diff --git a/.circle/tests.sh b/.circle/tests.sh index 202f9c5918..e6e9861ab7 100644 --- a/.circle/tests.sh +++ b/.circle/tests.sh @@ -30,8 +30,8 @@ case ${CIRCLE_NODE_INDEX} in exitcode=$? ;; 2) - docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \ - docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline + docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py36 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \ + docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline exitcode=$? ;; 3) diff --git a/doc/users/config_file.rst b/doc/users/config_file.rst index 7d55cc522d..8fccf7e42a 100644 --- a/doc/users/config_file.rst +++ b/doc/users/config_file.rst @@ -14,48 +14,52 @@ Logging ~~~~~~~ *workflow_level* - How detailed the logs regarding workflow should be (possible values: - ``INFO`` and ``DEBUG``; default value: ``INFO``) -*filemanip_level* - How detailed the logs regarding file operations (for example overwriting - warning) should be (possible values: ``INFO`` and ``DEBUG``; default value: - ``INFO``) + How detailed the logs regarding workflow should be (possible values: + ``INFO`` and ``DEBUG``; default value: ``INFO``) +*utils_level* + How detailed the logs regarding nipype utils, like file operations + (for example overwriting warning) or the resource profiler, should be + (possible values: ``INFO`` and ``DEBUG``; default value: + ``INFO``) *interface_level* - How detailed the logs regarding interface execution should be (possible - values: ``INFO`` and ``DEBUG``; default value: ``INFO``) + How detailed the logs regarding interface execution should be (possible + values: ``INFO`` and ``DEBUG``; default value: ``INFO``) +*filemanip_level* (deprecated as of 0.13.2) + How detailed the logs regarding file operations (for example overwriting + warning) should be (possible values: ``INFO`` and ``DEBUG``) *log_to_file* Indicates whether logging should also send the output to a file (possible values: ``true`` and ``false``; default value: ``false``) *log_directory* - Where to store logs. (string, default value: home directory) + Where to store logs. (string, default value: home directory) *log_size* - Size of a single log file. (integer, default value: 254000) + Size of a single log file. (integer, default value: 254000) *log_rotate* - How many rotation should the log file make. (integer, default value: 4) + How many rotation should the log file make. (integer, default value: 4) Execution ~~~~~~~~~ *plugin* - This defines which execution plugin to use. (possible values: ``Linear``, - ``MultiProc``, ``SGE``, ``IPython``; default value: ``Linear``) + This defines which execution plugin to use. (possible values: ``Linear``, + ``MultiProc``, ``SGE``, ``IPython``; default value: ``Linear``) *stop_on_first_crash* - Should the workflow stop upon first node crashing or try to execute as many - nodes as possible? (possible values: ``true`` and ``false``; default value: - ``false``) + Should the workflow stop upon first node crashing or try to execute as many + nodes as possible? (possible values: ``true`` and ``false``; default value: + ``false``) *stop_on_first_rerun* - Should the workflow stop upon first node trying to recompute (by that we - mean rerunning a node that has been run before - this can happen due changed - inputs and/or hash_method since the last run). (possible values: ``true`` - and ``false``; default value: ``false``) + Should the workflow stop upon first node trying to recompute (by that we + mean rerunning a node that has been run before - this can happen due changed + inputs and/or hash_method since the last run). (possible values: ``true`` + and ``false``; default value: ``false``) *hash_method* - Should the input files be checked for changes using their content (slow, but - 100% accurate) or just their size and modification date (fast, but - potentially prone to errors)? (possible values: ``content`` and - ``timestamp``; default value: ``timestamp``) + Should the input files be checked for changes using their content (slow, but + 100% accurate) or just their size and modification date (fast, but + potentially prone to errors)? (possible values: ``content`` and + ``timestamp``; default value: ``timestamp``) *keep_inputs* Ensures that all inputs that are created in the nodes working directory are @@ -63,44 +67,44 @@ Execution value: ``false``) *single_thread_matlab* - Should all of the Matlab interfaces (including SPM) use only one thread? - This is useful if you are parallelizing your workflow using MultiProc or - IPython on a single multicore machine. (possible values: ``true`` and - ``false``; default value: ``true``) + Should all of the Matlab interfaces (including SPM) use only one thread? + This is useful if you are parallelizing your workflow using MultiProc or + IPython on a single multicore machine. (possible values: ``true`` and + ``false``; default value: ``true``) *display_variable* - What ``DISPLAY`` variable should all command line interfaces be - run with. This is useful if you are using `xnest - `_ - or `Xvfb `_ - and you would like to redirect all spawned windows to - it. (possible values: any X server address; default value: not - set) + What ``DISPLAY`` variable should all command line interfaces be + run with. This is useful if you are using `xnest + `_ + or `Xvfb `_ + and you would like to redirect all spawned windows to + it. (possible values: any X server address; default value: not + set) *remove_unnecessary_outputs* - This will remove any interface outputs not needed by the workflow. If the - required outputs from a node changes, rerunning the workflow will rerun the - node. Outputs of leaf nodes (nodes whose outputs are not connected to any - other nodes) will never be deleted independent of this parameter. (possible - values: ``true`` and ``false``; default value: ``true``) + This will remove any interface outputs not needed by the workflow. If the + required outputs from a node changes, rerunning the workflow will rerun the + node. Outputs of leaf nodes (nodes whose outputs are not connected to any + other nodes) will never be deleted independent of this parameter. (possible + values: ``true`` and ``false``; default value: ``true``) *try_hard_link_datasink* - When the DataSink is used to produce an orginized output file outside - of nipypes internal cache structure, a file system hard link will be - attempted first. A hard link allow multiple file paths to point to the - same physical storage location on disk if the conditions allow. By - refering to the same physical file on disk (instead of copying files - byte-by-byte) we can avoid unnecessary data duplication. If hard links - are not supported for the source or destination paths specified, then - a standard byte-by-byte copy is used. (possible values: ``true`` and - ``false``; default value: ``true``) + When the DataSink is used to produce an orginized output file outside + of nipypes internal cache structure, a file system hard link will be + attempted first. A hard link allow multiple file paths to point to the + same physical storage location on disk if the conditions allow. By + refering to the same physical file on disk (instead of copying files + byte-by-byte) we can avoid unnecessary data duplication. If hard links + are not supported for the source or destination paths specified, then + a standard byte-by-byte copy is used. (possible values: ``true`` and + ``false``; default value: ``true``) *use_relative_paths* - Should the paths stored in results (and used to look for inputs) - be relative or absolute. Relative paths allow moving the whole - working directory around but may cause problems with - symlinks. (possible values: ``true`` and ``false``; default - value: ``false``) + Should the paths stored in results (and used to look for inputs) + be relative or absolute. Relative paths allow moving the whole + working directory around but may cause problems with + symlinks. (possible values: ``true`` and ``false``; default + value: ``false``) *local_hash_check* Perform the hash check on the job submission machine. This option minimizes @@ -115,10 +119,10 @@ Execution done after a job finish is detected. (float in seconds; default value: 5) *remove_node_directories (EXPERIMENTAL)* - Removes directories whose outputs have already been used - up. Doesn't work with IdentiInterface or any node that patches - data through (without copying) (possible values: ``true`` and - ``false``; default value: ``false``) + Removes directories whose outputs have already been used + up. Doesn't work with IdentiInterface or any node that patches + data through (without copying) (possible values: ``true`` and + ``false``; default value: ``false``) *stop_on_unknown_version* If this is set to True, an underlying interface will raise an error, when no @@ -146,18 +150,26 @@ Execution crashfiles allow portability across machines and shorter load time. (possible values: ``pklz`` and ``txt``; default value: ``pklz``) +*resource_monitor* + Enables monitoring the resources occupation (possible values: ``true`` and + ``false``; default value: ``false``) + +*resource_monitor_frequency* + Sampling period (in seconds) between measurements of resources (memory, cpus) + being used by an interface. Requires ``resource_monitor`` to be ``true``. + Example ~~~~~~~ :: - [logging] - workflow_level = DEBUG + [logging] + workflow_level = DEBUG - [execution] - stop_on_first_crash = true - hash_method = timestamp - display_variable = :1 + [execution] + stop_on_first_crash = true + hash_method = timestamp + display_variable = :1 Workflow.config property has a form of a nested dictionary reflecting the structure of the .cfg file. diff --git a/doc/users/plugins.rst b/doc/users/plugins.rst index 6c825aa8f8..4c0960c554 100644 --- a/doc/users/plugins.rst +++ b/doc/users/plugins.rst @@ -74,6 +74,14 @@ Optional arguments:: n_procs : Number of processes to launch in parallel, if not set number of processors/threads will be automatically detected + memory_gb : Total memory available to be shared by all simultaneous tasks + currently running, if not set it will be automatically set to 90\% of + system RAM. + + raise_insufficient : Raise exception when the estimated resources of a node + exceed the total amount of resources available (memory and threads), when + ``False`` (default), only a warning will be issued. + To distribute processing on a multicore machine, simply call:: workflow.run(plugin='MultiProc') diff --git a/doc/users/resource_sched_profiler.rst b/doc/users/resource_sched_profiler.rst index 37404b27da..7fa0819c19 100644 --- a/doc/users/resource_sched_profiler.rst +++ b/doc/users/resource_sched_profiler.rst @@ -82,7 +82,7 @@ by setting the ``status_callback`` parameter to point to this function in the :: - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb args_dict = {'n_procs' : 8, 'memory_gb' : 10, 'status_callback' : log_nodes_cb} To set the filepath for the callback log the ``'callback'`` logger must be @@ -141,7 +141,7 @@ The pandas_ Python package is required to use this feature. :: - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb args_dict = {'n_procs' : 8, 'memory_gb' : 10, 'status_callback' : log_nodes_cb} workflow.run(plugin='MultiProc', plugin_args=args_dict) diff --git a/docker/files/run_examples.sh b/docker/files/run_examples.sh index a23c27e76b..f71ac60dde 100644 --- a/docker/files/run_examples.sh +++ b/docker/files/run_examples.sh @@ -12,10 +12,16 @@ mkdir -p ${HOME}/.nipype ${WORKDIR}/logs/example_${example_id} ${WORKDIR}/tests echo "[logging]" > ${HOME}/.nipype/nipype.cfg echo "workflow_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg echo "interface_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg -echo "filemanip_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg +echo "utils_level = DEBUG" >> ${HOME}/.nipype/nipype.cfg echo "log_to_file = true" >> ${HOME}/.nipype/nipype.cfg echo "log_directory = ${WORKDIR}/logs/example_${example_id}" >> ${HOME}/.nipype/nipype.cfg +if [[ "${NIPYPE_RESOURCE_MONITOR:-0}" == "1" ]]; then + echo '[execution]' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor_frequency = 3' >> ${HOME}/.nipype/nipype.cfg +fi + # Set up coverage export COVERAGE_FILE=${WORKDIR}/tests/.coverage.${example_id} if [ "$2" == "MultiProc" ]; then diff --git a/docker/files/run_pytests.sh b/docker/files/run_pytests.sh index f76734ad45..622772d3ae 100644 --- a/docker/files/run_pytests.sh +++ b/docker/files/run_pytests.sh @@ -17,10 +17,10 @@ echo '[logging]' > ${HOME}/.nipype/nipype.cfg echo 'log_to_file = true' >> ${HOME}/.nipype/nipype.cfg echo "log_directory = ${WORKDIR}/logs/py${PYTHON_VERSION}" >> ${HOME}/.nipype/nipype.cfg -# Enable profile_runtime tests only for python 2.7 +# Enable resource_monitor tests only for python 2.7 if [[ "${PYTHON_VERSION}" -lt "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg - echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg fi # Run tests using pytest @@ -31,9 +31,9 @@ exit_code=$? # Workaround: run here the profiler tests in python 3 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then echo '[execution]' >> ${HOME}/.nipype/nipype.cfg - echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg + echo 'resource_monitor = true' >> ${HOME}/.nipype/nipype.cfg export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra - py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py + py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/utils/tests/test_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py exit_code=$(( $exit_code + $? )) fi diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index 5c44844cf9..0e04841ad7 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -30,6 +30,9 @@ def test_ACompCor_inputs(): regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_pre_filter=dict(), use_regress_poly=dict(deprecated='0.15.0', new_name='pre_filter', diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index f38319040b..e9ed0f5ba8 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -11,6 +11,9 @@ def test_AddCSVRow_inputs(): ), in_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = AddCSVRow.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 054bc1da99..6468176307 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -27,6 +27,9 @@ def test_ArtifactDetect_inputs(): ), realignment_parameters=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_threshold=dict(mandatory=True, xor=['norm_threshold'], ), diff --git a/nipype/algorithms/tests/test_auto_CalculateMedian.py b/nipype/algorithms/tests/test_auto_CalculateMedian.py index 88888d5bbe..21ed0d19ae 100644 --- a/nipype/algorithms/tests/test_auto_CalculateMedian.py +++ b/nipype/algorithms/tests/test_auto_CalculateMedian.py @@ -11,6 +11,9 @@ def test_CalculateMedian_inputs(): median_file=dict(), median_per_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = CalculateMedian.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index 7c59f851d1..729f9a1f40 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -21,6 +21,9 @@ def test_ComputeDVARS_inputs(): ), remove_zerovariance=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_all=dict(usedefault=True, ), save_nstd=dict(usedefault=True, diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 61f64de033..5e30acf0ad 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -13,6 +13,9 @@ def test_ComputeMeshWarp_inputs(): ), out_warp=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), surface1=dict(mandatory=True, ), surface2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index 3e365b8894..e8a7139526 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -12,6 +12,9 @@ def test_CreateNifti_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = CreateNifti.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 5cf8c425c8..3f9398a777 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -10,6 +10,9 @@ def test_Distance_inputs(): mask_volume=dict(), method=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index e230992eec..b4f8f0ddeb 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -23,6 +23,9 @@ def test_FramewiseDisplacement_inputs(): ), radius=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_plot=dict(usedefault=True, ), series_tr=dict(), diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index 764d821bc6..dd57ef5c4f 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -13,6 +13,9 @@ def test_FuzzyOverlap_inputs(): ), out_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), weighting=dict(usedefault=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index 6b06654f1d..9d84480279 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -9,6 +9,9 @@ def test_Gunzip_inputs(): ), in_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Gunzip.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index da3110fd76..4e629376b3 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -9,6 +9,9 @@ def test_ICC_inputs(): ), mask=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_sessions=dict(mandatory=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index 3c6077922b..65ae52f5f9 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -18,6 +18,9 @@ def test_MeshWarpMaths_inputs(): ), out_warp=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = MeshWarpMaths.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index c7b4b25d0c..fa0daec97c 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -7,6 +7,9 @@ def test_ModifyAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), transformation_matrix=dict(usedefault=True, ), volumes=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index 7b12363ee8..1380ea134e 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -9,6 +9,9 @@ def test_NonSteadyStateDetector_inputs(): ), in_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = NonSteadyStateDetector.input_spec() diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 59c749da30..bf0c3cb1b8 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -13,6 +13,9 @@ def test_P2PDistance_inputs(): ), out_warp=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), surface1=dict(mandatory=True, ), surface2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 990b71e289..e8c7a77258 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -16,6 +16,9 @@ def test_PickAtlas_inputs(): labels=dict(mandatory=True, ), output_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = PickAtlas.input_spec() diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index 4dce363864..61184a3330 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -11,6 +11,9 @@ def test_Similarity_inputs(): mask2=dict(), metric=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index 0031f4bb7f..746759cef8 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -7,6 +7,9 @@ def test_SimpleThreshold_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), threshold=dict(mandatory=True, ), volumes=dict(mandatory=True, diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index 33d5435b5f..512b3cbb65 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -23,6 +23,9 @@ def test_SpecifyModel_inputs(): ), realignment_parameters=dict(copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_info=dict(mandatory=True, xor=['subject_info', 'event_files'], ), diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index 7a33ac63c4..3337a9ee49 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -27,6 +27,9 @@ def test_SpecifySPMModel_inputs(): ), realignment_parameters=dict(copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_info=dict(mandatory=True, xor=['subject_info', 'event_files'], ), diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index 4caf1c1033..43508b7ff3 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -24,6 +24,9 @@ def test_SpecifySparseModel_inputs(): ), realignment_parameters=dict(copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_plot=dict(), scale_regressors=dict(usedefault=True, ), diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index 95581bb111..d988df85af 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -13,6 +13,9 @@ def test_StimulusCorrelation_inputs(): ), realignment_parameters=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(mandatory=True, ), ) diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index b39c946d9d..4eb731b766 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -32,6 +32,9 @@ def test_TCompCor_inputs(): regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_pre_filter=dict(), use_regress_poly=dict(deprecated='0.15.0', new_name='pre_filter', diff --git a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py index d6e38722fe..36548065de 100644 --- a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py +++ b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py @@ -7,6 +7,9 @@ def test_TVTKBaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = TVTKBaseInterface.input_spec() diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index ab59d22cff..fd65a3c7b8 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -17,6 +17,9 @@ def test_WarpPoints_inputs(): ), points=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), warp=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index 3ab5756f03..b834b34163 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -45,6 +45,7 @@ def version(): """ try: clout = CommandLine(command='afni --version', + resource_monitor=False, terminal_output='allatonce').run() except IOError: # If afni_vcheck is not present, return None @@ -106,6 +107,8 @@ def standard_image(img_name): Could be made more fancy to allow for more relocatability''' clout = CommandLine('which afni', + ignore_exception=True, + resource_monitor=False, terminal_output='allatonce').run() if clout.runtime.returncode is not 0: return None @@ -295,4 +298,4 @@ def cmd(self): @property def cmdline(self): - return "{} {}".format(self.inputs.py27_path, super(AFNIPythonCommand, self).cmdline) \ No newline at end of file + return "{} {}".format(self.inputs.py27_path, super(AFNIPythonCommand, self).cmdline) diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py index 93219fe3dc..72a0d77eea 100644 --- a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py +++ b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py @@ -30,6 +30,9 @@ def test_ABoverlap_inputs(): outputtype=dict(), quiet=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verb=dict(argstr='-verb', diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index aef42ee585..1e22ac7cbf 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -17,6 +17,9 @@ def test_AFNICommand_inputs(): name_template='%s_afni', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py index 37efbcee2d..5a8376af07 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py @@ -12,6 +12,9 @@ def test_AFNICommandBase_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py index e8efb62f5d..337ef9de50 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py @@ -17,6 +17,9 @@ def test_AFNIPythonCommand_inputs(): name_template='%s_afni', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 5fe66e9df7..587eeb4b8c 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -33,6 +33,9 @@ def test_AFNItoNIFTI_inputs(): outputtype=dict(), pure=dict(argstr='-pure', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py index 8193270c5d..0a0f080922 100644 --- a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py +++ b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py @@ -32,6 +32,9 @@ def test_AlignEpiAnatPy_inputs(): outputtype=dict(), py27_path=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_skullstrip=dict(argstr='-save_skullstrip', ), suffix=dict(argstr='-suffix %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index d1a8ae2187..c8df1643ae 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -97,6 +97,9 @@ def test_Allineate_inputs(): ), replacemeth=dict(argstr='-replacemeth %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_automask=dict(argstr='-source_automask+%d', ), source_mask=dict(argstr='-source_mask %s', diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py index 3c95374697..18e87a49a7 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py @@ -22,6 +22,9 @@ def test_AutoTLRC_inputs(): no_ss=dict(argstr='-no_ss', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index f7a3d89278..f77cfe17cf 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -34,6 +34,9 @@ def test_AutoTcorrelate_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index 91479c241d..c5a0a88577 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -25,6 +25,9 @@ def test_Autobox_inputs(): outputtype=dict(), padding=dict(argstr='-npad %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index f0a76037c2..3e1571624b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -32,6 +32,9 @@ def test_Automask_inputs(): name_template='%s_mask', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Axialize.py b/nipype/interfaces/afni/tests/test_auto_Axialize.py index 6d04decdaa..f70c3771a3 100644 --- a/nipype/interfaces/afni/tests/test_auto_Axialize.py +++ b/nipype/interfaces/afni/tests/test_auto_Axialize.py @@ -30,6 +30,9 @@ def test_Axialize_inputs(): name_template='%s_axialize', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sagittal=dict(argstr='-sagittal', xor=['coronal', 'axial'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index 5310eaa256..c8ee04bde6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -55,6 +55,9 @@ def test_Bandpass_inputs(): position=1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tr=dict(argstr='-dt %f', diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index eb4a571079..7224a8fb66 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -39,6 +39,9 @@ def test_BlurInMask_inputs(): outputtype=dict(), preserve=dict(argstr='-preserve', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index bf4d2a194c..ef54b9b30a 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -30,6 +30,9 @@ def test_BlurToFWHM_inputs(): name_template='%s_afni', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index f15a8d972d..937d5c4e4f 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -28,6 +28,9 @@ def test_BrickStat_inputs(): ), percentile=dict(argstr='-percentile %.3f %.3f %.3f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slow=dict(argstr='-slow', ), sum=dict(argstr='-sum', diff --git a/nipype/interfaces/afni/tests/test_auto_Bucket.py b/nipype/interfaces/afni/tests/test_auto_Bucket.py index 1cf812fd73..f50c3e742b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bucket.py +++ b/nipype/interfaces/afni/tests/test_auto_Bucket.py @@ -20,6 +20,9 @@ def test_Bucket_inputs(): name_template='buck', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index aa9d1222b7..d6f9488624 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -35,6 +35,9 @@ def test_Calc_inputs(): outputtype=dict(), overwrite=dict(argstr='-overwrite', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), single_idx=dict(), start_idx=dict(requires=['stop_idx'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index c35c3e86b9..a4ebbd3620 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -42,6 +42,9 @@ def test_Cat_inputs(): xor=['out_format', 'out_int', 'out_double', 'out_fint', 'out_cint'], ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sel=dict(argstr='-sel %s', ), stack=dict(argstr='-stack', diff --git a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py index d3d94569be..9ddfd91b85 100644 --- a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py +++ b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py @@ -35,6 +35,9 @@ def test_CatMatvec_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 8bd4cd346a..8a11bce555 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -27,6 +27,9 @@ def test_ClipLevel_inputs(): mfrac=dict(argstr='-mfrac %s', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index 80338ccc57..05e56803a0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -23,6 +23,9 @@ def test_Copy_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py index 0dfbec8deb..10073109a2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py +++ b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py @@ -81,6 +81,9 @@ def test_Deconvolve_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rmsmin=dict(argstr='-rmsmin %f', ), rout=dict(argstr='-rout', diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index cd4146a7b9..c60bfcf508 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -32,6 +32,9 @@ def test_DegreeCentrality_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sparsity=dict(argstr='-sparsity %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index aedb50b684..972942cabd 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -22,6 +22,9 @@ def test_Despike_inputs(): name_template='%s_despike', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 3fb771cbfc..77474e4fe2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -22,6 +22,9 @@ def test_Detrend_inputs(): name_template='%s_detrend', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Dot.py b/nipype/interfaces/afni/tests/test_auto_Dot.py index 21cebb28fe..08ee9592d7 100644 --- a/nipype/interfaces/afni/tests/test_auto_Dot.py +++ b/nipype/interfaces/afni/tests/test_auto_Dot.py @@ -39,6 +39,9 @@ def test_Dot_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), show_labels=dict(argstr='-show_labels', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index 39bdefe0ba..64ce4c45e7 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -40,6 +40,9 @@ def test_ECM_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='-scale %f', ), shift=dict(argstr='-shift %f', diff --git a/nipype/interfaces/afni/tests/test_auto_Edge3.py b/nipype/interfaces/afni/tests/test_auto_Edge3.py index 51a4dc865d..cd7a1d47c6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Edge3.py +++ b/nipype/interfaces/afni/tests/test_auto_Edge3.py @@ -32,6 +32,9 @@ def test_Edge3_inputs(): position=-1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale_floats=dict(argstr='-scale_floats %f', xor=['fscale', 'gscale', 'nscale'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 490b09e486..2e10a1702e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -35,6 +35,9 @@ def test_Eval_inputs(): name_template='%s_calc', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), single_idx=dict(), start_idx=dict(requires=['stop_idx'], ), diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 527c7fdb22..10084c1736 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -56,6 +56,9 @@ def test_FWHMx_inputs(): name_source='in_file', name_template='%s_subbricks.out', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), unif=dict(argstr='-unif', diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index e80adb6801..7080d0b483 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -32,6 +32,9 @@ def test_Fim_inputs(): name_template='%s_fim', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 0573252de4..fd22a63b59 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -28,6 +28,9 @@ def test_Fourier_inputs(): name_template='%s_fourier', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), retrend=dict(argstr='-retrend', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_GCOR.py b/nipype/interfaces/afni/tests/test_auto_GCOR.py index 5cc9bf390c..bbf7eecd8e 100644 --- a/nipype/interfaces/afni/tests/test_auto_GCOR.py +++ b/nipype/interfaces/afni/tests/test_auto_GCOR.py @@ -24,6 +24,9 @@ def test_GCOR_inputs(): ), no_demean=dict(argstr='-no_demean', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index 91f4238834..cf300d45ad 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -38,6 +38,9 @@ def test_Hist_inputs(): name_template='%s_hist.out', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), showhist=dict(argstr='-showhist', usedefault=True, ), diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index c3690b8fd5..195269bfd8 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -30,6 +30,9 @@ def test_LFCD_inputs(): outputtype=dict(), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresh=dict(argstr='-thresh %f', diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 0121d68d7d..b4234c0536 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -40,6 +40,9 @@ def test_MaskTool_inputs(): name_template='%s_mask', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), union=dict(argstr='-union', diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index 9c58ea432b..b6844372b0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -30,6 +30,9 @@ def test_Maskave_inputs(): quiet=dict(argstr='-quiet', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 03bab07dcc..524ae33d0a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -34,6 +34,9 @@ def test_Means_inputs(): name_template='%s_mean', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='-%sscale', ), sqr=dict(argstr='-sqr', diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index f943128da9..2a2a6cd82e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -27,6 +27,9 @@ def test_Merge_inputs(): name_template='%s_merge', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index ca08111696..ae7e3876d8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -30,6 +30,9 @@ def test_Notes_inputs(): rep_history=dict(argstr='-HH "%s"', xor=['add_history'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ses=dict(argstr='-ses', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index 273d0fed47..8b79cfadf7 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -30,6 +30,9 @@ def test_NwarpApply_inputs(): quiet=dict(argstr='-quiet', xor=['verb'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), short=dict(argstr='-short', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index fd6aed4b12..85f2875473 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -29,6 +29,9 @@ def test_OneDToolPy_inputs(): outputtype=dict(), py27_path=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), set_nruns=dict(argstr='-set_nruns %d', ), show_censor_count=dict(argstr='-show_censor_count', diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index 23f768f3dd..3d842f7ab6 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -52,6 +52,9 @@ def test_OutlierCount_inputs(): ), qthr=dict(argstr='-qthr %.5f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_outliers=dict(usedefault=True, ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index 2659fc8d91..a55370728e 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -41,6 +41,9 @@ def test_QualityIndex_inputs(): quadrant=dict(argstr='-quadrant', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spearman=dict(argstr='-spearman', usedefault=True, ), diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index 2848fe97f8..d973f4b18f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -122,6 +122,9 @@ def test_Qwarp_inputs(): ), resample=dict(argstr='-resample', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verb=dict(argstr='-verb', diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index 04f12426de..5b8a5008db 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -26,6 +26,9 @@ def test_QwarpPlusMinus_inputs(): ), pblur=dict(argstr='-pblur %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='-source %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 1e5de5806f..32f780c2a6 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -25,6 +25,9 @@ def test_ROIStats_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(mandatory=True, nohash=True, usedefault=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index b6c167198c..522b521979 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -31,6 +31,9 @@ def test_Refit_inputs(): ), nosaveatr=dict(argstr='-nosaveatr', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveatr=dict(argstr='-saveatr', ), space=dict(argstr='-space %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index a061a01449..36fbf91ca3 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -79,6 +79,9 @@ def test_Remlfit_inputs(): ), rbeta_file=dict(argstr='-Rbeta %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rout=dict(argstr='-rout', ), slibase=dict(argstr='-slibase %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 4fabc2749c..c769ddee4b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -28,6 +28,9 @@ def test_Resample_inputs(): outputtype=dict(), resample_mode=dict(argstr='-rmode %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel_size=dict(argstr='-dxyz %f %f %f', diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 6822425f00..49214e8de8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -33,6 +33,9 @@ def test_Retroicor_inputs(): position=1, ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resp=dict(argstr='-resp %s', position=-3, ), diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 496f947a28..5a907560fe 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -32,6 +32,9 @@ def test_SVMTest_inputs(): name_template='%s_predictions', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), testlabels=dict(argstr='-testlabels %s', diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index 25973372e6..517aafcd46 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -46,6 +46,9 @@ def test_SVMTrain_inputs(): suffix='_bucket', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trainlabels=dict(argstr='-trainlabels %s', diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index e8114e5838..9dcf8a0217 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -39,6 +39,9 @@ def test_Seg_inputs(): ), prefix=dict(argstr='-prefix %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index 37b24cfb76..3265f955dd 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -22,6 +22,9 @@ def test_SkullStrip_inputs(): name_template='%s_skullstrip', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 9c72dcd545..aa7619909e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -22,6 +22,9 @@ def test_TCat_inputs(): name_template='%s_tcat', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rlt=dict(argstr='-rlt%s', position=1, ), diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index e42ac2b7d5..19cd65e053 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -30,6 +30,9 @@ def test_TCorr1D_inputs(): position=1, xor=['pearson', 'spearman', 'ktaub'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spearman=dict(argstr=' -spearman', position=1, xor=['pearson', 'quadrant', 'ktaub'], diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 8c80f15080..75c00044aa 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -72,6 +72,9 @@ def test_TCorrMap_inputs(): ), regress_out_timeseries=dict(argstr='-ort %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seeds=dict(argstr='-seed %s', xor='seeds_width', ), diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index e2e100cdb7..e16a089fd2 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -21,6 +21,9 @@ def test_TCorrelate_inputs(): ), polort=dict(argstr='-polort %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xset=dict(argstr='%s', diff --git a/nipype/interfaces/afni/tests/test_auto_TNorm.py b/nipype/interfaces/afni/tests/test_auto_TNorm.py index 3b9fac4b98..55a16754f3 100644 --- a/nipype/interfaces/afni/tests/test_auto_TNorm.py +++ b/nipype/interfaces/afni/tests/test_auto_TNorm.py @@ -34,6 +34,9 @@ def test_TNorm_inputs(): outputtype=dict(), polort=dict(argstr='-polort %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index e167205995..63976b11cd 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -26,6 +26,9 @@ def test_TShift_inputs(): name_template='%s_tshift', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rlt=dict(argstr='-rlt', ), rltplus=dict(argstr='-rlt+', diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index f09fb5b4af..5945a0858c 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -26,6 +26,9 @@ def test_TStat_inputs(): name_template='%s_tstat', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 0df075d87f..3ea2e120e4 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -29,6 +29,9 @@ def test_To3D_inputs(): name_template='%s', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skipoutliers=dict(argstr='-skip_outliers', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Undump.py b/nipype/interfaces/afni/tests/test_auto_Undump.py index 808de86daf..3b30bd9111 100644 --- a/nipype/interfaces/afni/tests/test_auto_Undump.py +++ b/nipype/interfaces/afni/tests/test_auto_Undump.py @@ -33,6 +33,9 @@ def test_Undump_inputs(): name_source='in_file', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), srad=dict(argstr='-srad -%f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index 2c37e13fb1..10ed9ff677 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -29,6 +29,9 @@ def test_Unifize_inputs(): name_source='in_file', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale_file=dict(argstr='-ssave %s', ), t2=dict(argstr='-T2', diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 314ac04743..9085e9f8ee 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -45,6 +45,9 @@ def test_Volreg_inputs(): name_template='%s_volreg', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeshift=dict(argstr='-tshift 0', diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index e370d32058..88cf4bd503 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -34,6 +34,9 @@ def test_Warp_inputs(): name_template='%s_warp', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tta2mni=dict(argstr='-tta2mni', diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 8019b1dcf8..27c7b86bab 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -24,6 +24,9 @@ def test_ZCutUp_inputs(): name_template='%s_zcutup', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/afni/tests/test_auto_Zcat.py b/nipype/interfaces/afni/tests/test_auto_Zcat.py index 48f742df5e..c99ec2b141 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zcat.py +++ b/nipype/interfaces/afni/tests/test_auto_Zcat.py @@ -29,6 +29,9 @@ def test_Zcat_inputs(): name_template='zcat', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verb=dict(argstr='-verb', diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index 551498e1ab..dc33e3a80c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -54,6 +54,9 @@ def test_Zeropad_inputs(): name_template='zeropad', ), outputtype=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), z=dict(argstr='-z %i', diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index e7fbe117ae..907a93d0e5 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -57,6 +57,9 @@ def test_ANTS_inputs(): ), regularization_gradient_field_sigma=dict(requires=['regularization'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smoothing_sigmas=dict(argstr='--gaussian-smoothing-sigmas %s', sep='x', ), diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index 4f6920645b..ecc4288a14 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -15,6 +15,9 @@ def test_ANTSCommand_inputs(): num_threads=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py index 319798e13f..00533675ad 100644 --- a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py +++ b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py @@ -43,6 +43,9 @@ def test_AffineInitializer_inputs(): position=5, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_factor=dict(argstr='%f', position=4, usedefault=True, diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index dcd115429f..6ad79d70b5 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -55,6 +55,9 @@ def test_AntsJointFusion_inputs(): maxlen=3, minlen=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), retain_atlas_voting_images=dict(argstr='-f', usedefault=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index 4b27963757..42cdf28e9e 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -43,6 +43,9 @@ def test_ApplyTransforms_inputs(): reference_image=dict(argstr='--reference-image %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transforms=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 5a20ac0f43..d727b9eb46 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -26,6 +26,9 @@ def test_ApplyTransformsToPoints_inputs(): name_source=['input_file'], name_template='%s_transformed.csv', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transforms=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 50fd85477d..41e58651d4 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -56,6 +56,9 @@ def test_Atropos_inputs(): prior_probability_threshold=dict(requires=['prior_weighting'], ), prior_weighting=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_posteriors=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 25a7f0b892..e087800c50 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -24,6 +24,9 @@ def test_AverageAffineTransform_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transforms=dict(argstr='%s', diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 47accd6758..8bb58062d1 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -32,6 +32,9 @@ def test_AverageImages_inputs(): position=1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index 86f652cbbe..d34a899530 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -40,6 +40,9 @@ def test_BrainExtraction_inputs(): out_prefix=dict(argstr='-o %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), use_floatingpoint_precision=dict(argstr='-q %d', diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index 42d049990b..17a8d35ab9 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -57,6 +57,9 @@ def test_ConvertScalarImageToRGB_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index 5fe224b494..44a1452a1f 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -53,6 +53,9 @@ def test_CorticalThickness_inputs(): ), quick_registration=dict(argstr='-q 1', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation_iterations=dict(argstr='-n %d', ), segmentation_priors=dict(argstr='-p %s', diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index f7aafb27be..398be1d292 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -31,6 +31,9 @@ def test_CreateJacobianDeterminantImage_inputs(): mandatory=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), useGeometric=dict(argstr='%d', diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index 09340f631f..bc2eee5ca0 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -33,6 +33,9 @@ def test_CreateTiledMosaic_inputs(): ), permute_axes=dict(argstr='-g', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rgb_image=dict(argstr='-r %s', mandatory=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index 6c28016de6..9786afbc08 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -35,6 +35,9 @@ def test_DenoiseImage_inputs(): name_source=['input_image'], name_template='%s_noise_corrected', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_noise=dict(mandatory=True, usedefault=True, xor=['noise_image'], diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index f5d79bd851..fc10358d49 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -41,6 +41,9 @@ def test_GenWarpFields_inputs(): copyfile=True, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), similarity_metric=dict(argstr='-s %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index cddfb487be..c0c330e161 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -49,6 +49,9 @@ def test_JointFusion_inputs(): maxlen=3, minlen=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_radius=dict(argstr='-rs %s', maxlen=3, minlen=3, diff --git a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py index 046d31d158..46089b0584 100644 --- a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py +++ b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py @@ -38,6 +38,9 @@ def test_KellyKapowski_inputs(): ), number_integration_points=dict(argstr='--number-of-integration-points %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation_image=dict(argstr='--segmentation-image "%s"', mandatory=True, ), diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index 71b0483f92..5120e689a0 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -39,6 +39,9 @@ def test_LaplacianThickness_inputs(): prior_thickness=dict(argstr='priorthickval=%d', position=5, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_param=dict(argstr='smoothparam=%d', position=4, ), diff --git a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py index 3dba65d8bb..6eede97bcc 100644 --- a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py +++ b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py @@ -35,6 +35,9 @@ def test_MeasureImageSimilarity_inputs(): radius_or_number_of_bins=dict(mandatory=True, requires=['metric'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_percentage=dict(mandatory=True, requires=['metric'], ), diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 2175db201d..11b9b56616 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -28,6 +28,9 @@ def test_MultiplyImages_inputs(): mandatory=True, position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), second_input=dict(argstr='%s', mandatory=True, position=2, diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index b863f888d9..b2b85441d8 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -40,6 +40,9 @@ def test_N4BiasFieldCorrection_inputs(): genfile=True, hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_bias=dict(mandatory=True, usedefault=True, xor=['bias_image'], diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index d437e437f3..7a70014b85 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -87,6 +87,9 @@ def test_Registration_inputs(): radius_or_number_of_bins=dict(requires=['metric_weight'], usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), restore_state=dict(argstr='--restore-state %s', ), restrict_deformation=dict(), diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index e016aac163..60a78ed4db 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -39,6 +39,9 @@ def test_WarpImageMultiTransform_inputs(): ), reslice_by_header=dict(argstr='--reslice-by-header', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tightest_box=dict(argstr='--tightest-bounding-box', diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index 79fbf89302..0e956145aa 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -32,6 +32,9 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): ), reslice_by_header=dict(argstr='--reslice-by-header', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tightest_box=dict(argstr='--tightest-bounding-box', diff --git a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py index 230176c856..1c6d3304d3 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py @@ -40,6 +40,9 @@ def test_antsBrainExtraction_inputs(): out_prefix=dict(argstr='-o %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), use_floatingpoint_precision=dict(argstr='-q %d', diff --git a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py index 02f2d46c59..80be6a63a0 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py @@ -53,6 +53,9 @@ def test_antsCorticalThickness_inputs(): ), quick_registration=dict(argstr='-q 1', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation_iterations=dict(argstr='-n %d', ), segmentation_priors=dict(argstr='-p %s', diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index 0a9646ae2c..7334aeda39 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -41,6 +41,9 @@ def test_antsIntroduction_inputs(): copyfile=True, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), similarity_metric=dict(argstr='-s %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 9232bb32b1..f4854948a3 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -42,6 +42,9 @@ def test_buildtemplateparallel_inputs(): parallelization=dict(argstr='-c %d', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigid_body_registration=dict(argstr='-r 1', ), similarity_metric=dict(argstr='-s %s', diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 19cf9ccaa6..4cb929ba7f 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -24,7 +24,7 @@ import platform from string import Template import select -import subprocess +import subprocess as sp import sys import time from textwrap import wrap @@ -44,30 +44,22 @@ File, Directory, DictStrStr, has_metadata, ImageFile) from ..external.due import due -runtime_profile = str2bool(config.get('execution', 'profile_runtime')) nipype_version = Version(__version__) iflogger = logging.getLogger('interface') FLOAT_FORMAT = '{:.10f}'.format PY35 = sys.version_info >= (3, 5) PY3 = sys.version_info[0] > 2 - -if runtime_profile: - try: - import psutil - except ImportError as exc: - iflogger.info('Unable to import packages needed for runtime profiling. '\ - 'Turning off runtime profiler. Reason: %s' % exc) - runtime_profile = False - __docformat__ = 'restructuredtext' class Str(traits.Unicode): pass + traits.Str = Str + class NipypeInterfaceError(Exception): def __init__(self, value): self.value = value @@ -75,6 +67,7 @@ def __init__(self, value): def __str__(self): return '{}'.format(self.value) + def _exists_in_path(cmd, environ): """ Based on a code snippet from @@ -144,7 +137,6 @@ class Bunch(object): """ - def __init__(self, *args, **kwargs): self.__dict__.update(*args, **kwargs) @@ -581,7 +573,6 @@ def get_hashval(self, hash_method=None): hash_files=hash_files))) return dict_withhash, md5(to_str(dict_nofilename).encode()).hexdigest() - def _get_sorteddict(self, objekt, dictwithhash=False, hash_method=None, hash_files=True): if isinstance(objekt, dict): @@ -738,9 +729,12 @@ def _get_filecopy_info(self): class BaseInterfaceInputSpec(TraitedSpec): - ignore_exception = traits.Bool(False, desc="Print an error message instead \ -of throwing an exception in case the interface fails to run", usedefault=True, - nohash=True) + ignore_exception = traits.Bool(False, usedefault=True, nohash=True, + desc='Print an error message instead of throwing an exception ' + 'in case the interface fails to run') + resource_monitor = traits.Bool(True, usedefault=True, nohash=True, + desc='Disable the resource monitor for this interface ' + '(overloads the default nipype config).') class BaseInterface(Interface): @@ -782,7 +776,6 @@ def __init__(self, from_file=None, **inputs): for name, value in list(inputs.items()): setattr(self.inputs, name, value) - @classmethod def help(cls, returnhelp=False): """ Prints class help @@ -903,7 +896,7 @@ def _outputs_help(cls): """ helpstr = ['Outputs::', ''] if cls.output_spec: - outputs = cls.output_spec() #pylint: disable=E1102 + outputs = cls.output_spec() # pylint: disable=E1102 for name, spec in sorted(outputs.traits(transient=None).items()): helpstr += cls._get_trait_desc(outputs, name, spec) if len(helpstr) == 2: @@ -915,7 +908,7 @@ def _outputs(self): """ outputs = None if self.output_spec: - outputs = self.output_spec() #pylint: disable=E1102 + outputs = self.output_spec() # pylint: disable=E1102 return outputs @@ -1011,7 +1004,6 @@ def _check_version_requirements(self, trait_object, raise_exception=True): return unavailable_traits def _run_wrapper(self, runtime): - sysdisplay = os.getenv('DISPLAY') if self._redirect_x: try: from xvfbwrapper import Xvfb @@ -1063,6 +1055,10 @@ def run(self, **inputs): results : an InterfaceResult object containing a copy of the instance that was executed, provenance information and, if successful, results """ + from ..utils.profiler import resource_monitor, ResourceMonitor + + enable_rm = resource_monitor and getattr(self.inputs, 'resource_monitor', True) + force_raise = not getattr(self.inputs, 'ignore_exception', False) self.inputs.trait_set(**inputs) self._check_mandatory_inputs() self._check_version_requirements(self.inputs) @@ -1070,6 +1066,8 @@ def run(self, **inputs): self._duecredit_cite() # initialize provenance tracking + store_provenance = str2bool(config.get( + 'execution', 'write_provenance', 'false')) env = deepcopy(dict(os.environ)) runtime = Bunch(cwd=os.getcwd(), returncode=None, @@ -1080,66 +1078,74 @@ def run(self, **inputs): platform=platform.platform(), hostname=platform.node(), version=self.version) + + mon_sp = None + if enable_rm: + mon_freq = config.get('execution', 'resource_monitor_frequency', 1) + proc_pid = os.getpid() + mon_fname = os.path.abspath('.prof-%d_freq-%0.3f' % (proc_pid, mon_freq)) + iflogger.debug('Creating a ResourceMonitor on a %s interface: %s', + self.__class__.__name__, mon_fname) + mon_sp = ResourceMonitor(proc_pid, freq=mon_freq, fname=mon_fname) + mon_sp.start() + + # Grab inputs now, as they should not change during execution + inputs = self.inputs.get_traitsfree() + outputs = None try: runtime = self._run_wrapper(runtime) outputs = self.aggregate_outputs(runtime) - runtime.endTime = dt.isoformat(dt.utcnow()) - timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) - runtime.duration = (timediff.days * 86400 + timediff.seconds + - timediff.microseconds / 100000.) - results = InterfaceResult(interface, runtime, - inputs=self.inputs.get_traitsfree(), - outputs=outputs) - prov_record = None - if str2bool(config.get('execution', 'write_provenance')): - prov_record = write_provenance(results) - results.provenance = prov_record except Exception as e: + import traceback + # Retrieve the maximum info fast + runtime.traceback = traceback.format_exc() + # Gather up the exception arguments and append nipype info. + exc_args = e.args if getattr(e, 'args') else tuple() + exc_args += ('An exception of type %s occurred while running interface %s.' % + (type(e).__name__, self.__class__.__name__), ) + if config.get('logging', 'interface_level', 'info').lower() == 'debug': + exc_args += ('Inputs: %s' % str(self.inputs),) + + runtime.traceback_args = ('\n'.join(['%s' % arg for arg in exc_args]),) + + if force_raise: + raise + finally: + # This needs to be done always runtime.endTime = dt.isoformat(dt.utcnow()) timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime) runtime.duration = (timediff.days * 86400 + timediff.seconds + - timediff.microseconds / 100000.) - if len(e.args) == 0: - e.args = ("") - - message = "\nInterface %s failed to run." % self.__class__.__name__ + timediff.microseconds / 1e6) + results = InterfaceResult(interface, runtime, inputs=inputs, outputs=outputs, + provenance=None) + + # Add provenance (if required) + if store_provenance: + # Provenance will only throw a warning if something went wrong + results.provenance = write_provenance(results) + + # Make sure runtime profiler is shut down + if enable_rm: + import numpy as np + mon_sp.stop() + + runtime.mem_peak_gb = None + runtime.nthreads_max = None + + # Read .prof file in and set runtime values + vals = np.loadtxt(mon_fname, delimiter=',') + if vals.tolist(): + vals = np.atleast_2d(vals) + _, mem_peak_mb, nthreads = vals.max(0).astype(float).tolist() + runtime.mem_peak_gb = mem_peak_mb / 1024 + runtime.nthreads_max = int(nthreads) + + runtime.prof_dict = { + 'time': vals[:, 0].tolist(), + 'mem_gb': (vals[:, 1] / 1024).tolist(), + 'cpus': vals[:, 2].astype(int).tolist(), + } - if config.has_option('logging', 'interface_level') and \ - config.get('logging', 'interface_level').lower() == 'debug': - inputs_str = "\nInputs:" + str(self.inputs) + "\n" - else: - inputs_str = '' - - if len(e.args) == 1 and isinstance(e.args[0], (str, bytes)): - e.args = (e.args[0] + " ".join([message, inputs_str]),) - else: - e.args += (message, ) - if inputs_str != '': - e.args += (inputs_str, ) - - # exception raising inhibition for special cases - import traceback - runtime.traceback = traceback.format_exc() - runtime.traceback_args = e.args - inputs = None - try: - inputs = self.inputs.get_traitsfree() - except Exception as e: - pass - results = InterfaceResult(interface, runtime, inputs=inputs) - prov_record = None - if str2bool(config.get('execution', 'write_provenance')): - try: - prov_record = write_provenance(results) - except Exception: - prov_record = None - results.provenance = prov_record - if hasattr(self.inputs, 'ignore_exception') and \ - isdefined(self.inputs.ignore_exception) and \ - self.inputs.ignore_exception: - pass - else: - raise return results def _list_outputs(self): @@ -1170,7 +1176,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None): self.__class__.__name__)) try: setattr(outputs, key, val) - _ = getattr(outputs, key) + getattr(outputs, key) except TraitError as error: if hasattr(error, 'info') and \ error.info.startswith("an existing"): @@ -1270,118 +1276,6 @@ def _read(self, drain): self._lastidx = len(self._rows) -# Get number of threads for process -def _get_num_threads(proc): - """Function to get the number of threads a process is using - NOTE: If - - Parameters - ---------- - proc : psutil.Process instance - the process to evaluate thead usage of - - Returns - ------- - num_threads : int - the number of threads that the process is using - """ - - # Import packages - import psutil - - # If process is running - if proc.status() == psutil.STATUS_RUNNING: - num_threads = proc.num_threads() - elif proc.num_threads() > 1: - tprocs = [psutil.Process(thr.id) for thr in proc.threads()] - alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] - num_threads = len(alive_tprocs) - else: - num_threads = 1 - - # Try-block for errors - try: - child_threads = 0 - # Iterate through child processes and get number of their threads - for child in proc.children(recursive=True): - # Leaf process - if len(child.children()) == 0: - # If process is running, get its number of threads - if child.status() == psutil.STATUS_RUNNING: - child_thr = child.num_threads() - # If its not necessarily running, but still multi-threaded - elif child.num_threads() > 1: - # Cast each thread as a process and check for only running - tprocs = [psutil.Process(thr.id) for thr in child.threads()] - alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] - child_thr = len(alive_tprocs) - # Otherwise, no threads are running - else: - child_thr = 0 - # Increment child threads - child_threads += child_thr - # Catch any NoSuchProcess errors - except psutil.NoSuchProcess: - pass - - # Number of threads is max between found active children and parent - num_threads = max(child_threads, num_threads) - - # Return number of threads found - return num_threads - - -# Get ram usage of process -def _get_ram_mb(pid, pyfunc=False): - """Function to get the RAM usage of a process and its children - - Parameters - ---------- - pid : integer - the PID of the process to get RAM usage of - pyfunc : boolean (optional); default=False - a flag to indicate if the process is a python function; - when Pythons are multithreaded via multiprocess or threading, - children functions include their own memory + parents. if this - is set, the parent memory will removed from children memories - - Reference: http://ftp.dev411.com/t/python/python-list/095thexx8g/multiprocessing-forking-memory-usage - - Returns - ------- - mem_mb : float - the memory RAM in MB utilized by the process PID - """ - - # Import packages - import psutil - - # Init variables - _MB = 1024.0**2 - - # Try block to protect against any dying processes in the interim - try: - # Init parent - parent = psutil.Process(pid) - # Get memory of parent - parent_mem = parent.memory_info().rss - mem_mb = parent_mem/_MB - - # Iterate through child processes - for child in parent.children(recursive=True): - child_mem = child.memory_info().rss - if pyfunc: - child_mem -= parent_mem - mem_mb += child_mem/_MB - - # Catch if process dies, return gracefully - except psutil.NoSuchProcess: - pass - - # Return memory - return mem_mb - - def _canonicalize_env(env): """Windows requires that environment be dicts with bytes as keys and values This function converts any unicode entries for Windows only, returning the @@ -1411,52 +1305,14 @@ def _canonicalize_env(env): return out_env -# Get max resources used for process -def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): - """Function to get the RAM and threads usage of a process - - Parameters - ---------- - pid : integer - the process ID of process to profile - mem_mb : float - the high memory watermark so far during process execution (in MB) - num_threads: int - the high thread watermark so far during process execution - - Returns - ------- - mem_mb : float - the new high memory watermark of process (MB) - num_threads : float - the new high thread watermark of process - """ - - # Import packages - import psutil - - try: - mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) - num_threads = max(num_threads, _get_num_threads(psutil.Process(pid))) - except Exception as exc: - iflogger.info('Could not get resources used by process. Error: %s'\ - % exc) - - # Return resources - return mem_mb, num_threads - - def run_command(runtime, output=None, timeout=0.01, redirect_x=False): """Run a command, read stdout and stderr, prefix with timestamp. The returned runtime contains a merged stdout+stderr log with timestamps """ - # Init logger - logger = logging.getLogger('workflow') - # Init variables - PIPE = subprocess.PIPE + PIPE = sp.PIPE cmdline = runtime.cmdline if redirect_x: @@ -1476,28 +1332,23 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False): stderr = open(errfile, 'wb') # t=='text'===default stdout = open(outfile, 'wb') - proc = subprocess.Popen(cmdline, - stdout=stdout, - stderr=stderr, - shell=True, - cwd=runtime.cwd, - env=env) + proc = sp.Popen(cmdline, + stdout=stdout, + stderr=stderr, + shell=True, + cwd=runtime.cwd, + env=env) else: - proc = subprocess.Popen(cmdline, - stdout=PIPE, - stderr=PIPE, - shell=True, - cwd=runtime.cwd, - env=env) + proc = sp.Popen(cmdline, + stdout=PIPE, + stderr=PIPE, + shell=True, + cwd=runtime.cwd, + env=env) result = {} errfile = os.path.join(runtime.cwd, 'stderr.nipype') outfile = os.path.join(runtime.cwd, 'stdout.nipype') - # Init variables for memory profiling - mem_mb = 0 - num_threads = 1 - interval = .5 - if output == 'stream': streams = [Stream('stdout', proc.stdout), Stream('stderr', proc.stderr)] @@ -1513,13 +1364,12 @@ def _process(drain=0): else: for stream in res[0]: stream.read(drain) + while proc.returncode is None: - if runtime_profile: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) proc.poll() _process() - time.sleep(interval) + time.sleep(0) + _process(drain=1) # collect results, merge and return @@ -1533,12 +1383,6 @@ def _process(drain=0): result['merged'] = [r[1] for r in temp] if output == 'allatonce': - if runtime_profile: - while proc.returncode is None: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) - proc.poll() - time.sleep(interval) stdout, stderr = proc.communicate() stdout = stdout.decode(default_encoding) stderr = stderr.decode(default_encoding) @@ -1546,32 +1390,20 @@ def _process(drain=0): result['stderr'] = stderr.split('\n') result['merged'] = '' if output == 'file': - if runtime_profile: - while proc.returncode is None: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) - proc.poll() - time.sleep(interval) - ret_code = proc.wait() + proc.wait() stderr.flush() stdout.flush() - result['stdout'] = [line.decode(default_encoding).strip() for line in open(outfile, 'rb').readlines()] - result['stderr'] = [line.decode(default_encoding).strip() for line in open(errfile, 'rb').readlines()] + result['stdout'] = [line.decode(default_encoding).strip() + for line in open(outfile, 'rb').readlines()] + result['stderr'] = [line.decode(default_encoding).strip() + for line in open(errfile, 'rb').readlines()] result['merged'] = '' if output == 'none': - if runtime_profile: - while proc.returncode is None: - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads) - proc.poll() - time.sleep(interval) proc.communicate() result['stdout'] = [] result['stderr'] = [] result['merged'] = '' - setattr(runtime, 'runtime_memory_gb', mem_mb/1024.0) - setattr(runtime, 'runtime_threads', num_threads) runtime.stderr = '\n'.join(result['stderr']) runtime.stdout = '\n'.join(result['stdout']) runtime.merged = result['merged'] @@ -1585,19 +1417,19 @@ def get_dependencies(name, environ): Uses otool on darwin, ldd on linux. Currently doesn't support windows. """ - PIPE = subprocess.PIPE + PIPE = sp.PIPE if sys.platform == 'darwin': - proc = subprocess.Popen('otool -L `which %s`' % name, - stdout=PIPE, - stderr=PIPE, - shell=True, - env=environ) + proc = sp.Popen('otool -L `which %s`' % name, + stdout=PIPE, + stderr=PIPE, + shell=True, + env=environ) elif 'linux' in sys.platform: - proc = subprocess.Popen('ldd `which %s`' % name, - stdout=PIPE, - stderr=PIPE, - shell=True, - env=environ) + proc = sp.Popen('ldd `which %s`' % name, + stdout=PIPE, + stderr=PIPE, + shell=True, + env=environ) else: return 'Platform %s not supported' % sys.platform o, e = proc.communicate() @@ -1607,7 +1439,7 @@ def get_dependencies(name, environ): class CommandLineInputSpec(BaseInterfaceInputSpec): args = Str(argstr='%s', desc='Additional parameters to the command') environ = DictStrStr(desc='Environment variables', usedefault=True, - nohash=True) + nohash=True) # This input does not have a "usedefault=True" so the set_default_terminal_output() # method would work terminal_output = traits.Enum('stream', 'allatonce', 'file', 'none', @@ -1647,6 +1479,7 @@ class must be instantiated with a command argument {'args': '-al', 'environ': {'DISPLAY': ':1'}, 'ignore_exception': False, + 'resource_monitor': True, 'terminal_output': 'stream'} >>> cli.inputs.get_hashval()[0][0] # doctest: +ALLOW_UNICODE @@ -1745,12 +1578,12 @@ def version_from_command(self, flag='-v'): if _exists_in_path(cmdname, env): out_environ = self._get_environ() env.update(out_environ) - proc = subprocess.Popen(' '.join((cmdname, flag)), - shell=True, - env=env, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - ) + proc = sp.Popen(' '.join((cmdname, flag)), + shell=True, + env=env, + stdout=sp.PIPE, + stderr=sp.PIPE, + ) o, e = proc.communicate() return o @@ -1905,7 +1738,7 @@ def _list_outputs(self): metadata = dict(name_source=lambda t: t is not None) traits = self.inputs.traits(**metadata) if traits: - outputs = self.output_spec().get() #pylint: disable=E1102 + outputs = self.output_spec().get() # pylint: disable=E1102 for name, trait_spec in list(traits.items()): out_name = name if trait_spec.output_name is not None: @@ -1953,8 +1786,8 @@ def _parse_inputs(self, skip=None): final_args[pos] = arg else: all_args.append(arg) - first_args = [arg for pos, arg in sorted(initial_args.items())] - last_args = [arg for pos, arg in sorted(final_args.items())] + first_args = [el for _, el in sorted(initial_args.items())] + last_args = [el for _, el in sorted(final_args.items())] return first_args + all_args + last_args @@ -2025,7 +1858,7 @@ class SEMLikeCommandLine(CommandLine): """ def _list_outputs(self): - outputs = self.output_spec().get() #pylint: disable=E1102 + outputs = self.output_spec().get() # pylint: disable=E1102 return self._outputs_from_inputs(outputs) def _outputs_from_inputs(self, outputs): @@ -2062,7 +1895,7 @@ def validate(self, object, name, value): # want to treat range and other sequences (except str) as list if not isinstance(value, (str, bytes)) and isinstance(value, collections.Sequence): - value = list(value) + value = list(value) if not isdefined(value) or \ (isinstance(value, list) and len(value) == 0): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index a2cbc2a440..875ed96064 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -94,6 +94,9 @@ def test_BDP_inputs(): ), phaseEncodingDirection=dict(argstr='--dir=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigidRegMeasure=dict(argstr='--rigid-reg-measure %s', ), skipDistortionCorr=dict(argstr='--no-distortion-correction', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index f24900c6a4..8644ea5785 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -60,6 +60,9 @@ def test_Bfc_inputs(): outputMaskedBiasField=dict(argstr='--maskedbias %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), splineLambda=dict(argstr='-w %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index a253bdcafc..129a07ee06 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -52,6 +52,9 @@ def test_Bse_inputs(): radius=dict(argstr='-r %f', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index f219aa82af..387e366b53 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -42,6 +42,9 @@ def test_Cerebro_inputs(): outputWarpTransformFile=dict(argstr='--warp %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), tempDirectory=dict(argstr='--tempdir %s', ), tempDirectoryBase=dict(argstr='--tempdirbase %s', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 6e0fe3851c..bef8d4f0af 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -29,6 +29,9 @@ def test_Cortex_inputs(): outputCerebrumMask=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index be334c7096..96ad0ca409 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -20,6 +20,9 @@ def test_Dewisp_inputs(): outputMaskFile=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sizeThreshold=dict(argstr='-t %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index 42887e8883..ab6552088a 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -30,6 +30,9 @@ def test_Dfs_inputs(): ), postSmoothFlag=dict(argstr='--postsmooth', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalingPercentile=dict(argstr='-f %f', ), smoothingConstant=dict(argstr='-a %f', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index 5bdfa45f0e..f6c55ccc03 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -32,6 +32,9 @@ def test_Hemisplit_inputs(): ), pialSurfaceFile=dict(argstr='-p %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index d4511fee33..3185157fe7 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -43,6 +43,9 @@ def test_Pialmesh_inputs(): ), recomputeNormals=dict(argstr='--norm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), searchRadius=dict(argstr='-r %f', usedefault=True, ), diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index 08c7f3b894..9ab6f77511 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -23,6 +23,9 @@ def test_Pvc_inputs(): outputTissueFractionFile=dict(argstr='-f %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialPrior=dict(argstr='-l %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py index 305fd26bf8..e898a2f3bd 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py @@ -31,6 +31,9 @@ def test_SVReg_inputs(): ), refineOutputs=dict(argstr="'-r'", ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shortMessages=dict(argstr="'-gui'", ), skipToIntensityReg=dict(argstr="'-p'", diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index 5a2b0931f8..bce9e758a6 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -26,6 +26,9 @@ def test_Scrubmask_inputs(): outputMaskFile=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index e96363e4f7..0588aca6ae 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -29,6 +29,9 @@ def test_Skullfinder_inputs(): ), performFinalOpening=dict(argstr='--finalOpening', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalpLabelValue=dict(argstr='--scalplabel %d', ), skullLabelValue=dict(argstr='--skulllabel %d', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index 498dd56e05..4c432fbcd1 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -26,6 +26,9 @@ def test_Tca_inputs(): outputMaskFile=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timer=dict(argstr='--timer', diff --git a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py index 8bd388c36c..0138cc0f83 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py @@ -12,6 +12,9 @@ def test_ThicknessPVC_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjectFilePrefix=dict(argstr='%s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index 39700f5304..e9b99a94ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -65,6 +65,9 @@ def test_AnalyzeHeader_inputs(): readheader=dict(argstr='-readheader %s', position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaleinter=dict(argstr='-scaleinter %d', units='NA', ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index 7016825269..8b8c568795 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -30,6 +30,9 @@ def test_ComputeEigensystem_inputs(): outputdatatype=dict(argstr='-outputdatatype %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 6bf41d7b95..a7be61e132 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -26,6 +26,9 @@ def test_ComputeFractionalAnisotropy_inputs(): ), outputdatatype=dict(argstr='-outputdatatype %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 16b3e6f163..fa66b9c213 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -26,6 +26,9 @@ def test_ComputeMeanDiffusivity_inputs(): ), outputdatatype=dict(argstr='-outputdatatype %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 3adc971f7b..3164e2c98b 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -26,6 +26,9 @@ def test_ComputeTensorTrace_inputs(): ), outputdatatype=dict(argstr='-outputdatatype %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index 715db443da..8f33d6a936 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -18,6 +18,9 @@ def test_Conmat_inputs(): output_root=dict(argstr='-outputroot %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalar_file=dict(argstr='-scalarfile %s', requires=['tract_stat'], ), diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index f0f1c789c4..10c98bc483 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -24,6 +24,9 @@ def test_DT2NIfTI_inputs(): genfile=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index e4a0115dc3..86c64c8fd3 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -25,6 +25,9 @@ def test_DTIFit_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', mandatory=True, position=2, diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 285891f0cf..eeb488cafb 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -31,6 +31,9 @@ def test_DTLUTGen_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samples=dict(argstr='-samples %d', units='NA', ), diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index ebde9241a1..c0b9038a61 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -29,6 +29,9 @@ def test_DTMetric_inputs(): outputfile=dict(argstr='-outputfile %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index efbaa1e95f..d96cc5c7ef 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -41,6 +41,9 @@ def test_FSL2Scheme_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), usegradmod=dict(argstr='-usegradmod', diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 2a17d57bc8..c6d214360c 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -24,6 +24,9 @@ def test_Image2Voxel_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index cd0aa1380e..014d66291e 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -22,6 +22,9 @@ def test_ImageStats_inputs(): output_root=dict(argstr='-outputroot %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), stat=dict(argstr='-stat %s', mandatory=True, units='NA', diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index a8f03034d3..69f31ea9b8 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -30,6 +30,9 @@ def test_LinRecon_inputs(): mandatory=True, position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', mandatory=True, position=2, diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index c9ac46d3d1..87356a90a8 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -39,6 +39,9 @@ def test_MESD_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index c3555de524..9267e72df3 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -42,6 +42,9 @@ def test_ModelFit_inputs(): ), residualmap=dict(argstr='-residualmap %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 999db17138..75db7a39cf 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -24,6 +24,9 @@ def test_NIfTIDT2Camino_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s0_file=dict(argstr='-s0 %s', ), scaleinter=dict(argstr='-scaleinter %s', diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index 1a64aa285c..58d9bd7103 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -39,6 +39,9 @@ def test_PicoPDFs_inputs(): position=4, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index da68661ea7..39a23b1b6c 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -78,6 +78,9 @@ def test_ProcStreamlines_inputs(): resamplestepsize=dict(argstr='-resamplestepsize %d', units='NA', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedfile=dict(argstr='-seedfile %s', ), seedpointmm=dict(argstr='-seedpointmm %s', diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index d55474e837..a9a3238401 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -28,6 +28,9 @@ def test_QBallMX_inputs(): rbfsigma=dict(argstr='-rbfsigma %f', units='NA', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index ca5044349d..212d5bf11c 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -39,6 +39,9 @@ def test_SFLUTGen_inputs(): pdf=dict(argstr='-pdf %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index ba9993d7bb..fa6fd83132 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -27,6 +27,9 @@ def test_SFPICOCalibData_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index f95f139256..7d0dc31929 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -45,6 +45,9 @@ def test_SFPeaks_inputs(): rbfpointset=dict(argstr='-rbfpointset %d', units='NA', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='%s', ), searchradius=dict(argstr='-searchradius %f', diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index f74dee86b3..af3ce192cf 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -28,6 +28,9 @@ def test_Shredder_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), space=dict(argstr='%d', position=3, units='NA', diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index 4903bbf163..02c69ae012 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -53,6 +53,9 @@ def test_Track_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 94b2abedaf..8d8a6f369d 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -53,6 +53,9 @@ def test_TrackBallStick_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 3855f8ecc1..75b8813817 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -70,6 +70,9 @@ def test_TrackBayesDirac_inputs(): ), pointset=dict(argstr='-pointset %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index e3572430b7..da710533b9 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -59,6 +59,9 @@ def test_TrackBedpostxDeter_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index bb4c0ed898..293384fb9c 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -62,6 +62,9 @@ def test_TrackBedpostxProba_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 30d87816b8..c0ded6c2ec 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -63,6 +63,9 @@ def test_TrackBootstrap_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scheme_file=dict(argstr='-schemefile %s', mandatory=True, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 1edd055921..a2b1fcf0e0 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -53,6 +53,9 @@ def test_TrackDT_inputs(): ), outputtracts=dict(argstr='-outputtracts %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index b62e25cd93..2409f7af48 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -58,6 +58,9 @@ def test_TrackPICo_inputs(): ), pdf=dict(argstr='-pdf %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seedfile %s', position=2, ), diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index 5f991d4090..13d7c31a7b 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -28,6 +28,9 @@ def test_TractShredder_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), space=dict(argstr='%d', position=3, units='NA', diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 775f3eedd9..aa9a488e78 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -29,6 +29,9 @@ def test_VtkStreamlines_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalar_file=dict(argstr='-scalarfile %s', position=3, ), diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index 258286bd9d..a0fb4c433a 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -32,6 +32,9 @@ def test_Camino2Trackvis_inputs(): genfile=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel_dims=dict(argstr='-x %s', diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 9ebd53f272..c0c0bec9fd 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -23,6 +23,9 @@ def test_Trackvis2Camino_inputs(): genfile=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index 6252ee9218..21408aa2d8 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -14,6 +14,9 @@ def test_AverageNetworks_inputs(): out_gexf_groupavg=dict(), out_gpickled_groupavg=dict(), resolution_network_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = AverageNetworks.input_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index ea97eaecd8..3f52c3dd10 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -23,6 +23,9 @@ def test_CFFConverter_inputs(): publisher=dict(), references=dict(), relation=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rights=dict(), script_files=dict(), species=dict(usedefault=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 3126066243..72d4bf0800 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -11,6 +11,9 @@ def test_CreateNodes_inputs(): ), resolution_network_file=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), roi_file=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index 18dd6c1ec6..11b86bedc3 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -11,6 +11,9 @@ def test_MergeCNetworks_inputs(): ), out_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = MergeCNetworks.input_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index e031b8cae2..0567c9a0ed 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -18,6 +18,9 @@ def test_NetworkBasedStatistic_inputs(): ), out_nbs_network=dict(), out_nbs_pval_network=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), t_tail=dict(usedefault=True, ), threshold=dict(usedefault=True, diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index 46c077af1b..7f3e803832 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -25,6 +25,9 @@ def test_NetworkXMetrics_inputs(): ), out_pickled_extra_measures=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), treat_as_weighted_graph=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index f62f98b51e..6f9d01889c 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -14,6 +14,9 @@ def test_Parcellate_inputs(): ), parcellation_name=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(mandatory=True, ), subjects_dir=dict(), diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index 41f99aa5bf..cfc645f105 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -17,6 +17,9 @@ def test_ROIGen_inputs(): ), out_roi_file=dict(genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_freesurfer_LUT=dict(xor=['LUT_file'], ), ) diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index 333578742e..4af5c8253c 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -36,6 +36,9 @@ def test_DTIRecon_inputs(): output_type=dict(argstr='-ot %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index ea20252ae3..728fa94aab 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -49,6 +49,9 @@ def test_DTITracker_inputs(): ), random_seed=dict(argstr='-rseed', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), step_length=dict(argstr='-l %f', ), swap_xy=dict(argstr='-sxy', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 699c5c920d..966479bce8 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -34,6 +34,9 @@ def test_HARDIMat_inputs(): ), reference_file=dict(argstr='-ref %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 8fa38aab42..1dd2897d9c 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -47,6 +47,9 @@ def test_ODFRecon_inputs(): output_type=dict(argstr='-ot %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sharpness=dict(argstr='-s %f', ), subtract_background=dict(argstr='-bg', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 647cb3767e..d775595ea0 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -56,6 +56,9 @@ def test_ODFTracker_inputs(): ), random_seed=dict(argstr='-rseed %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), runge_kutta2=dict(argstr='-rk2', ), slice_order=dict(argstr='-sorder %d', diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 0ce7d67281..7dd679c810 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -16,6 +16,9 @@ def test_SplineFilter_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), step_length=dict(argstr='%f', mandatory=True, position=1, diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index 296c311663..926804ffcf 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -16,6 +16,9 @@ def test_TrackMerge_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), track_files=dict(argstr='%s...', diff --git a/nipype/interfaces/dipy/tests/test_auto_APMQball.py b/nipype/interfaces/dipy/tests/test_auto_APMQball.py index 934bc3efff..673c825dbd 100644 --- a/nipype/interfaces/dipy/tests/test_auto_APMQball.py +++ b/nipype/interfaces/dipy/tests/test_auto_APMQball.py @@ -17,6 +17,9 @@ def test_APMQball_inputs(): ), mask_file=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = APMQball.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index 658294df02..a724fa94e3 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -18,6 +18,9 @@ def test_CSD_inputs(): in_mask=dict(), out_fods=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response=dict(), save_fods=dict(usedefault=True, ), diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index fddaeb3bcb..cd4e7ebb96 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -17,6 +17,9 @@ def test_DTI_inputs(): ), mask_file=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = DTI.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py index 5b98c1353d..a4b4e636ff 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py @@ -7,6 +7,9 @@ def test_DipyBaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = DipyBaseInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index 6bee2dde83..27106b1c08 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -16,6 +16,9 @@ def test_DipyDiffusionInterface_inputs(): in_file=dict(mandatory=True, ), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = DipyDiffusionInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index d03508c8ce..26566c314c 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -27,6 +27,9 @@ def test_EstimateResponseSH_inputs(): out_prefix=dict(), recursive=dict(xor=['auto'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response=dict(usedefault=True, ), roi_radius=dict(usedefault=True, diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index 5458d5bb98..1dc8d9d407 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -18,6 +18,9 @@ def test_RESTORE_inputs(): in_mask=dict(), noise_mask=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = RESTORE.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index a3d708fb71..03c07bd158 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -37,6 +37,9 @@ def test_SimulateMultiTensor_inputs(): ), out_mask=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), snr=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index 80ef4ecab4..2b9ad2cdc2 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -27,6 +27,9 @@ def test_StreamlineTractography_inputs(): peak_threshold=dict(mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_seeds=dict(mandatory=True, usedefault=True, ), diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index 02000714a1..957f78da57 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -17,6 +17,9 @@ def test_TensorMode_inputs(): ), mask_file=dict(), out_prefix=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = TensorMode.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 8308be79e8..ec71c7ddee 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -15,6 +15,9 @@ def test_TrackDensityMap_inputs(): points_space=dict(usedefault=True, ), reference=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), voxel_dims=dict(), ) inputs = TrackDensityMap.input_spec() diff --git a/nipype/interfaces/dynamic_slicer.py b/nipype/interfaces/dynamic_slicer.py index d38f4171f3..4d1df1e136 100644 --- a/nipype/interfaces/dynamic_slicer.py +++ b/nipype/interfaces/dynamic_slicer.py @@ -25,7 +25,8 @@ class SlicerCommandLine(CommandLine): output_spec = DynamicTraitedSpec def _grab_xml(self, module): - cmd = CommandLine(command="Slicer3", args="--launch %s --xml" % module) + cmd = CommandLine(command="Slicer3", resource_monitor=False, + args="--launch %s --xml" % module) ret = cmd.run() if ret.runtime.returncode == 0: return xml.dom.minidom.parseString(ret.runtime.stdout) diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index 1be5007b28..8898ddfff1 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -19,6 +19,9 @@ def test_AnalyzeWarp_inputs(): mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transform_file=dict(argstr='-tp %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index eb88b4c7e5..4901a73053 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -22,6 +22,9 @@ def test_ApplyWarp_inputs(): mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transform_file=dict(argstr='-tp %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index cd995b8aa2..25e78b48d6 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -16,6 +16,9 @@ def test_EditTransform_inputs(): output_type=dict(argstr='ResultImagePixelType', ), reference_image=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), transform_file=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index 713f912ef7..2ea6803da2 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -22,6 +22,9 @@ def test_PointsWarp_inputs(): points_file=dict(argstr='-def %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transform_file=dict(argstr='-tp %s', diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index b14af447c8..b9c261981c 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -34,6 +34,9 @@ def test_Registration_inputs(): parameters=dict(argstr='-p %s...', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index 5961ef84cc..86400f7812 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -22,6 +22,9 @@ def test_AddXFormToHeader_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index bcab8391db..c85f3dd3a3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -35,6 +35,9 @@ def test_Aparc2Aseg_inputs(): out_file=dict(argstr='--o %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_annotation=dict(mandatory=True, ), rh_pial=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index 802ebbc1d3..b5b7b0a02c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -18,6 +18,9 @@ def test_Apas2Aseg_inputs(): out_file=dict(argstr='--o %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 2910fbdc62..37065c3621 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -33,6 +33,9 @@ def test_ApplyMask_inputs(): name_template='%s_masked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index e4f93a1ce2..a507947805 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -55,6 +55,9 @@ def test_ApplyVolTransform_inputs(): mandatory=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--mov %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 4550cb071b..857132d39b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -55,6 +55,9 @@ def test_Binarize_inputs(): ), out_type=dict(argstr='', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rmax=dict(argstr='--rmax %f', ), rmin=dict(argstr='--rmin %f', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index 17028f990d..188654ecbe 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -37,6 +37,9 @@ def test_CALabel_inputs(): ), relabel_unlikely=dict(argstr='-relabel_unlikely %d %.1f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index ab6912accf..7932397f8e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -33,6 +33,9 @@ def test_CANormalize_inputs(): name_template='%s_norm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index e76437e24d..5bc8fa3217 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -36,6 +36,9 @@ def test_CARegister_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', position=-2, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index 19b38b0273..e3992d793c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -17,6 +17,9 @@ def test_CheckTalairachAlignment_inputs(): position=-1, xor=['subject'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject=dict(argstr='-subj %s', mandatory=True, position=-1, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index 8f702078ea..7c17ea8787 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -40,6 +40,9 @@ def test_Concatenate_inputs(): ), paired_stats=dict(argstr='--paired-%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sign=dict(argstr='--%s', ), sort=dict(argstr='--sort', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index b15dfee307..a3662b584b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -27,6 +27,9 @@ def test_ConcatenateLTA_inputs(): name_template='%s-long', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 57d56b9726..e4bf7756d1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -24,6 +24,9 @@ def test_Contrast_inputs(): ), rawavg=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--s %s', mandatory=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index 03474551d6..8c892bd5bf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -24,6 +24,9 @@ def test_Curvature_inputs(): ), n=dict(argstr='-n', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save=dict(argstr='-w', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index 9bb6f9fc50..7737fe66d0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -32,6 +32,9 @@ def test_CurvatureStats_inputs(): name_source=['hemisphere'], name_template='%s.curv.stats', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', mandatory=True, position=-4, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index a0e7b0fbdb..da2f91336e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -22,6 +22,9 @@ def test_DICOMConvert_inputs(): ), out_type=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seq_list=dict(requires=['dicom_info'], ), subject_dir_template=dict(usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index 97e5910c17..af82ac8f2c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -28,6 +28,9 @@ def test_EMRegister_inputs(): name_template='%s_transform.lta', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skull=dict(argstr='-skull', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index 081856a5fa..72b4627a6e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -26,6 +26,9 @@ def test_EditWMwithAseg_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seg_file=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index d2eba7ed16..b6dbb51e3d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -16,6 +16,9 @@ def test_EulerNumber_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index eb85cba81b..49b6c9a2f9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -21,6 +21,9 @@ def test_ExtractMainComponent_inputs(): name_template='%s.maincmp', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index e718c1c4cb..4137399e28 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -12,6 +12,9 @@ def test_FSCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py index 072161bd52..323b39a53a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py @@ -13,6 +13,9 @@ def test_FSCommandOpenMP_inputs(): usedefault=True, ), num_threads=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py index b685a4d82a..789999d08e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py @@ -12,6 +12,9 @@ def test_FSScriptCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 8496ca2ae5..519290bc7f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -21,6 +21,9 @@ def test_FitMSParams_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), te_list=dict(), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index ec064372eb..3fe86e03ff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -30,6 +30,9 @@ def test_FixTopology_inputs(): ), mgz=dict(argstr='-mgz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), sphere=dict(argstr='-sphere %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 24c8214fba..f93292317d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -24,6 +24,9 @@ def test_FuseSegmentations_inputs(): out_file=dict(mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', position=-3, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index e99a1de407..f26aadb064 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -88,6 +88,9 @@ def test_GLMFit_inputs(): prune_thresh=dict(argstr='--prune_thr %f', xor=['noprune'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resynth_test=dict(argstr='--resynthtest %d', ), save_cond=dict(argstr='--save-cond', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index c479c7727a..9f9dee34db 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -15,6 +15,9 @@ def test_ImageInfo_inputs(): in_file=dict(argstr='%s', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 4f986f6a93..e69ce01446 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -27,6 +27,9 @@ def test_Jacobian_inputs(): name_template='%s.jacobian', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py index a7e4a121af..4f4cf94c7f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py @@ -51,6 +51,9 @@ def test_LTAConvert_inputs(): ), out_reg=dict(argstr='--outreg %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--src %s', ), target_conform=dict(argstr='--trgconform', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index bba05d8690..0b4bd7a406 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -28,6 +28,9 @@ def test_Label2Annot_inputs(): out_annot=dict(argstr='--a %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--s %s', mandatory=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index ab1a98f286..3353b02aff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -25,6 +25,9 @@ def test_Label2Label_inputs(): registration_method=dict(argstr='--regmethod %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_label=dict(argstr='--srclabel %s', mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index c58fd71532..20327f2aa7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -53,6 +53,9 @@ def test_Label2Vol_inputs(): reg_header=dict(argstr='--regheader %s', xor=('reg_file', 'reg_header', 'identity'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seg_file=dict(argstr='--seg %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index acf272a603..aee3cc1636 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -31,6 +31,9 @@ def test_MNIBiasCorrection_inputs(): ), protocol_iterations=dict(argstr='--proto-iters %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shrink=dict(argstr='--shrink %d', ), stop=dict(argstr='--stop %f', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index b0b1b39a36..2af45858a0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -18,6 +18,9 @@ def test_MPRtoMNI305_inputs(): reference_dir=dict(mandatory=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), target=dict(mandatory=True, usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 9a1f011d77..223456e780 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -144,6 +144,9 @@ def test_MRIConvert_inputs(): ), reslice_like=dict(argstr='--reslice_like %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sdcm_list=dict(argstr='--sdcmlist %s', ), skip_n=dict(argstr='--nskip %d', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py index 5ba95570c8..c48de3868b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py @@ -65,6 +65,9 @@ def test_MRICoreg_inputs(): reference_mask=dict(argstr='--ref-mask %s', position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saturation_threshold=dict(argstr='--sat %g', ), sep=dict(argstr='--sep %s...', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index 1302f7a2dd..f1429e60a4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -22,6 +22,9 @@ def test_MRIFill_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation=dict(argstr='-segmentation %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index 13c70086df..d66ae62824 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -28,6 +28,9 @@ def test_MRIMarchingCubes_inputs(): genfile=True, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 85db09eb46..4db4d5ab0c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -35,6 +35,9 @@ def test_MRIPretess_inputs(): name_template='%s_pretesswm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index a35c091e04..9c9d1c759f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -35,6 +35,9 @@ def test_MRISPreproc_inputs(): ), proj_frac=dict(argstr='--projfrac %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index e3a266d61a..94fe364872 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -38,6 +38,9 @@ def test_MRISPreprocReconAll_inputs(): ), proj_frac=dict(argstr='--projfrac %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_surfreg_target=dict(requires=['surfreg_files'], ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 58979a75a7..945b35d11b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -24,6 +24,9 @@ def test_MRITessellate_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 50897b18a7..79f87e3cdb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -39,6 +39,9 @@ def test_MRIsCALabel_inputs(): name_template='%s.aparc.annot', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), smoothwm=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index ad45ba32ed..c15c91db95 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -35,6 +35,9 @@ def test_MRIsCalc_inputs(): out_file=dict(argstr='-o %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py index 2eae71deea..fbc627ff11 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py @@ -21,6 +21,9 @@ def test_MRIsCombine_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 6d4501c8ca..0e27b2956d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -45,6 +45,9 @@ def test_MRIsConvert_inputs(): ), rescale=dict(argstr='-r', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scalarcurv_file=dict(argstr='-c %s', ), scale=dict(argstr='-s %.3f', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py index c74f31bd59..99ff1791a1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py @@ -32,6 +32,9 @@ def test_MRIsExpand_inputs(): pial=dict(argstr='-pial %s', copyfile=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_averages=dict(argstr='-A %d', ), sphere=dict(copyfile=False, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index a2ea82a4f0..62cb3386ac 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -29,6 +29,9 @@ def test_MRIsInflate_inputs(): ), out_sulc=dict(xor=['no_save_sulc'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index cf4f27522e..367a2fff60 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -27,6 +27,9 @@ def test_MS_LDA_inputs(): ), mask_file=dict(argstr='-mask %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shift=dict(argstr='-shift %d', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index a230fac5f4..f68334c203 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -15,6 +15,9 @@ def test_MakeAverageSubject_inputs(): out_name=dict(argstr='--out %s', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), subjects_ids=dict(argstr='--subjects %s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index ff49e627ba..ed9b9e450b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -49,6 +49,9 @@ def test_MakeSurfaces_inputs(): ), orig_white=dict(argstr='-orig_white %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index c081e76912..068e0053e3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -28,6 +28,9 @@ def test_Normalize_inputs(): name_template='%s_norm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentation=dict(argstr='-aseg %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index e5d7c18980..5e42735f03 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -88,6 +88,9 @@ def test_OneSampleTTest_inputs(): prune_thresh=dict(argstr='--prune_thr %f', xor=['noprune'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resynth_test=dict(argstr='--resynthtest %d', ), save_cond=dict(argstr='--save-cond', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index 3713464c7c..730b4ccf6a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -25,6 +25,9 @@ def test_Paint_inputs(): name_template='%s.avg_curv', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index 28de43ee39..c1c57f31a8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -44,6 +44,9 @@ def test_ParcellationStats_inputs(): genfile=True, requires=['tabular_output'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_pial=dict(mandatory=True, ), rh_white=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index 54bf4467e5..1c81ac4e0b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -18,6 +18,9 @@ def test_ParseDICOMDir_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sortbyrun=dict(argstr='--sortbyrun', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 9a84bf9f28..942322631f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -96,6 +96,9 @@ def test_ReconAll_inputs(): ), parallel=dict(argstr='-parallel', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='-subjid %s', usedefault=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index 33c6e0c941..7090037d5c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -29,6 +29,9 @@ def test_Register_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), target=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index c10b12911c..2196294c63 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -20,6 +20,9 @@ def test_RegisterAVItoTalairach_inputs(): position=3, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), target=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index 4e46bbc03d..aea7cc51b8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -26,6 +26,9 @@ def test_RelabelHypointensities_inputs(): name_template='%s.hypos.mgz', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_white=dict(copyfile=True, mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index 14a9cd8edb..439888c525 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -24,6 +24,9 @@ def test_RemoveIntersection_inputs(): name_template='%s', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index 023bf6552a..9a5a01e32c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -25,6 +25,9 @@ def test_RemoveNeck_inputs(): ), radius=dict(argstr='-radius %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), template=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 811fb85cde..02593f33ac 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -20,6 +20,9 @@ def test_Resample_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index c8b7080c26..aac06d6347 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -63,6 +63,9 @@ def test_RobustRegister_inputs(): ), registered_file=dict(argstr='--warp %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--mov %s', mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index d2b89e3235..4e0c742a57 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -42,6 +42,9 @@ def test_RobustTemplate_inputs(): mandatory=True, xor=['auto_detect_sensitivity'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaled_intensity_outputs=dict(argstr='--iscaleout %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index a257fd7e2e..013a87d58c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -74,6 +74,9 @@ def test_SampleToSurface_inputs(): ), reshape_slices=dict(argstr='--rf %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_method=dict(argstr='%s', mandatory=True, requires=['sampling_range', 'sampling_units'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 04e9f830d1..f3383237ed 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -76,6 +76,9 @@ def test_SegStats_inputs(): ), partial_volume_file=dict(argstr='--pv %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict(argstr='--seg %s', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index eecc3aa4e5..4e2f3875ac 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -85,6 +85,9 @@ def test_SegStatsReconAll_inputs(): partial_volume_file=dict(argstr='--pv %s', ), presurf_seg=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_orig_nofix=dict(mandatory=True, ), rh_pial=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index f54484b5b7..101356461d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -27,6 +27,9 @@ def test_SegmentCC_inputs(): out_rotation=dict(argstr='-lta %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='%s', mandatory=True, position=-1, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index 450ad4f95b..cff075eef3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -20,6 +20,9 @@ def test_SegmentWM_inputs(): mandatory=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 5720c12975..141c6e3e0d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -28,6 +28,9 @@ def test_Smooth_inputs(): reg_file=dict(argstr='--reg %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smoothed_file=dict(argstr='--o %s', genfile=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 2419164f5f..5ac3782ce9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -35,6 +35,9 @@ def test_SmoothTessellation_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), smoothing_iterations=dict(argstr='-n %d', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index 8afabb96e6..af2a0a40ff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -28,6 +28,9 @@ def test_Sphere_inputs(): name_template='%s.sphere', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='-seed %d', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index 928a2a5127..777c51961c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -36,6 +36,9 @@ def test_SphericalAverage_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='-o %s', mandatory=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 2590827648..4aec7985b0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -24,6 +24,9 @@ def test_Surface2VolTransform_inputs(): mandatory=True, xor=['subject_id'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='--surfval %s', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index 835d4bc601..977d2e62c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -29,6 +29,9 @@ def test_SurfaceSmooth_inputs(): ), reshape=dict(argstr='--reshape', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth_iters=dict(argstr='--smooth %d', xor=['fwhm'], ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 2043603124..637be86cc0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -58,6 +58,9 @@ def test_SurfaceSnapshots_inputs(): ), patch_file=dict(argstr='-patch %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), reverse_overlay=dict(argstr='-revphaseflag 1', ), screenshot_stem=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 99c54a8f78..52a0ca1a53 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -22,6 +22,9 @@ def test_SurfaceTransform_inputs(): ), reshape_factor=dict(argstr='--reshape-factor', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_annot_file=dict(argstr='--sval-annot %s', mandatory=True, xor=['source_file'], diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index bc5fb23eb7..23c3abddae 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -26,6 +26,9 @@ def test_SynthesizeFLASH_inputs(): mandatory=True, position=6, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), t1_image=dict(argstr='%s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index f301168b01..7c168986ab 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -20,6 +20,9 @@ def test_TalairachAVI_inputs(): out_file=dict(argstr='--xfm %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index a6ae75b3ff..4f8d39e993 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -16,6 +16,9 @@ def test_TalairachQC_inputs(): mandatory=True, position=0, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index c5e3d65274..b8917c826a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -36,6 +36,9 @@ def test_Tkregister2_inputs(): ), reg_header=dict(argstr='--regheader', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--s %s', ), subjects_dir=dict(), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index 8a1aecaa22..5bc42a466e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -26,6 +26,9 @@ def test_UnpackSDICOMDir_inputs(): ), output_dir=dict(argstr='-targ %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), run_info=dict(argstr='-run %d %s %s %s', mandatory=True, xor=('run_info', 'config', 'seq_config'), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index b1bcaa4e40..3ebb182f5f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -28,6 +28,9 @@ def test_VolumeMask_inputs(): ), lh_white=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rh_pial=dict(mandatory=True, ), rh_white=dict(mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index 53ff443424..e76ade04ba 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -24,6 +24,9 @@ def test_WatershedSkullStrip_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subjects_dir=dict(), t1=dict(argstr='-T1', ), diff --git a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py index 2c3eda86cb..9de2144826 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py +++ b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py @@ -35,6 +35,9 @@ def test_AR1Image_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index 1e4fb9406c..ab3e679421 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -21,6 +21,9 @@ def test_AccuracyTester_inputs(): mandatory=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trained_wts_file=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 0a74d811c3..f6c96c596f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -35,6 +35,9 @@ def test_ApplyMask_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 7b08c18c28..5f7bee70e6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -40,6 +40,9 @@ def test_ApplyTOPUP_inputs(): name_template='%s_corrected', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index bcdcc670ac..d2f784f5fc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -46,6 +46,9 @@ def test_ApplyWarp_inputs(): position=-1, xor=['abswarp'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), superlevel=dict(argstr='--superlevel=%s', ), supersample=dict(argstr='--super', diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py index 438f4ce486..52d5a32dc1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py @@ -109,6 +109,9 @@ def test_ApplyXFM_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigid2D=dict(argstr='-2D', ), save_log=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index e19577b71f..f33bd9ee75 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -20,6 +20,9 @@ def test_AvScale_inputs(): ref_file=dict(argstr='%s', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index ee6b749d7e..c29318f3c0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -33,6 +33,9 @@ def test_B0Calc_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), x_b0=dict(argstr='--b0x=%0.2f', diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 782c1a9317..38b147d924 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -69,6 +69,9 @@ def test_BEDPOSTX5_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rician=dict(argstr='--rician', ), sample_every=dict(argstr='-s %d', diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index 98af74707d..fa0e2a2ecc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -50,6 +50,9 @@ def test_BET_inputs(): remove_eyes=dict(argstr='-S', xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), robust=dict(argstr='-R', xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index aae4a436dd..0dde4928d0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -45,6 +45,9 @@ def test_BinaryMaths_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index 6d2952c073..ecc5270c90 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -32,6 +32,9 @@ def test_ChangeDataType_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Classifier.py b/nipype/interfaces/fsl/tests/test_auto_Classifier.py index 713666b754..6acae3c3c9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Classifier.py +++ b/nipype/interfaces/fsl/tests/test_auto_Classifier.py @@ -17,6 +17,9 @@ def test_Classifier_inputs(): copyfile=False, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresh=dict(argstr='%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index 76487d6adc..7680f29830 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -35,6 +35,9 @@ def test_Cleaner_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index 886ef8885b..c44784bbe0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -65,6 +65,9 @@ def test_Cluster_inputs(): pthreshold=dict(argstr='--pthresh=%.10f', requires=['dlh', 'volume'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), std_space_file=dict(argstr='--stdvol=%s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index c0544c799d..a1cabb7248 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -83,6 +83,9 @@ def test_Complex_inputs(): position=1, xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), start_vol=dict(argstr='%d', position=-2, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index 5fa6e7828c..d4964186b9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -28,6 +28,9 @@ def test_ContrastMgr_inputs(): copyfile=False, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigmasquareds=dict(argstr='', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 97c0a06315..5f9bb4c208 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -47,6 +47,9 @@ def test_ConvertWarp_inputs(): relwarp=dict(argstr='--rel', xor=['abswarp'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shift_direction=dict(argstr='--shiftdir=%s', requires=['shift_in_file'], ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index 5146d1f718..0ea43bd196 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -39,6 +39,9 @@ def test_ConvertXFM_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 70922a9da9..49e79b0287 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -28,6 +28,9 @@ def test_CopyGeom_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 4badbfb2dc..b440a17341 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -51,6 +51,9 @@ def test_DTIFit_inputs(): min_z=dict(argstr='-z %d', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_tensor=dict(argstr='--save_tensor', ), sse=dict(argstr='--sse', diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 40da7affbe..774289c011 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -46,6 +46,9 @@ def test_DilateImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 87cde59644..73e4f8ffcb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -27,6 +27,9 @@ def test_DistanceMap_inputs(): mask_file=dict(argstr='--mask=%s', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py index 02c68ebc24..546b68ec43 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py +++ b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py @@ -44,6 +44,9 @@ def test_DualRegression_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 5f49d5a89e..7632e44a93 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -38,6 +38,9 @@ def test_EPIDeWarp_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='--sigma %s', usedefault=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index c5f521045f..30cb1abf43 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -70,6 +70,9 @@ def test_Eddy_inputs(): output_type=dict(), repol=dict(argstr='--repol', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), session=dict(argstr='--session=%s', ), slm=dict(argstr='--slm=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index c7606a2cea..e7eb3dca4d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -28,6 +28,9 @@ def test_EddyCorrect_inputs(): position=2, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index c34014dd57..c15960b141 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -36,6 +36,9 @@ def test_EpiReg_inputs(): output_type=dict(), pedir=dict(argstr='--pedir=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), t1_brain=dict(argstr='--t1brain=%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index a64c6f5d9e..2202a1b2e1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -46,6 +46,9 @@ def test_ErodeImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 77be2edb95..176a4f62ab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -21,6 +21,9 @@ def test_ExtractROI_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), roi_file=dict(argstr='%s', genfile=True, hash_files=False, diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 11e6cec5de..d47d4afda5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -53,6 +53,9 @@ def test_FAST_inputs(): output_type=dict(), probability_maps=dict(argstr='-p', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segment_iters=dict(argstr='-W %d', ), segments=dict(argstr='-g', diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index f2c5e46e7e..50fbe55433 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -17,6 +17,9 @@ def test_FEAT_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index e0956ee674..e402831f41 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -23,6 +23,9 @@ def test_FEATModel_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index a0f5e09177..4a021bcab7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -13,6 +13,9 @@ def test_FEATRegister_inputs(): ), reg_image=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = FEATRegister.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 7b98ac128c..a441709d8d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -45,6 +45,9 @@ def test_FIRST_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-v', diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index ed8093853d..ed7c29e3a6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -44,6 +44,9 @@ def test_FLAMEO_inputs(): outlier_iter=dict(argstr='--ioni=%d', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), run_mode=dict(argstr='--runmode=%s', mandatory=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index fabfa4054c..ffd85d95a4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -108,6 +108,9 @@ def test_FLIRT_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigid2D=dict(argstr='-2D', ), save_log=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 8e4cf47fc3..e273a5dfb5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -94,6 +94,9 @@ def test_FNIRT_inputs(): ), regularization_model=dict(argstr='--regmod=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skip_implicit_in_masking=dict(argstr='--impinm=0', ), skip_implicit_ref_masking=dict(argstr='--imprefm=0', diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index 2ade472bfa..617f3ad140 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -13,6 +13,9 @@ def test_FSLCommand_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index 280cf3a588..819f31e453 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -66,6 +66,9 @@ def test_FSLXCommand_inputs(): xor=('no_spat', 'non_linear', 'cnlinear'), ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rician=dict(argstr='--rician', ), sample_every=dict(argstr='--sampleevery=%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 93b41ea6de..01e221d454 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -57,6 +57,9 @@ def test_FUGUE_inputs(): ), poly_order=dict(argstr='--poly=%d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_fmap=dict(xor=['save_unmasked_fmap'], ), save_shift=dict(xor=['save_unmasked_shift'], diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index c0e763640c..59582898ad 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -16,6 +16,9 @@ def test_FeatureExtractor_inputs(): copyfile=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index ac62586ec5..c52b6dadbc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -40,6 +40,9 @@ def test_FilterRegressor_inputs(): out_vnscales=dict(argstr='--out_vnscales', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), var_norm=dict(argstr='--vn', diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index ef7e14fcbf..e2aa619d60 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -22,6 +22,9 @@ def test_FindTheBiggest_inputs(): position=2, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index d9ab6bc168..de64bc16b8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -61,6 +61,9 @@ def test_GLM_inputs(): out_z_name=dict(argstr='--out_z=%s', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), var_norm=dict(argstr='--vn', diff --git a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py index 9102d667b3..884b2f30c0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py +++ b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py @@ -46,6 +46,9 @@ def test_ICA_AROMA_inputs(): out_dir=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 8c1aef8b5c..5e500a2947 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -31,6 +31,9 @@ def test_ImageMaths_inputs(): position=4, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), suffix=dict(), terminal_output=dict(nohash=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 73deecb7e5..38ba476069 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -30,6 +30,9 @@ def test_ImageMeants_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), show_all=dict(argstr='--showall', ), spatial_coord=dict(argstr='-c %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 1a4739a320..5fcb8cf070 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -23,6 +23,9 @@ def test_ImageStats_inputs(): position=3, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), split_4d=dict(argstr='-t', position=1, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index 02624a6d2c..55e2aef927 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -37,6 +37,9 @@ def test_InvWarp_inputs(): relative=dict(argstr='--rel', xor=['absolute'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warp=dict(argstr='--warp=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 0d33d852a2..c324d7b250 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -36,6 +36,9 @@ def test_IsotropicSmooth_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='-s %.5f', mandatory=True, position=4, diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 81f74cc923..fd1de91739 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -9,6 +9,9 @@ def test_L2Model_inputs(): ), num_copes=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = L2Model.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index f5fcfe4093..da42942fab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -15,6 +15,9 @@ def test_Level1Design_inputs(): model_serial_correlations=dict(mandatory=True, ), orthogonalization=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), session_info=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index 300f829bfa..ddfaf2d411 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -37,6 +37,9 @@ def test_MCFLIRT_inputs(): ), ref_vol=dict(argstr='-refvol %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation=dict(argstr='-rotation %d', ), save_mats=dict(argstr='-mats', diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index 1c14c441d9..a873dfaf6d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -93,6 +93,9 @@ def test_MELODIC_inputs(): ), report_maps=dict(argstr='--report_maps=%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s_con=dict(argstr='--Scon=%s', ), s_des=dict(argstr='--Sdes=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index ed921d092a..48cb0c2a10 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -28,6 +28,9 @@ def test_MakeDyadicVectors_inputs(): mandatory=True, position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), theta_vol=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index 1962cd5ad9..dfe53cbf87 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -31,6 +31,9 @@ def test_MathsCommand_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 22ba2f24ad..fd0e5a6e48 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -35,6 +35,9 @@ def test_MaxImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py index 12444f2e3b..c621aa2bf6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py @@ -35,6 +35,9 @@ def test_MaxnImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 86b23eb8b9..fd448b1684 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -35,6 +35,9 @@ def test_MeanImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py index c4be8d6687..70fce4a5d3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py @@ -35,6 +35,9 @@ def test_MedianImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 32c966edaf..5a2b008edc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -27,6 +27,9 @@ def test_Merge_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tr=dict(argstr='%.2f', diff --git a/nipype/interfaces/fsl/tests/test_auto_MinImage.py b/nipype/interfaces/fsl/tests/test_auto_MinImage.py index 973bc9a369..9ac450018e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MinImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MinImage.py @@ -35,6 +35,9 @@ def test_MinImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index a4268fd930..5fe4695d07 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -42,6 +42,9 @@ def test_MotionOutliers_inputs(): name_template='%s_metrics.txt', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--thresh=%g', diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 964605e726..6b6edab63d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -37,6 +37,9 @@ def test_MultiImageMaths_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 69ef20f16c..1ae400cfcd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -12,6 +12,9 @@ def test_MultipleRegressDesign_inputs(): ), regressors=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = MultipleRegressDesign.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 84885f6c10..6b93e456e7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -41,6 +41,9 @@ def test_Overlay_inputs(): usedefault=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), show_negative_stats=dict(argstr='%s', position=8, xor=['stat_image2'], diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 38d8f7bdf3..97c6826220 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -47,6 +47,9 @@ def test_PRELUDE_inputs(): ), removeramps=dict(argstr='--removeramps', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), savemask_file=dict(argstr='--savemask=%s', hash_files=False, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py index 49f1ed3538..9ff68fb02c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py @@ -39,6 +39,9 @@ def test_PercentileImage_inputs(): position=5, usedefault=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 9dc7a30fd0..3d4aca5d15 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -28,6 +28,9 @@ def test_PlotMotionParams_inputs(): plot_type=dict(argstr='%s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 03467e1dcf..ea24858481 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -36,6 +36,9 @@ def test_PlotTimeSeries_inputs(): plot_start=dict(argstr='--start=%d', xor=('plot_range',), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sci_notation=dict(argstr='--sci', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 114feac427..eced97b4c5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -22,6 +22,9 @@ def test_PowerSpectrum_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index 8400c376e6..5c34ea2f3d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -33,6 +33,9 @@ def test_PrepareFieldmap_inputs(): position=4, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scanner=dict(argstr='%s', position=1, usedefault=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index d88ab0b0b9..2e39bc2e58 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -65,6 +65,9 @@ def test_ProbTrackX_inputs(): ), random_seed=dict(argstr='--rseed', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s2tastext=dict(argstr='--s2tastext', ), sample_random_points=dict(argstr='--sampvox', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index 770eafe3cb..0256789574 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -82,6 +82,9 @@ def test_ProbTrackX2_inputs(): ), random_seed=dict(argstr='--rseed', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s2tastext=dict(argstr='--s2tastext', ), sample_random_points=dict(argstr='--sampvox', diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index 318e67c9d9..470da8bfb8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -17,6 +17,9 @@ def test_ProjThresh_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 53e999893c..8f75d74b5c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -48,6 +48,9 @@ def test_Randomise_inputs(): ), raw_stats_imgs=dict(argstr='-R', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='--seed=%d', ), show_info_parallel_mode=dict(argstr='-Q', diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index fd37a51ecb..069bba1691 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -20,6 +20,9 @@ def test_Reorient2Std_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 26d3c45c6f..58491ab7f1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -29,6 +29,9 @@ def test_RobustFOV_inputs(): name_template='%s_to_ROI', ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 301a5fdd47..a9dd76b9a5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -21,6 +21,9 @@ def test_SMM_inputs(): position=2, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatial_data_file=dict(argstr='--sdf="%s"', copyfile=False, mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index bdaba2cad6..d576fed82c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -34,6 +34,9 @@ def test_SUSAN_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), usans=dict(argstr='', diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index c2b645b540..8d5f85eec3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -23,6 +23,9 @@ def test_SigLoss_inputs(): genfile=True, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_direction=dict(argstr='-d %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 681e9157b2..894692e63f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -31,6 +31,9 @@ def test_SliceTimer_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_direction=dict(argstr='--direction=%d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index d00aeafbaf..b2ec44662f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -53,6 +53,9 @@ def test_Slicer_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sample_axial=dict(argstr='-S %d', position=10, requires=['image_width'], diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index af09615294..0e7fc4c864 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -22,6 +22,9 @@ def test_Smooth_inputs(): position=0, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='-kernel gauss %.03f -fmean', mandatory=True, position=1, diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index 066af89a60..fbbe43909b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -23,6 +23,9 @@ def test_SmoothEstimate_inputs(): residual_fit_file=dict(argstr='--res=%s', requires=['dof'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), zstat_file=dict(argstr='--zstat=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 949254bdcc..d53d58d85c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -46,6 +46,9 @@ def test_SpatialFilter_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index 7eb80a9f12..761506bb0c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -24,6 +24,9 @@ def test_Split_inputs(): position=1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 5fd80d2dc0..fc7fd50eca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -35,6 +35,9 @@ def test_StdImage_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 1fe20d3351..3eb2ff9da4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -24,6 +24,9 @@ def test_SwapDimensions_inputs(): hash_files=False, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 8223b5dac4..d1206866f3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -83,6 +83,9 @@ def test_TOPUP_inputs(): ), regrid=dict(argstr='--regrid=%d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='--scale=%d', ), splineorder=dict(argstr='--splineorder=%d', diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index f5a4f5835a..6b20f6b3ba 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -39,6 +39,9 @@ def test_TemporalFilter_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index bd56d6270b..778d6ede61 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -33,6 +33,9 @@ def test_Threshold_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresh=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 360a5b9b57..cdeb8c39e7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -26,6 +26,9 @@ def test_TractSkeleton_inputs(): requires=['threshold', 'distance_map', 'data_file'], ), projected_data=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_mask_file=dict(xor=['use_cingulum_mask'], ), skeleton_file=dict(argstr='-o %s', diff --git a/nipype/interfaces/fsl/tests/test_auto_Training.py b/nipype/interfaces/fsl/tests/test_auto_Training.py index c5b1f12874..3b712ab176 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Training.py +++ b/nipype/interfaces/fsl/tests/test_auto_Training.py @@ -19,6 +19,9 @@ def test_Training_inputs(): copyfile=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trained_wts_filestem=dict(argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py index abe2237832..6099379f55 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py +++ b/nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py @@ -11,6 +11,9 @@ def test_TrainingSetCreator_inputs(): copyfile=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = TrainingSetCreator.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 9ac8a42d7f..659c4db2ef 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -35,6 +35,9 @@ def test_UnaryMaths_inputs(): position=-1, ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 9ea57c1677..2a96f49641 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -31,6 +31,9 @@ def test_VecReg_inputs(): ref_vol=dict(argstr='-r %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_mat=dict(argstr='--rotmat=%s', ), rotation_warp=dict(argstr='--rotwarp=%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 3c5e999c51..861eeebbfe 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -29,6 +29,9 @@ def test_WarpPoints_inputs(): name_template='%s_warped', output_name='out_file', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), src_file=dict(argstr='-src %s', mandatory=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index aa9d63ceca..5ab79eeb6c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -31,6 +31,9 @@ def test_WarpPointsToStd_inputs(): ), premat_file=dict(argstr='-premat %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), std_file=dict(argstr='-std %s', mandatory=True, ), diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index a32d067588..3c69784764 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -30,6 +30,9 @@ def test_WarpUtils_inputs(): reference=dict(argstr='--ref=%s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warp_resolution=dict(argstr='--warpres=%0.4f,%0.4f,%0.4f', diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 6a3022ed2d..90c64b56f6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -68,6 +68,9 @@ def test_XFibres5_inputs(): xor=('no_spat', 'non_linear', 'cnlinear'), ), output_type=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rician=dict(argstr='--rician', ), sample_every=dict(argstr='--sampleevery=%d', diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py index 7d3d6a9dce..32f0266ddb 100644 --- a/nipype/interfaces/fsl/tests/test_preprocess.py +++ b/nipype/interfaces/fsl/tests/test_preprocess.py @@ -258,7 +258,8 @@ def test_flirt(setup_flirt): if key in ('trait_added', 'trait_modified', 'in_file', 'reference', 'environ', 'output_type', 'out_file', 'out_matrix_file', 'in_matrix_file', 'apply_xfm', 'ignore_exception', - 'terminal_output', 'out_log', 'save_log'): + 'resource_monitor', 'terminal_output', 'out_log', + 'save_log'): continue param = None value = None diff --git a/nipype/interfaces/matlab.py b/nipype/interfaces/matlab.py index d3f6f26993..b56ef3ce17 100644 --- a/nipype/interfaces/matlab.py +++ b/nipype/interfaces/matlab.py @@ -22,6 +22,7 @@ def get_matlab_command(): try: res = CommandLine(command='which', args=matlab_cmd, + resource_monitor=False, terminal_output='allatonce').run() matlab_path = res.runtime.stdout.strip() except Exception as e: diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 5b9f60d0d3..efdacbe423 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -92,6 +92,9 @@ def test_Average_inputs(): quiet=dict(argstr='-quiet', xor=('verbose', 'quiet'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sdfile=dict(argstr='-sdfile %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index 3ef4392a2c..cd98a54dc8 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -35,6 +35,9 @@ def test_BBox_inputs(): name_template='%s_bbox.txt', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='-threshold', diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index 10a804e98f..006b4003f3 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -52,6 +52,9 @@ def test_Beast_inputs(): ), probability_map=dict(argstr='-probability', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), same_resolution=dict(argstr='-same_resolution', ), search_area=dict(argstr='-search_area %s', diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index 0bec968390..6104e85eb6 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -31,6 +31,9 @@ def test_BestLinReg_inputs(): name_template='%s_bestlinreg.xfm', position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source=dict(argstr='%s', mandatory=True, position=-4, diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index 1fc965370c..787a8757e0 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -29,6 +29,9 @@ def test_BigAverage_inputs(): ), output_float=dict(argstr='--float', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), robust=dict(argstr='-robust', ), sd_file=dict(argstr='--sdfile %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index 0f87d37bb2..b698723ed4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -27,6 +27,9 @@ def test_Blob_inputs(): name_template='%s_blob.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trace=dict(argstr='-trace', diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index 77342e4f9d..7908162c3b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -44,6 +44,9 @@ def test_Blur_inputs(): rect=dict(argstr='-rect', xor=('gaussian', 'rect'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), standard_dev=dict(argstr='-standarddev %s', mandatory=True, xor=('fwhm', 'fwhm3d', 'standard_dev'), diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 6ac13c47b1..e79ddf0f56 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -103,6 +103,9 @@ def test_Calc_inputs(): quiet=dict(argstr='-quiet', xor=('verbose', 'quiet'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), two=dict(argstr='-2', diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index 10bbdad6a6..c927d2aec6 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -31,6 +31,9 @@ def test_Convert_inputs(): name_template='%s_convert_output.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template=dict(argstr='-template', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index 62fa8b7470..52f6c31790 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -29,6 +29,9 @@ def test_Copy_inputs(): real_values=dict(argstr='-real_values', xor=('pixel_values', 'real_values'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index 07e183e009..a50c6cf9ca 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -45,6 +45,9 @@ def test_Dump_inputs(): ), precision=dict(argstr='%s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), variables=dict(argstr='-v %s', diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index f4fb2c6e2b..8530d6eb52 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -77,6 +77,9 @@ def test_Extract_inputs(): name_template='%s.raw', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), start=dict(argstr='-start %s', sep=',', ), diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index 77ffe4d114..89e921ed51 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -26,6 +26,9 @@ def test_Gennlxfm_inputs(): name_template='%s_gennlxfm.xfm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), step=dict(argstr='-step %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index b12e3cd60a..c09318f7e2 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -126,6 +126,9 @@ def test_Math_inputs(): ), propagate_nan=dict(argstr='-propagate_nan', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scale=dict(argstr='-scale -const2 %s %s', ), segment=dict(argstr='-segment -const2 %s %s', diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index a30e856276..e48268b2c8 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -26,6 +26,9 @@ def test_NlpFit_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source=dict(argstr='%s', mandatory=True, position=-3, diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 410309a364..99c8dc9d3d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -44,6 +44,9 @@ def test_Norm_inputs(): name_source=['input_file'], name_template='%s_norm_threshold_mask.mnc', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='-threshold', diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index b3f5e6cf78..100ff9aaa1 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -48,6 +48,9 @@ def test_Pik_inputs(): ), png=dict(xor=('jpg', 'png'), ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sagittal_offset=dict(argstr='--sagittal_offset %s', ), sagittal_offset_perc=dict(argstr='--sagittal_offset_perc %d', diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index dd3e788557..d7e8805a03 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -92,6 +92,9 @@ def test_Resample_inputs(): ), output_range=dict(argstr='-range %s %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sagittal_slices=dict(argstr='-sagittal', xor=('transverse', 'sagittal', 'coronal'), ), diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index 11ee473e78..8192222731 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -26,6 +26,9 @@ def test_Reshape_inputs(): name_template='%s_reshape.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index dea6132cdf..0bd0ff72e2 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -38,6 +38,9 @@ def test_ToEcat_inputs(): name_template='%s_to_ecat.v', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxels_as_integers=dict(argstr='-label', diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index d92ee7322b..2622ad80f3 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -32,6 +32,9 @@ def test_ToRaw_inputs(): name_template='%s.raw', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), write_byte=dict(argstr='-byte', diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index cf0550b1b1..6b4986c1ce 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -35,6 +35,9 @@ def test_VolSymm_inputs(): name_template='%s_vol_symm.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trans_file=dict(argstr='%s', diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index 89bd7bda04..33d19c9731 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -30,6 +30,9 @@ def test_Volcentre_inputs(): name_template='%s_volcentre.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index 74efb575c1..c997f851b6 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -32,6 +32,9 @@ def test_Voliso_inputs(): name_template='%s_voliso.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 063db70230..aec28a9749 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -32,6 +32,9 @@ def test_Volpad_inputs(): name_template='%s_volpad.mnc', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth=dict(argstr='-smooth', ), smooth_distance=dict(argstr='-smooth_distance %s', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index e90331196f..d48443c650 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -33,6 +33,9 @@ def test_XfmAvg_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index 1e7702b92e..f8e81b1ace 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -28,6 +28,9 @@ def test_XfmConcat_inputs(): name_template='%s_xfmconcat.xfm', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index 2ee570e7fe..dd93bc55ad 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -23,6 +23,9 @@ def test_XfmInvert_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='-verbose', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index 7aa5289887..99cf618f98 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -58,6 +58,9 @@ def test_JistBrainMgdmSegmentation_inputs(): outSegmented=dict(argstr='--outSegmented %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index dae7e339d7..f2659ec465 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -25,6 +25,9 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): outDura=dict(argstr='--outDura %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index 077ec1f574..d60ed9b2f0 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -36,6 +36,9 @@ def test_JistBrainMp2rageSkullStripping_inputs(): outMasked3=dict(argstr='--outMasked3 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 10e55ce20e..1c9f51377b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -23,6 +23,9 @@ def test_JistBrainPartialVolumeFilter_inputs(): outPartial=dict(argstr='--outPartial %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index 1fef3cc678..3a6658f2a3 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -34,6 +34,9 @@ def test_JistCortexSurfaceMeshInflation_inputs(): outOriginal=dict(argstr='--outOriginal %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index 0fd3ed52e4..98cbf1c090 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -38,6 +38,9 @@ def test_JistIntensityMp2rageMasking_inputs(): outSignal2=dict(argstr='--outSignal_Mask %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 54c3909e85..7dbd011ea5 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -23,6 +23,9 @@ def test_JistLaminarProfileCalculator_inputs(): outResult=dict(argstr='--outResult %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index 34b8b80569..2c3acecbab 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -27,6 +27,9 @@ def test_JistLaminarProfileGeometry_inputs(): outResult=dict(argstr='--outResult %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index cc2b743f3e..f2adb4344f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -26,6 +26,9 @@ def test_JistLaminarProfileSampling_inputs(): outProfilemapped=dict(argstr='--outProfilemapped %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index e51df02dc1..99153da4ca 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -25,6 +25,9 @@ def test_JistLaminarROIAveraging_inputs(): outROI3=dict(argstr='--outROI3 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 562e5846d0..c06bf175d6 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -45,6 +45,9 @@ def test_JistLaminarVolumetricLayering_inputs(): outLayer=dict(argstr='--outLayer %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 8254b959fd..f4b4b9d060 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -23,6 +23,9 @@ def test_MedicAlgorithmImageCalculator_inputs(): outResult=dict(argstr='--outResult %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 328072d54d..1d111f73d9 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -83,6 +83,9 @@ def test_MedicAlgorithmLesionToads_inputs(): outWM=dict(argstr='--outWM %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index 9422fda7ac..b6c23dfc26 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -36,6 +36,9 @@ def test_MedicAlgorithmMipavReorient_inputs(): outReoriented=dict(argstr='--outReoriented %s', sep=';', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index cbe6f4e2d5..d5f2057a86 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -38,6 +38,9 @@ def test_MedicAlgorithmN3_inputs(): outInhomogeneity2=dict(argstr='--outInhomogeneity2 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index c273c2f223..f1ec227970 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -109,6 +109,9 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): outd0=dict(argstr='--outd0 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py index 9b98541542..0cf3dabbfe 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py @@ -26,6 +26,9 @@ def test_MedicAlgorithmThresholdToBinaryMask_inputs(): outBinary=dict(argstr='--outBinary %s', sep=';', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index 19ea1c4c89..35b3302f07 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -35,6 +35,9 @@ def test_RandomVol_inputs(): outRand1=dict(argstr='--outRand1 %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), xDefaultMem=dict(argstr='-xDefaultMem %d', diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 8f5f876b73..6cd546b026 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -17,6 +17,9 @@ def test_WatershedBEM_inputs(): overwrite=dict(argstr='--overwrite', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(argstr='--subject %s', mandatory=True, ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 400f79676c..733f33d978 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -43,6 +43,9 @@ def test_ConstrainedSphericalDeconvolution_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response_file=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 4593e247bb..791c9b29cd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -29,6 +29,9 @@ def test_DWI2SphericalHarmonicsImage_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index c7d5675bc1..73ec54052f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -39,6 +39,9 @@ def test_DWI2Tensor_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 1a3dcc9edb..18ae66cd00 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -83,6 +83,9 @@ def test_DiffusionTensorStreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index 4a88fd9cb3..da5392481a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -36,6 +36,9 @@ def test_Directions2Amplitude_inputs(): ), quiet_display=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 7580cfd40c..6a1e876e09 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -31,6 +31,9 @@ def test_Erode_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index b0ee191fe1..8ab5587837 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -36,6 +36,9 @@ def test_EstimateResponseForSH_inputs(): ), quiet=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 7b9dd09517..dfdaf207bc 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -53,6 +53,9 @@ def test_FilterTracks_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 5f14e69f35..798479dd67 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -42,6 +42,9 @@ def test_FindShPeaks_inputs(): ), quiet_display=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index ab805c35cb..83ab7ac124 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -32,6 +32,9 @@ def test_GenerateDirections_inputs(): ), quiet_display=dict(argstr='-quiet', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 2aa1a3cffa..eff3328fe1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -30,6 +30,9 @@ def test_GenerateWhiteMatterMask_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 7f970f0dc4..98b34adf82 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -50,6 +50,9 @@ def test_MRConvert_inputs(): position=3, units='mm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel_dims=dict(argstr='-vox %s', diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index 9074271d16..a295728da4 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -26,6 +26,9 @@ def test_MRMultiply_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index 28985f43b2..71f1c906aa 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -38,6 +38,9 @@ def test_MRTransform_inputs(): replace_transform=dict(argstr='-replace', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_image=dict(argstr='-template %s', position=1, ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 09ffc2a900..cf72940b0b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -16,6 +16,9 @@ def test_MRTrixInfo_inputs(): mandatory=True, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index a6fe757114..526e99ad7b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -22,6 +22,9 @@ def test_MRTrixViewer_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 796c607791..2b8148ebea 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -26,6 +26,9 @@ def test_MedianFilter3D_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 64605ad510..f4bdd96511 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -81,6 +81,9 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index fd23f4479d..7c9e4a7609 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -79,6 +79,9 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index 3e466057b0..1dec4525fd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -79,6 +79,9 @@ def test_StreamlineTrack_inputs(): output_name='tracked', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed_file=dict(argstr='-seed %s', xor=['seed_file', 'seed_spec'], ), diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 8ffdad429f..1af2a6295d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -26,6 +26,9 @@ def test_Tensor2ApparentDiffusion_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index e234065864..329f508e0f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -26,6 +26,9 @@ def test_Tensor2FractionalAnisotropy_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 08f0837540..11842c914f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -26,6 +26,9 @@ def test_Tensor2Vector_inputs(): quiet=dict(argstr='-quiet', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 4ff6fa9759..51314b4fc6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -36,6 +36,9 @@ def test_Threshold_inputs(): replace_zeros_with_NaN=dict(argstr='-nan', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index 079273f9e2..240837a242 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -33,6 +33,9 @@ def test_Tracks2Prob_inputs(): position=3, units='mm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_file=dict(argstr='-template %s', position=1, ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index 91af4ef87e..a3e3682fc3 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -21,6 +21,9 @@ def test_ACTPrepareFSL_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 33de89ccbb..aaaeaa8c00 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -33,6 +33,9 @@ def test_BrainMask_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 9e44d4134a..2d2309df43 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -35,6 +35,9 @@ def test_BuildConnectome_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search_forward=dict(argstr='-assignment_forward_search %f', ), search_radius=dict(argstr='-assignment_radial_search %f', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 18c6868538..9ebf19c72f 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -43,6 +43,9 @@ def test_ComputeTDI_inputs(): ), reference=dict(argstr='-template %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), stat_tck=dict(argstr='-stat_tck %s', ), stat_vox=dict(argstr='-stat_vox %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index daaddaceca..5fac437c07 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -43,6 +43,9 @@ def test_EstimateFOD_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), response=dict(argstr='%s', mandatory=True, position=-2, diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index fa7126432b..8ef82fd44b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -39,6 +39,9 @@ def test_FitTensor_inputs(): ), reg_term=dict(argstr='-regularisation %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index 6ad81cc00c..70b2f79ecb 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -24,6 +24,9 @@ def test_Generate5tt_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 564a986116..1e29d9d880 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -35,6 +35,9 @@ def test_LabelConfig_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spine=dict(argstr='-spine %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py index 63de8538d0..52d2f3e85d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py @@ -12,6 +12,9 @@ def test_MRTrix3Base_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 1e3c6983ed..a46e3d0a88 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -27,6 +27,9 @@ def test_Mesh2PVE_inputs(): mandatory=True, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index ddefa4361e..a1522c7a78 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -28,6 +28,9 @@ def test_ReplaceFSwithFIRST_inputs(): position=-1, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 216e905c11..38765e7fa6 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -47,6 +47,9 @@ def test_ResponseSD_inputs(): ), out_sf=dict(argstr='-sf %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shell=dict(argstr='-shell %s', sep=',', ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index 558a90df40..aac61137f5 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -25,6 +25,9 @@ def test_TCK2VTK_inputs(): ), reference=dict(argstr='-image %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), voxel=dict(argstr='-image %s', diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 2719e25ea6..abf1f929c3 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -31,6 +31,9 @@ def test_TensorMetrics_inputs(): ), out_fa=dict(argstr='-fa %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index dcbc5a0489..f5194de88b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -72,6 +72,9 @@ def test_Tractography_inputs(): ), power=dict(argstr='-power %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), roi_excl=dict(argstr='-exclude %s', ), roi_incl=dict(argstr='-include %s', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py index 8d5d0e2b14..a20a9c76e6 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_DwiTool.py @@ -77,6 +77,9 @@ def test_DwiTool_inputs(): position=6, xor=['mono_flag', 'ivim_flag', 'dti_flag', 'dti_flag2', 'ball_flag', 'ballv_flag', 'nod_flag'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rgbmap_file=dict(argstr='-rgbmap %s', name_source=['source_file'], name_template='%s_rgbmap.nii.gz', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py index aa67c92149..7c12d60c76 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitAsl.py @@ -67,6 +67,9 @@ def test_FitAsl_inputs(): ), pv_threshold=dict(argstr='-pvthreshold', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seg=dict(argstr='-seg %s', ), segstyle=dict(argstr='-segstyle', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py index e03d999463..c2bc5ee025 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitDwi.py @@ -106,6 +106,9 @@ def test_FitDwi_inputs(): name_source=['source_file'], name_template='%s_resmap.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rgbmap_file=dict(argstr='-rgbmap %s', name_source=['source_file'], name_template='%s_rgbmap.nii.gz', diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index 86c15efaa5..292b84860a 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -68,6 +68,9 @@ def test_FitQt1_inputs(): name_source=['source_file'], name_template='%s_res.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_no=dict(argstr='-slice %d', position=9, ), diff --git a/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py b/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py index a89cdf40ce..9055062ee8 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py @@ -12,6 +12,9 @@ def test_NiftyFitCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py b/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py index e18211fee7..2b5a2dc1d4 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py @@ -15,6 +15,9 @@ def test_NiftyRegCommand_inputs(): omp_core_val=dict(argstr='-omp %i', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py index b4910d1a1e..5f383b0bf9 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py @@ -61,6 +61,9 @@ def test_RegAladin_inputs(): name_source=['flo_file'], name_template='%s_res.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rig_only_flag=dict(argstr='-rigOnly', ), rmask_file=dict(argstr='-rmask %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py index 119b6c5e82..4626a8ec28 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py @@ -49,6 +49,9 @@ def test_RegAverage_inputs(): genfile=True, position=0, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warp_files=dict(argstr='%s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py index 660532fb15..bf053d7c32 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py @@ -95,6 +95,9 @@ def test_RegF3D_inputs(): name_source=['flo_file'], name_template='%s_res.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rlwth2_thr_val=dict(argstr='-rLwTh %d %f', ), rlwth_thr_val=dict(argstr='--rLwTh %f', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py index b5eb132c39..ba91924f57 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py @@ -22,6 +22,9 @@ def test_RegJacobian_inputs(): ), ref_file=dict(argstr='-ref %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trans_file=dict(argstr='-trans %s', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py index f0504cb3dc..9359b86092 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py @@ -28,6 +28,9 @@ def test_RegMeasure_inputs(): ref_file=dict(argstr='-ref %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py index e1ca405567..5d5f3459ea 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py @@ -34,6 +34,9 @@ def test_RegResample_inputs(): ref_file=dict(argstr='-ref %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), tensor_flag=dict(argstr='-tensor ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py index 495e0854d7..8162c95308 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py @@ -40,6 +40,9 @@ def test_RegTools_inputs(): name_source=['in_file'], name_template='%s_tools.nii.gz', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rms_val=dict(argstr='-rms %s', ), smo_g_val=dict(argstr='-smoG %f %f %f', diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py index 00c017d1d3..b1553b28ef 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py @@ -70,6 +70,9 @@ def test_RegTransform_inputs(): position=1, requires=['ref1_file'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upd_s_form_input=dict(argstr='-updSform %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py index 714e201fc3..e465b176df 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py @@ -43,6 +43,9 @@ def test_BinaryMaths_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py index 484f2ac3b4..223c536ffb 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py @@ -32,6 +32,9 @@ def test_BinaryMathsInteger_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py index 14ea5463b0..3fb7cb25d9 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py @@ -36,6 +36,9 @@ def test_BinaryStats_inputs(): mandatory=True, position=4, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py index a54501c730..f3bae45fb8 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py @@ -26,6 +26,9 @@ def test_CalcTopNCC_inputs(): mandatory=True, position=2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), top_templates=dict(argstr='-n %s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_EM.py b/nipype/interfaces/niftyseg/tests/test_auto_EM.py index c42acf6a70..5950c76423 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_EM.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_EM.py @@ -58,6 +58,9 @@ def test_EM_inputs(): ), relax_priors=dict(argstr='-rf %s %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py index aae126636a..eea089b911 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py @@ -39,6 +39,9 @@ def test_FillLesions_inputs(): name_template='%s_lesions_filled.nii.gz', position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), search=dict(argstr='-search %f', ), size=dict(argstr='-size %d', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py index b572ac940c..2e98bf6723 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py @@ -42,6 +42,9 @@ def test_LabelFusion_inputs(): ), proportion=dict(argstr='-prop %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), set_pq=dict(argstr='-setPQ %f %f', ), sm_ranking=dict(argstr='-%s', diff --git a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py index 640c7088bf..ee121879ea 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py @@ -24,6 +24,9 @@ def test_MathsCommand_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py index 3980bc9ac3..4b7eba953c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py @@ -30,6 +30,9 @@ def test_Merge_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py index 55dc5d9d1d..45021be8ff 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py @@ -12,6 +12,9 @@ def test_NiftySegCommand_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py index f535133dee..528c733789 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py @@ -22,6 +22,9 @@ def test_StatsCommand_inputs(): mask_file=dict(argstr='-m %s', position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py index 9bd5ca771d..99e8237713 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py @@ -48,6 +48,9 @@ def test_TupleMaths_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py index ed98de196f..792a310115 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py @@ -28,6 +28,9 @@ def test_UnaryMaths_inputs(): output_datatype=dict(argstr='-odt %s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py index 17252084c6..41266c950c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py @@ -26,6 +26,9 @@ def test_UnaryStats_inputs(): mandatory=True, position=4, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 915f2c85d2..4e1e1e300e 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -13,6 +13,9 @@ def test_ComputeMask_inputs(): mean_volume=dict(mandatory=True, ), reference_volume=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = ComputeMask.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 7d44248cbc..77d9fe79ee 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -22,6 +22,9 @@ def test_EstimateContrast_inputs(): ), reg_names=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), s2=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 5c3f881179..959e7e0ee6 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -22,6 +22,9 @@ def test_FitGLM_inputs(): ), plot_design_matrix=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_residuals=dict(usedefault=True, ), session_info=dict(mandatory=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index 80902a7d0c..4a5444736c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -13,6 +13,9 @@ def test_FmriRealign4d_inputs(): ), loops=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_order=dict(requires=['time_interp'], ), speedup=dict(usedefault=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index f9c815fedb..fd6474c09d 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -11,6 +11,9 @@ def test_Similarity_inputs(): mask2=dict(), metric=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index b4e495a434..3325ffa67c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -10,6 +10,9 @@ def test_SpaceTimeRealigner_inputs(): in_file=dict(mandatory=True, min_ver='0.4.0.dev', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_info=dict(requires=['slice_times'], ), slice_times=dict(), diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index c1bc16e103..e052b9cec3 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -14,6 +14,9 @@ def test_Trim_inputs(): in_file=dict(mandatory=True, ), out_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), suffix=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 4d970500d2..72d36fb8e3 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -21,6 +21,9 @@ def test_CoherenceAnalyzer_inputs(): ), output_csv_file=dict(), output_figure_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = CoherenceAnalyzer.input_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 9c3d3928e5..867e937dc3 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -29,6 +29,9 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index 273d140224..29444a14a5 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -40,6 +40,9 @@ def test_BRAINSTalairach_inputs(): outputGrid=dict(argstr='--outputGrid %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index daee0ded09..50f11b8c5f 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -21,6 +21,9 @@ def test_BRAINSTalairachMask_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), talairachBox=dict(argstr='--talairachBox %s', ), talairachParameters=dict(argstr='--talairachParameters %s', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index f5275319a6..7a86062f31 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -30,6 +30,9 @@ def test_GenerateEdgeMapImage_inputs(): outputMaximumGradientImage=dict(argstr='--outputMaximumGradientImage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upperPercentileMatching=dict(argstr='--upperPercentileMatching %f', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index 262ef2c485..3481277f7f 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -20,6 +20,9 @@ def test_GeneratePurePlugMask_inputs(): outputMaskFile=dict(argstr='--outputMaskFile %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--threshold %f', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index c2d76581be..64783a16fb 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -29,6 +29,9 @@ def test_HistogramMatchingFilter_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose ', diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index c7bac4f4f6..0e74ef5eb9 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -18,6 +18,9 @@ def test_SimilarityIndex_inputs(): ), outputCSVFilename=dict(argstr='--outputCSVFilename %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdInterval=dict(argstr='--thresholdInterval %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index b355239d30..28950f2130 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -43,6 +43,9 @@ def test_DWIConvert_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smallGradientThreshold=dict(argstr='--smallGradientThreshold %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index 209c267fdc..a4d357c8b2 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -18,6 +18,9 @@ def test_compareTractInclusion_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), standardFiber=dict(argstr='--standardFiber %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index c3bff362a2..b2dab2104b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -16,6 +16,9 @@ def test_dtiaverage_inputs(): ), inputs=dict(argstr='--inputs %s...', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), tensor_output=dict(argstr='--tensor_output %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 74c63221dc..14b596d206 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -36,6 +36,9 @@ def test_dtiestim_inputs(): ), method=dict(argstr='--method %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shiftNeg=dict(argstr='--shiftNeg ', ), shiftNegCoeff=dict(argstr='--shiftNegCoeff %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index f6822c5558..e6caee54b4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -76,6 +76,9 @@ def test_dtiprocess_inputs(): ), reorientation=dict(argstr='--reorientation %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rot_output=dict(argstr='--rot_output %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index b6a904d649..5eeb234494 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -19,6 +19,9 @@ def test_extractNrrdVectorIndex_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), setImageOrientation=dict(argstr='--setImageOrientation %s', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index c9a1a591cc..741ee46e1b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -21,6 +21,9 @@ def test_gtractAnisotropyMap_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 318ad5fea4..5e77d4f61a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -23,6 +23,9 @@ def test_gtractAverageBvalues_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index 0b3f2ec979..489243f9be 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -23,6 +23,9 @@ def test_gtractClipAnisotropy_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 9453af96ea..a5ff744bdf 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -46,6 +46,9 @@ def test_gtractCoRegAnatomy_inputs(): ), relaxationFactor=dict(argstr='--relaxationFactor %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samplingPercentage=dict(argstr='--samplingPercentage %f', ), spatialScale=dict(argstr='--spatialScale %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 68d85d66b6..2af2f82f90 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -21,6 +21,9 @@ def test_gtractConcatDwi_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index 13fa034804..a2f60ebb74 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -21,6 +21,9 @@ def test_gtractCopyImageOrientation_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index fa7444c2a2..6d7ce9d9d8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -42,6 +42,9 @@ def test_gtractCoregBvalues_inputs(): ), relaxationFactor=dict(argstr='--relaxationFactor %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samplingPercentage=dict(argstr='--samplingPercentage %f', ), spatialScale=dict(argstr='--spatialScale %f', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 6cdb0ca6b8..fc77653036 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -28,6 +28,9 @@ def test_gtractCostFastMarching_inputs(): outputSpeedVolume=dict(argstr='--outputSpeedVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedThreshold=dict(argstr='--seedThreshold %f', ), startingSeedsLabel=dict(argstr='--startingSeedsLabel %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index 1d2da52d72..4c82e1cef4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -21,6 +21,9 @@ def test_gtractCreateGuideFiber_inputs(): outputFiber=dict(argstr='--outputFiber %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index 9b30f161c6..1c3eee20dd 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -33,6 +33,9 @@ def test_gtractFastMarchingTracking_inputs(): outputTract=dict(argstr='--outputTract %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedThreshold=dict(argstr='--seedThreshold %f', ), startingSeedsLabel=dict(argstr='--startingSeedsLabel %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index e3db9ee6d2..7b6bcf5ced 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -47,6 +47,9 @@ def test_gtractFiberTracking_inputs(): ), randomSeed=dict(argstr='--randomSeed %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedThreshold=dict(argstr='--seedThreshold %f', ), startingSeedsLabel=dict(argstr='--startingSeedsLabel %d', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index a78b5bb9f9..62f9c07799 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -21,6 +21,9 @@ def test_gtractImageConformity_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index de662d068b..74d6b44fe3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -24,6 +24,9 @@ def test_gtractInvertBSplineTransform_inputs(): outputTransform=dict(argstr='--outputTransform %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index 10b14f9def..fb2e08674b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -21,6 +21,9 @@ def test_gtractInvertDisplacementField_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subsamplingFactor=dict(argstr='--subsamplingFactor %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index a995a4e4cd..b41fa4153e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -19,6 +19,9 @@ def test_gtractInvertRigidTransform_inputs(): outputTransform=dict(argstr='--outputTransform %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index e9b668a716..7d9a96fe5a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -23,6 +23,9 @@ def test_gtractResampleAnisotropy_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformType=dict(argstr='--transformType %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index edc706cf4e..cb59797fa3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -23,6 +23,9 @@ def test_gtractResampleB0_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformType=dict(argstr='--transformType %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index 860e96fd09..fe9bde4fdc 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -23,6 +23,9 @@ def test_gtractResampleCodeImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformType=dict(argstr='--transformType %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index 3ecd5742e5..58f5567780 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -31,6 +31,9 @@ def test_gtractResampleDWIInPlace_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warpDWITransform=dict(argstr='--warpDWITransform %s', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index 34997e8799..efa141c3de 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -23,6 +23,9 @@ def test_gtractResampleFibers_inputs(): outputTract=dict(argstr='--outputTract %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 0cd3f101db..b3c9d0b682 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -37,6 +37,9 @@ def test_gtractTensor_inputs(): ), resampleIsotropic=dict(argstr='--resampleIsotropic ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), size=dict(argstr='--size %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 7feeabae6f..921f56142c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -21,6 +21,9 @@ def test_gtractTransformToDisplacementField_inputs(): outputDeformationFieldVolume=dict(argstr='--outputDeformationFieldVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index 7ded2e168c..e94813ed60 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -17,6 +17,9 @@ def test_maxcurvature_inputs(): output=dict(argstr='--output %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='--sigma %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 0927be112c..63ca97942c 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -61,6 +61,9 @@ def test_UKFTractography_inputs(): ), recordTrace=dict(argstr='--recordTrace ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedFALimit=dict(argstr='--seedFALimit %f', ), seedsFile=dict(argstr='--seedsFile %s', diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index 11c67161dc..af0e2dd827 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -29,6 +29,9 @@ def test_fiberprocess_inputs(): ), no_warp=dict(argstr='--no_warp ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveProperties=dict(argstr='--saveProperties ', ), tensor_volume=dict(argstr='--tensor_volume %s', diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index 613664bb15..f0aa1d7f2f 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -14,6 +14,9 @@ def test_fiberstats_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose ', diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index 3dda03843f..28b10d1c79 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -29,6 +29,9 @@ def test_fibertrack_inputs(): ), really_verbose=dict(argstr='--really_verbose ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_label=dict(argstr='--source_label %d', ), step_size=dict(argstr='--step_size %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index 446f520077..4c5621231f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -19,6 +19,9 @@ def test_CannyEdge_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upperThreshold=dict(argstr='--upperThreshold %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index 6014c01238..355b623ff5 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -32,6 +32,9 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 6690a83005..31b9ed1f46 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -21,6 +21,9 @@ def test_DilateImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 80c7fe1636..9a9d28cc28 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -21,6 +21,9 @@ def test_DilateMask_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sizeStructuralElement=dict(argstr='--sizeStructuralElement %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index ad886bd5c5..1ee1484880 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -21,6 +21,9 @@ def test_DistanceMaps_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index 017f27c3af..1d4589a1e6 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -16,6 +16,9 @@ def test_DumpBinaryTrainingVectors_inputs(): ), inputVectorFilename=dict(argstr='--inputVectorFilename %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index c5cbd6fc35..1b77316f68 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -21,6 +21,9 @@ def test_ErodeImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 6e73eb584a..7633350f63 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -19,6 +19,9 @@ def test_FlippedDifference_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 5a3bcbd888..2c1220677b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -21,6 +21,9 @@ def test_GenerateBrainClippedImage_inputs(): outputFileName=dict(argstr='--outputFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index ddca6453e8..ba15282815 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -23,6 +23,9 @@ def test_GenerateSummedGradientImage_inputs(): outputFileName=dict(argstr='--outputFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index 09915d813c..6edb1d58ec 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -21,6 +21,9 @@ def test_GenerateTestImage_inputs(): ), outputVolumeSize=dict(argstr='--outputVolumeSize %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), upperBoundOfOutputVolume=dict(argstr='--upperBoundOfOutputVolume %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index 625a0fe338..f0d1c5bfea 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -21,6 +21,9 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeStep=dict(argstr='--timeStep %f', diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 128d3d62d1..bd72549a2e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -24,6 +24,9 @@ def test_HammerAttributeCreator_inputs(): ), outputVolumeBase=dict(argstr='--outputVolumeBase %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index c029f33409..565e0b8dd4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -21,6 +21,9 @@ def test_NeighborhoodMean_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 4a80af0377..f6ea39bf50 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -21,6 +21,9 @@ def test_NeighborhoodMedian_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 03ffe65d04..b2cf49922b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -19,6 +19,9 @@ def test_STAPLEAnalysis_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index de0816897c..8e78238b32 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -19,6 +19,9 @@ def test_TextureFromNoiseImageFilter_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index de8a74c45e..01b616fe5e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -23,6 +23,9 @@ def test_TextureMeasureFilter_inputs(): outputFilename=dict(argstr='--outputFilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index f20b6b5ca7..f591f04dc9 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -26,6 +26,9 @@ def test_UnbiasedNonLocalMeans_inputs(): rc=dict(argstr='--rc %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rs=dict(argstr='--rs %s', sep=',', ), diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 83aaec5ea3..fd4b5da5c6 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -25,6 +25,9 @@ def test_scalartransform_inputs(): output_image=dict(argstr='--output_image %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), transformation=dict(argstr='--transformation %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index 9aee3d80d1..1ec3021f74 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_BRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 7447f574af..3758413206 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -118,6 +118,9 @@ def test_BRAINSFit_inputs(): ), reproportionScale=dict(argstr='--reproportionScale %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), samplingPercentage=dict(argstr='--samplingPercentage %f', ), scaleOutputValues=dict(argstr='--scaleOutputValues ', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 6e10f86ca0..f20909a41b 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -34,6 +34,9 @@ def test_BRAINSResample_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warpTransform=dict(argstr='--warpTransform %s', diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 4c90eaf915..2b176c5ddc 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -19,6 +19,9 @@ def test_BRAINSResize_inputs(): ), pixelType=dict(argstr='--pixelType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaleFactor=dict(argstr='--scaleFactor %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index bc0ead4e53..bbaa6cf436 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -22,6 +22,9 @@ def test_BRAINSTransformFromFiducials_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveTransform=dict(argstr='--saveTransform %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index 96e28abafa..bda28deeee 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_VBRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 110cfcef77..68060131d6 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -77,6 +77,9 @@ def test_BRAINSABC_inputs(): ), purePlugsThreshold=dict(argstr='--purePlugsThreshold %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), restoreState=dict(argstr='--restoreState %s', ), saveState=dict(argstr='--saveState %s', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 30ffbaa945..dc9cf1a974 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -91,6 +91,9 @@ def test_BRAINSConstellationDetector_inputs(): rescaleIntensitiesOutputRange=dict(argstr='--rescaleIntensitiesOutputRange %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultsDir=dict(argstr='--resultsDir %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 5a8f506310..51da71bbec 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -30,6 +30,9 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): priorLabelCodes=dict(argstr='--priorLabelCodes %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index 6e7652979e..806c4a6d55 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -38,6 +38,9 @@ def test_BRAINSCut_inputs(): ), randomTreeDepth=dict(argstr='--randomTreeDepth %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), trainModel=dict(argstr='--trainModel ', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 1cd57a8267..0a7d620e0b 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -28,6 +28,9 @@ def test_BRAINSMultiSTAPLE_inputs(): ), resampledVolumePrefix=dict(argstr='--resampledVolumePrefix %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), skipResampling=dict(argstr='--skipResampling ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index fe1ce50a3d..e25820b7e8 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -34,6 +34,9 @@ def test_BRAINSROIAuto_inputs(): ), outputVolumePixelType=dict(argstr='--outputVolumePixelType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdCorrectionFactor=dict(argstr='--thresholdCorrectionFactor %f', diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index 2e754dd1b1..7b620aac56 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -25,6 +25,9 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): outputBinaryVolume=dict(argstr='--outputBinaryVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), setCutDirectionForLandmark=dict(argstr='--setCutDirectionForLandmark %s', sep=',', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 4ebd23e30f..317cbd994c 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -29,6 +29,9 @@ def test_ESLR_inputs(): ), preserveOutside=dict(argstr='--preserveOutside ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), safetySize=dict(argstr='--safetySize %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 2d50880990..7662bfffe6 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -16,6 +16,9 @@ def test_DWICompare_inputs(): ), inputVolume2=dict(argstr='--inputVolume2 %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index 437d2d9087..adacb240a3 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -18,6 +18,9 @@ def test_DWISimpleCompare_inputs(): ), inputVolume2=dict(argstr='--inputVolume2 %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index 0ae702b805..f5a43a29af 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -17,6 +17,9 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index 9636e284f7..7a72ae3256 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -30,6 +30,9 @@ def test_BRAINSAlignMSP_inputs(): rescaleIntensitiesOutputRange=dict(argstr='--rescaleIntensitiesOutputRange %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultsDir=dict(argstr='--resultsDir %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index d08f270b5e..9304d97b9b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -23,6 +23,9 @@ def test_BRAINSClipInferior_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index ff5447109c..246a1f9420 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -30,6 +30,9 @@ def test_BRAINSConstellationModeler_inputs(): rescaleIntensitiesOutputRange=dict(argstr='--rescaleIntensitiesOutputRange %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultsDir=dict(argstr='--resultsDir %s', hash_files=False, ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index b9286e8835..d4af5fb35d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -21,6 +21,9 @@ def test_BRAINSEyeDetector_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index d8288ff86f..c2ff4f215e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -24,6 +24,9 @@ def test_BRAINSInitializedControlPoints_inputs(): permuteOrder=dict(argstr='--permuteOrder %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), splineGridSize=dict(argstr='--splineGridSize %s', sep=',', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 332534edf8..8cf8b49dfa 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -21,6 +21,9 @@ def test_BRAINSLandmarkInitializer_inputs(): outputTransformFilename=dict(argstr='--outputTransformFilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index 9bcf5409c7..ec44e1a7ac 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -16,6 +16,9 @@ def test_BRAINSLinearModelerEPCA_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 048b66b32b..cd71b5c734 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -28,6 +28,9 @@ def test_BRAINSLmkTransform_inputs(): outputResampledVolume=dict(argstr='--outputResampledVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 31548abd1c..528775dfe7 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -43,6 +43,9 @@ def test_BRAINSMush_inputs(): outputWeightsFile=dict(argstr='--outputWeightsFile %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='--seed %s', sep=',', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index a4fd3abf5d..882e44fa20 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -31,6 +31,9 @@ def test_BRAINSSnapShotWriter_inputs(): outputFilename=dict(argstr='--outputFilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index 5c168fbb6a..901daed765 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -26,6 +26,9 @@ def test_BRAINSTransformConvert_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index 364747314a..507da98cca 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -29,6 +29,9 @@ def test_BRAINSTrimForegroundInDirection_inputs(): outputVolume=dict(argstr='--outputVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py index bf91238a1d..ed022450cd 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py @@ -17,6 +17,9 @@ def test_CleanUpOverlapLabels_inputs(): outputBinaryVolumes=dict(argstr='--outputBinaryVolumes %s...', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index d15f647808..2e60991a5b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -50,6 +50,9 @@ def test_FindCenterOfBrain_inputs(): ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index cda3720812..928b90c2f3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -19,6 +19,9 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): outputLabelVolume=dict(argstr='--outputLabelVolume %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 6823172b50..c07cae9efe 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -24,6 +24,9 @@ def test_ImageRegionPlotter_inputs(): ), outputJointHistogramData=dict(argstr='--outputJointHistogramData %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), useIntensityForHistogram=dict(argstr='--useIntensityForHistogram ', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index 9b8df83880..68e8759fea 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -22,6 +22,9 @@ def test_JointHistogram_inputs(): ), outputJointHistogramImage=dict(argstr='--outputJointHistogramImage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), verbose=dict(argstr='--verbose ', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 1cf264afcc..22a851a5ed 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -19,6 +19,9 @@ def test_ShuffleVectorsModule_inputs(): ), resampleProportion=dict(argstr='--resampleProportion %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 927a33fd04..985296aa5d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -24,6 +24,9 @@ def test_fcsv_to_hdf5_inputs(): ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), versionID=dict(argstr='--versionID %s', diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index abb847e478..4c57c439a4 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -17,6 +17,9 @@ def test_insertMidACPCpoint_inputs(): outputLandmarkFile=dict(argstr='--outputLandmarkFile %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index 3122d627ed..8bc07fb12d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -17,6 +17,9 @@ def test_landmarksConstellationAligner_inputs(): outputLandmarksPaired=dict(argstr='--outputLandmarksPaired %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index 49772ca873..2dedbf2f06 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -21,6 +21,9 @@ def test_landmarksConstellationWeights_inputs(): outputWeightsList=dict(argstr='--outputWeightsList %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 649b1db802..9016a579c4 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -19,6 +19,9 @@ def test_DTIexport_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index 05f18b318e..3c3b575046 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -19,6 +19,9 @@ def test_DTIimport_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), testingmode=dict(argstr='--testingmode ', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index 9cf7cc1008..346c5b826b 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -26,6 +26,9 @@ def test_DWIJointRicianLMMSEFilter_inputs(): re=dict(argstr='--re %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rf=dict(argstr='--rf %s', sep=',', ), diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 97c015d7f4..29f3adc716 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -36,6 +36,9 @@ def test_DWIRicianLMMSEFilter_inputs(): re=dict(argstr='--re %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rf=dict(argstr='--rf %s', sep=',', ), diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index ba807a5052..7a6f93dc76 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -27,6 +27,9 @@ def test_DWIToDTIEstimation_inputs(): hash_files=False, position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shiftNeg=dict(argstr='--shiftNeg ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index 0b997a9c40..8ec3d8f77e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -21,6 +21,9 @@ def test_DiffusionTensorScalarMeasurements_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index 0deaf6543e..c098d4ce9f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -23,6 +23,9 @@ def test_DiffusionWeightedVolumeMasking_inputs(): ), removeislands=dict(argstr='--removeislands ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdMask=dict(argstr='%s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index d54f99f55d..ae7d3a1646 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -46,6 +46,9 @@ def test_ResampleDTIVolume_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_point=dict(argstr='--rotation_point %s', ), size=dict(argstr='--size %s', diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 55f127a6c9..64fe0e391f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -38,6 +38,9 @@ def test_TractographyLabelMapSeeding_inputs(): ), randomgrid=dict(argstr='--randomgrid ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedspacing=dict(argstr='--seedspacing %f', ), stoppingcurvature=dict(argstr='--stoppingcurvature %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 7914b71736..fbc6addebe 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -24,6 +24,9 @@ def test_AddScalarVolumes_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index eed01c2996..64174e81d6 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -19,6 +19,9 @@ def test_CastScalarVolume_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), type=dict(argstr='--type %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index be6ae4ba84..d8a1193d1e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -25,6 +25,9 @@ def test_CheckerBoardFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index 01c28d842f..3f0c3f837e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -23,6 +23,9 @@ def test_CurvatureAnisotropicDiffusion_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeStep=dict(argstr='--timeStep %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 8ec1aa362c..b05e6e0240 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -25,6 +25,9 @@ def test_ExtractSkeleton_inputs(): ), pointsFile=dict(argstr='--pointsFile %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), type=dict(argstr='--type %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index c5aa979bc6..8f5b51f783 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -19,6 +19,9 @@ def test_GaussianBlurImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sigma=dict(argstr='--sigma %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index ce307bde81..20e5753aa8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -23,6 +23,9 @@ def test_GradientAnisotropicDiffusion_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), timeStep=dict(argstr='--timeStep %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 115c25ceab..39500d65aa 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -19,6 +19,9 @@ def test_GrayscaleFillHoleImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 12c4c5402f..78c431092e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -19,6 +19,9 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index 00ef1b26dc..cc60f4b6fd 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -26,6 +26,9 @@ def test_HistogramMatching_inputs(): referenceVolume=dict(argstr='%s', position=-2, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--threshold ', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 9640cf5457..358a04dcc4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -24,6 +24,9 @@ def test_ImageLabelCombine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index c9f6c1bd8a..29482142ea 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -26,6 +26,9 @@ def test_MaskScalarVolume_inputs(): ), replace=dict(argstr='--replace %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 07f11bddae..8f1cef1c0e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -22,6 +22,9 @@ def test_MedianImageFilter_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index f53fe36ef0..560bf28903 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -24,6 +24,9 @@ def test_MultiplyScalarVolumes_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index a9cf9f449d..9a6f012822 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -35,6 +35,9 @@ def test_N4ITKBiasFieldCorrection_inputs(): outputimage=dict(argstr='--outputimage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), shrinkfactor=dict(argstr='--shrinkfactor %d', ), splinedistance=dict(argstr='--splinedistance %f', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index d317e139f8..388daafe55 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -44,6 +44,9 @@ def test_ResampleScalarVectorDWIVolume_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rotation_point=dict(argstr='--rotation_point %s', ), size=dict(argstr='--size %s', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 78fd010e43..de96efb3aa 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -24,6 +24,9 @@ def test_SubtractScalarVolumes_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index 840f527211..22ebe5aa1d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -23,6 +23,9 @@ def test_ThresholdScalarVolume_inputs(): ), outsidevalue=dict(argstr='--outsidevalue %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), threshold=dict(argstr='--threshold %d', diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 9d8a717dac..986592cc9e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -28,6 +28,9 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): radius=dict(argstr='--radius %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index de89d21763..a712864f18 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -29,6 +29,9 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): re=dict(argstr='--re %s', sep=',', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rs=dict(argstr='--rs %s', sep=',', ), diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index 1095a2169b..71532612fa 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -34,6 +34,9 @@ def test_AffineRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 2965724b45..e7fb49ea0b 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -41,6 +41,9 @@ def test_BSplineDeformableRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 9b0c0cb41e..117468b129 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -17,6 +17,9 @@ def test_BSplineToDeformationField_inputs(): ), refImage=dict(argstr='--refImage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), tfm=dict(argstr='--tfm %s', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 5c6ca38748..bde2730d11 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -61,6 +61,9 @@ def test_ExpertAutomatedRegistration_inputs(): resampledImage=dict(argstr='--resampledImage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rigidMaxIterations=dict(argstr='--rigidMaxIterations %d', ), rigidSamplingRatio=dict(argstr='--rigidSamplingRatio %f', diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index e62a728d7d..659b4944c3 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -38,6 +38,9 @@ def test_LinearRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index cea84022e4..70b1f13b01 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -31,6 +31,9 @@ def test_MultiResolutionAffineRegistration_inputs(): resampledImage=dict(argstr='--resampledImage %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveTransform=dict(argstr='--saveTransform %s', hash_files=False, ), diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index a598be2eee..298b6bf46c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -25,6 +25,9 @@ def test_OtsuThresholdImageFilter_inputs(): ), outsideValue=dict(argstr='--outsideValue %d', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index ee088157b2..4bba73c371 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -27,6 +27,9 @@ def test_OtsuThresholdSegmentation_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 6084ba5d83..c89ce07e4b 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -21,6 +21,9 @@ def test_ResampleScalarVolume_inputs(): ), interpolation=dict(argstr='--interpolation %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spacing=dict(argstr='--spacing %s', sep=',', ), diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index ef5b7f2168..725711ec20 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -38,6 +38,9 @@ def test_RigidRegistration_inputs(): resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index fc174efcfa..678c64dc30 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -30,6 +30,9 @@ def test_IntensityDifferenceMetric_inputs(): reportFileName=dict(argstr='--reportFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sensitivityThreshold=dict(argstr='--sensitivityThreshold %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 0b66af94f3..58c58ca846 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -33,6 +33,9 @@ def test_PETStandardUptakeValueComputation_inputs(): ), petVolume=dict(argstr='--petVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 35e08a6db1..3624fb5cd5 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -21,6 +21,9 @@ def test_ACPCTransform_inputs(): outputTransform=dict(argstr='--outputTransform %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index 9aee3d80d1..1ec3021f74 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_BRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index f7521f7551..38e482a47a 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -114,6 +114,9 @@ def test_BRAINSFit_inputs(): ), reproportionScale=dict(argstr='--reproportionScale %f', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), scaleOutputValues=dict(argstr='--scaleOutputValues ', ), skewScale=dict(argstr='--skewScale %f', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 6e10f86ca0..f20909a41b 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -34,6 +34,9 @@ def test_BRAINSResample_inputs(): ), referenceVolume=dict(argstr='--referenceVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), warpTransform=dict(argstr='--warpTransform %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index ee3db65e07..142c4703c8 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -18,6 +18,9 @@ def test_FiducialRegistration_inputs(): ), outputMessage=dict(argstr='--outputMessage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), rms=dict(argstr='--rms %f', ), saveTransform=dict(argstr='--saveTransform %s', diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index 96e28abafa..bda28deeee 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -91,6 +91,9 @@ def test_VBRAINSDemonWarp_inputs(): ), registrationFilterType=dict(argstr='--registrationFilterType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seedForBOBF=dict(argstr='--seedForBOBF %s', sep=',', ), diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 8792856f51..66ccf7f87d 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -30,6 +30,9 @@ def test_BRAINSROIAuto_inputs(): ), outputVolumePixelType=dict(argstr='--outputVolumePixelType %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), thresholdCorrectionFactor=dict(argstr='--thresholdCorrectionFactor %f', diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 3e51e217f2..e89c2bcc17 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -43,6 +43,9 @@ def test_EMSegmentCommandLine_inputs(): ), registrationPackage=dict(argstr='--registrationPackage %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), resultMRMLSceneFileName=dict(argstr='--resultMRMLSceneFileName %s', hash_files=False, ), diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 844bf8a0e0..6ed3a6e4e2 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -28,6 +28,9 @@ def test_RobustStatisticsSegmenter_inputs(): originalImageFileName=dict(argstr='%s', position=-3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), segmentedImageFileName=dict(argstr='%s', hash_files=False, position=-1, diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 9600134d40..5ae3f611e0 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -27,6 +27,9 @@ def test_SimpleRegionGrowingSegmentation_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), seed=dict(argstr='--seed %s...', ), smoothingIterations=dict(argstr='--smoothingIterations %d', diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index b533e70237..5892977f6b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -19,6 +19,9 @@ def test_DicomToNrrdConverter_inputs(): ), outputVolume=dict(argstr='--outputVolume %s', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smallGradientThreshold=dict(argstr='--smallGradientThreshold %f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index fd8a401276..9ecf032b4d 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -17,6 +17,9 @@ def test_EMSegmentTransformToNewFormat_inputs(): outputMRMLFileName=dict(argstr='--outputMRMLFileName %s', hash_files=False, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), templateFlag=dict(argstr='--templateFlag ', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 7c9d4b027d..4f5e38f6b5 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -25,6 +25,9 @@ def test_GrayscaleModelMaker_inputs(): ), pointnormals=dict(argstr='--pointnormals ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), smooth=dict(argstr='--smooth %d', ), splitnormals=dict(argstr='--splitnormals ', diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index b066a5081f..1ebdca13d1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -27,6 +27,9 @@ def test_LabelMapSmoothing_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 2102c77cdf..89ce57b851 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -22,6 +22,9 @@ def test_MergeModels_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index 4e84c252a9..6a37b524b1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -41,6 +41,9 @@ def test_ModelMaker_inputs(): ), pointnormals=dict(argstr='--pointnormals ', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), saveIntermediateModels=dict(argstr='--saveIntermediateModels ', ), skipUnNamed=dict(argstr='--skipUnNamed ', diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 1b7dcd8076..1595d99ae6 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -21,6 +21,9 @@ def test_ModelToLabelMap_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), surface=dict(argstr='%s', position=-2, ), diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index a75c12d463..7d1338a038 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -21,6 +21,9 @@ def test_OrientScalarVolume_inputs(): hash_files=False, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index d5e50cf6c9..ff04f1fd72 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -22,6 +22,9 @@ def test_ProbeVolumeWithModel_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index 1a24d5901e..6a81f1bc19 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -12,6 +12,9 @@ def test_SlicerCommandLine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index 6c3fbab32e..391528e83b 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -151,19 +151,14 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): returns None of path not found """ - if use_mcr or 'FORCE_SPMMCR' in os.environ: - use_mcr = True - if matlab_cmd is None: - try: - matlab_cmd = os.environ['SPMMCRCMD'] - except KeyError: - pass - if matlab_cmd is None: - try: - matlab_cmd = os.environ['MATLABCMD'] - except KeyError: - matlab_cmd = 'matlab -nodesktop -nosplash' - mlab = MatlabCommand(matlab_cmd=matlab_cmd) + + use_mcr = use_mcr or 'FORCE_SPMMCR' in os.environ + matlab_cmd = ((use_mcr and os.getenv('SPMMCRCMD')) or + os.getenv('MATLABCMD') or + 'matlab -nodesktop -nosplash') + + mlab = MatlabCommand(matlab_cmd=matlab_cmd, + resource_monitor=False) mlab.inputs.mfile = False if paths: mlab.inputs.paths = paths @@ -187,7 +182,7 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): except (IOError, RuntimeError) as e: # if no Matlab at all -- exception could be raised # No Matlab -- no spm - logger.debug(str(e)) + logger.debug('%s', e) return None else: out = sd._strip_header(out.runtime.stdout) @@ -276,11 +271,12 @@ def _find_mlab_cmd_defaults(self): def _matlab_cmd_update(self): # MatlabCommand has to be created here, - # because matlab_cmb is not a proper input + # because matlab_cmd is not a proper input # and can be set only during init self.mlab = MatlabCommand(matlab_cmd=self.inputs.matlab_cmd, mfile=self.inputs.mfile, - paths=self.inputs.paths) + paths=self.inputs.paths, + resource_monitor=False) self.mlab.inputs.script_file = 'pyscript_%s.m' % \ self.__class__.__name__.split('.')[-1].lower() if isdefined(self.inputs.use_mcr) and self.inputs.use_mcr: diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index c5064f2f59..2ebb74f4a7 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -13,6 +13,9 @@ def test_Analyze2nii_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, @@ -34,6 +37,9 @@ def test_Analyze2nii_outputs(): ), nifti_file=dict(), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index 5847ad98fe..b9b5bf2acd 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -22,6 +22,9 @@ def test_ApplyDeformations_inputs(): reference_volume=dict(field='comp{2}.id.space', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index 849c5580db..e08957db57 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -24,6 +24,9 @@ def test_ApplyInverseDeformation_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), target=dict(field='comp{1}.inv.space', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index 8100981604..0d22e8bc70 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -18,6 +18,9 @@ def test_ApplyTransform_inputs(): out_file=dict(genfile=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 04bae31f0d..dbb2ef21d0 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -16,6 +16,9 @@ def test_CalcCoregAffine_inputs(): mandatory=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), target=dict(mandatory=True, ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 468ad7e3e3..c9680d6438 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -23,6 +23,9 @@ def test_Coregister_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), separation=dict(field='eoptions.sep', ), source=dict(copyfile=True, diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index c1a8d34725..251df4707c 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -25,6 +25,9 @@ def test_CreateWarped_inputs(): modulate=dict(field='crt_warped.jactransf', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index c7197a586f..1dc974bc81 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -21,6 +21,9 @@ def test_DARTEL_inputs(): paths=dict(), regularization_form=dict(field='warp.settings.rform', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_prefix=dict(field='warp.settings.template', usedefault=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index d3e7815756..d7be1bcbd5 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -24,6 +24,9 @@ def test_DARTELNorm2MNI_inputs(): modulate=dict(field='mni_norm.preserve', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), template_file=dict(copyfile=False, field='mni_norm.template', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index dff4b04d06..3c65bcb9dd 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -26,6 +26,9 @@ def test_DicomImport_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index 76d4a25bf5..3c5b040cc8 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -21,6 +21,9 @@ def test_EstimateContrast_inputs(): residual_image=dict(copyfile=False, mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, field='spmmat', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 703c97c6fc..6e143e19bc 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -15,6 +15,9 @@ def test_EstimateModel_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, field='spmmat', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index eaa4272d8d..21b4421273 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -28,6 +28,9 @@ def test_FactorialDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 908672beb7..28bb7b196c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -31,6 +31,9 @@ def test_Level1Design_inputs(): model_serial_correlations=dict(field='cvi', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), session_info=dict(field='sess', mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 54ec275450..4d3b20d1a2 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -34,6 +34,9 @@ def test_MultipleRegressionDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 4c77c5d203..b2d839daec 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -19,6 +19,9 @@ def test_NewSegment_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='warp.samp', ), tissues=dict(field='tissue', diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index f6cb425d6a..4436ad5c26 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -32,6 +32,9 @@ def test_Normalize_inputs(): xor=['source', 'template'], ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source=dict(copyfile=True, field='subj.source', mandatory=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index 9d537e34b1..a37d596871 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -35,6 +35,9 @@ def test_Normalize12_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='eoptions.samp', ), smoothness=dict(field='eoptions.fwhm', diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 1148cbf9fa..19eb4562cf 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -31,6 +31,9 @@ def test_OneSampleTTestDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index f9cce92a37..f1562df787 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -35,6 +35,9 @@ def test_PairedTTestDesign_inputs(): mandatory=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 6c54c4a945..5fe77d6977 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -28,6 +28,9 @@ def test_Realign_inputs(): ), register_to_mean=dict(field='eoptions.rtm', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), separation=dict(field='eoptions.sep', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 4a433e5b3d..d64785469b 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -16,6 +16,9 @@ def test_Reslice_inputs(): ), out_file=dict(), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), space_defining=dict(mandatory=True, ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 06e8f2e607..5ea5d2af27 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -18,6 +18,9 @@ def test_ResliceToReference_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), target=dict(field='comp{1}.id.space', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index ed841142dd..874aeda7db 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -11,6 +11,9 @@ def test_SPMCommand_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index 739a4e1ca9..e4c9a274c1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -31,6 +31,9 @@ def test_Segment_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='opts.samp', ), save_bias_corrected=dict(field='output.biascor', diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index 739d0157a1..9f0373978c 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -24,6 +24,9 @@ def test_SliceTiming_inputs(): ref_slice=dict(field='refslice', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), slice_order=dict(field='so', mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index 378f504328..e5fb9e1fbb 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -24,6 +24,9 @@ def test_Smooth_inputs(): usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index e30b163857..1927ba29a0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -23,6 +23,9 @@ def test_Threshold_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index d73cd4f98f..82d0d81ac5 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -17,6 +17,9 @@ def test_ThresholdStatistics_inputs(): mfile=dict(usedefault=True, ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_file=dict(copyfile=True, mandatory=True, ), diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index cb19a35f62..2dbcd8304d 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -36,6 +36,9 @@ def test_TwoSampleTTestDesign_inputs(): no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict(field='masking.tm.tma.athresh', diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index f02579b66c..52f98a2586 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -82,6 +82,9 @@ def test_VBMSegment_inputs(): pve_label_normalized=dict(field='estwrite.output.label.warped', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sampling_distance=dict(field='estwrite.opts.samp', usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py new file mode 100644 index 0000000000..36d02d5fe9 --- /dev/null +++ b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py @@ -0,0 +1,28 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..bids_utils import BIDSDataGrabber + + +def test_BIDSDataGrabber_inputs(): + input_map = dict(base_dir=dict(mandatory=True, + ), + output_query=dict(), + raise_on_empty=dict(usedefault=True, + ), + return_type=dict(usedefault=True, + ), + ) + inputs = BIDSDataGrabber.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value + + +def test_BIDSDataGrabber_outputs(): + output_map = dict() + outputs = BIDSDataGrabber.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/tests/test_auto_BaseInterface.py index 9c1f2cfaa6..670ea84cc7 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/tests/test_auto_BaseInterface.py @@ -7,6 +7,9 @@ def test_BaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = BaseInterface.input_spec() diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index b67b83bf5f..30c361226e 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -25,6 +25,9 @@ def test_Bru2_inputs(): output_filename=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 2acfbfbaab..847c88bcac 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -22,6 +22,9 @@ def test_C3dAffineTool_inputs(): reference_file=dict(argstr='-ref %s', position=1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_file=dict(argstr='-src %s', position=2, ), diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/tests/test_auto_CommandLine.py index 01f7c8f6fb..e42d5984a9 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/tests/test_auto_CommandLine.py @@ -12,6 +12,9 @@ def test_CommandLine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index f402bdc53d..a9621efbad 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -12,6 +12,9 @@ def test_DataFinder_inputs(): ), max_depth=dict(), min_depth=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), root_paths=dict(mandatory=True, ), unpack_single=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index 5795ce969d..72f0378392 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -10,6 +10,9 @@ def test_DataGrabber_inputs(): ), raise_on_empty=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(mandatory=True, ), template=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 0ea2b71a6d..98c69b7065 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -20,6 +20,9 @@ def test_DataSink_inputs(): regexp_substitutions=dict(), remove_dest_dir=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), strip_dir=dict(), substitutions=dict(), ) diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index eb155ff975..775fde2497 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -50,6 +50,9 @@ def test_Dcm2nii_inputs(): reorient_and_crop=dict(argstr='-x', usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), source_dir=dict(argstr='%s', mandatory=True, position=-1, diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py index a396853b70..5e6b5118de 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2niix.py +++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py @@ -33,6 +33,9 @@ def test_Dcm2niix_inputs(): output_dir=dict(argstr='-o %s', genfile=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), single_file=dict(argstr='-s', usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 1af0874410..30bfa03a45 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -9,6 +9,9 @@ def test_FreeSurferSource_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), subject_id=dict(mandatory=True, ), subjects_dir=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index 02e45692a9..a6ac687661 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -7,6 +7,9 @@ def test_IOBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = IOBase.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index 3a93359459..a5be775470 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -9,6 +9,9 @@ def test_JSONFileGrabber_inputs(): usedefault=True, ), in_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = JSONFileGrabber.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 32b51c9dc5..6d22a770f4 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -12,6 +12,9 @@ def test_JSONFileSink_inputs(): in_dict=dict(usedefault=True, ), out_file=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = JSONFileSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index 6801f40353..fdbc90b304 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -29,6 +29,9 @@ def test_MatlabCommand_inputs(): ), prescript=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), script=dict(argstr='-r "%s;exit"', mandatory=True, position=-1, diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 7abd5878a0..acc5f6e0fb 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -67,6 +67,9 @@ def test_MeshFix_inputs(): ), remove_handles=dict(argstr='--remove-handles', ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), save_as_freesurfer_mesh=dict(argstr='--fsmesh', xor=['save_as_vrml', 'save_as_stl'], ), diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/tests/test_auto_MpiCommandLine.py index f1bc2486b2..12d3f98117 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/tests/test_auto_MpiCommandLine.py @@ -13,6 +13,9 @@ def test_MpiCommandLine_inputs(): usedefault=True, ), n_procs=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), use_mpi=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 1218d8fac0..0405d6d5ea 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -18,6 +18,9 @@ def test_MySQLSink_inputs(): usedefault=True, ), password=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), table_name=dict(mandatory=True, ), username=dict(), diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 773e7e24a3..6841df94ad 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -7,6 +7,9 @@ def test_NiftiGeneratorBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = NiftiGeneratorBase.input_spec() diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index 9c62a83a23..2c31794e11 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -43,6 +43,9 @@ def test_PETPVC_inputs(): pvc=dict(argstr='-p %s', mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), stop_crit=dict(argstr='-a %.4f', ), terminal_output=dict(nohash=True, diff --git a/nipype/interfaces/tests/test_auto_Quickshear.py b/nipype/interfaces/tests/test_auto_Quickshear.py index 7debd4dd84..df68cfd506 100644 --- a/nipype/interfaces/tests/test_auto_Quickshear.py +++ b/nipype/interfaces/tests/test_auto_Quickshear.py @@ -29,6 +29,9 @@ def test_Quickshear_inputs(): name_template='%s_defaced', position=3, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index a3c918c465..d3953457dc 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -18,6 +18,9 @@ def test_S3DataGrabber_inputs(): ), region=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(mandatory=True, ), template=dict(mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py index c7aee569d5..31a7144c85 100644 --- a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py @@ -12,6 +12,9 @@ def test_SEMLikeCommandLine_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 74c9caaa46..ba3835e2f3 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -9,6 +9,9 @@ def test_SQLiteSink_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), table_name=dict(mandatory=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py index 99e71d1ffe..73f1ac8b6e 100644 --- a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py @@ -16,6 +16,9 @@ def test_SSHDataGrabber_inputs(): password=dict(), raise_on_empty=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(mandatory=True, ), ssh_log_to_file=dict(usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index da119bfcf6..25593366fa 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -12,6 +12,9 @@ def test_SelectFiles_inputs(): ), raise_on_empty=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), sort_filelist=dict(usedefault=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index 4f101450b0..fc60690d30 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -21,6 +21,9 @@ def test_SignalExtraction_inputs(): ), out_file=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = SignalExtraction.input_spec() diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index 891eff2394..4bec246b86 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -13,6 +13,9 @@ def test_SlicerCommandLine_inputs(): usedefault=True, ), module=dict(), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py index 46a0974b34..27b8618241 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py @@ -16,6 +16,9 @@ def test_StdOutCommandLine_inputs(): genfile=True, position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index 286c8b2ca9..39b698a955 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -22,6 +22,9 @@ def test_XNATSink_inputs(): pwd=dict(), reconstruction_id=dict(xor=['assessor_id'], ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), server=dict(mandatory=True, requires=['user', 'pwd'], xor=['config'], diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index b399d143aa..514d21ac45 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -16,6 +16,9 @@ def test_XNATSource_inputs(): ), query_template_args=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), server=dict(mandatory=True, requires=['user', 'pwd'], xor=['config'], diff --git a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py index 739725a417..b1403216c6 100644 --- a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py @@ -7,6 +7,9 @@ def test_AssertEqual_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, diff --git a/nipype/interfaces/utility/tests/test_auto_Function.py b/nipype/interfaces/utility/tests/test_auto_Function.py index 649d626a5f..27ca7ed1b3 100644 --- a/nipype/interfaces/utility/tests/test_auto_Function.py +++ b/nipype/interfaces/utility/tests/test_auto_Function.py @@ -9,6 +9,9 @@ def test_Function_inputs(): ignore_exception=dict(nohash=True, usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Function.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Merge.py b/nipype/interfaces/utility/tests/test_auto_Merge.py index f98e70892b..dd9247ebc6 100644 --- a/nipype/interfaces/utility/tests/test_auto_Merge.py +++ b/nipype/interfaces/utility/tests/test_auto_Merge.py @@ -13,6 +13,9 @@ def test_Merge_inputs(): ), ravel_inputs=dict(usedefault=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Merge.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Select.py b/nipype/interfaces/utility/tests/test_auto_Select.py index 3c67785702..b3041ecfce 100644 --- a/nipype/interfaces/utility/tests/test_auto_Select.py +++ b/nipype/interfaces/utility/tests/test_auto_Select.py @@ -11,6 +11,9 @@ def test_Select_inputs(): ), inlist=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), ) inputs = Select.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Split.py b/nipype/interfaces/utility/tests/test_auto_Split.py index 663ff65b13..33ae28bda4 100644 --- a/nipype/interfaces/utility/tests/test_auto_Split.py +++ b/nipype/interfaces/utility/tests/test_auto_Split.py @@ -9,6 +9,9 @@ def test_Split_inputs(): ), inlist=dict(mandatory=True, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), splits=dict(mandatory=True, ), squeeze=dict(usedefault=True, diff --git a/nipype/interfaces/utility/wrappers.py b/nipype/interfaces/utility/wrappers.py index 4de11d7ea8..4fa10205d2 100644 --- a/nipype/interfaces/utility/wrappers.py +++ b/nipype/interfaces/utility/wrappers.py @@ -20,21 +20,13 @@ from builtins import str, bytes from ... import logging -from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile, - BaseInterfaceInputSpec, get_max_resources_used) +from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, + BaseInterfaceInputSpec) from ..io import IOBase, add_traits from ...utils.filemanip import filename_to_list from ...utils.misc import getsource, create_function_from_source logger = logging.getLogger('interface') -if runtime_profile: - try: - import psutil - except ImportError as exc: - logger.info('Unable to import packages needed for runtime profiling. '\ - 'Turning off runtime profiler. Reason: %s' % exc) - runtime_profile = False - class FunctionInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec): function_str = traits.Str(mandatory=True, desc='code for function') @@ -137,22 +129,9 @@ def _add_output_traits(self, base): return base def _run_interface(self, runtime): - # Get workflow logger for runtime profile error reporting - logger = logging.getLogger('workflow') - # Create function handle function_handle = create_function_from_source(self.inputs.function_str, self.imports) - - # Wrapper for running function handle in multiprocessing.Process - # Can catch exceptions and report output via multiprocessing.Queue - def _function_handle_wrapper(queue, **kwargs): - try: - out = function_handle(**kwargs) - queue.put(out) - except Exception as exc: - queue.put(exc) - # Get function args args = {} for name in self._input_names: @@ -160,37 +139,7 @@ def _function_handle_wrapper(queue, **kwargs): if isdefined(value): args[name] = value - # Profile resources if set - if runtime_profile: - import multiprocessing - # Init communication queue and proc objs - queue = multiprocessing.Queue() - proc = multiprocessing.Process(target=_function_handle_wrapper, - args=(queue,), kwargs=args) - - # Init memory and threads before profiling - mem_mb = 0 - num_threads = 0 - - # Start process and profile while it's alive - proc.start() - while proc.is_alive(): - mem_mb, num_threads = \ - get_max_resources_used(proc.pid, mem_mb, num_threads, - pyfunc=True) - - # Get result from process queue - out = queue.get() - # If it is an exception, raise it - if isinstance(out, Exception): - raise out - - # Function ran successfully, populate runtime stats - setattr(runtime, 'runtime_memory_gb', mem_mb / 1024.0) - setattr(runtime, 'runtime_threads', num_threads) - else: - out = function_handle(**args) - + out = function_handle(**args) if len(self._output_names) == 1: self._out[self._output_names[0]] = out else: diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 460c1eac79..2603a5b567 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -26,6 +26,9 @@ def test_Vnifti2Image_inputs(): name_template='%s.v', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 055e665abc..af7b5d1f27 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -23,6 +23,9 @@ def test_VtoMat_inputs(): name_template='%s.mat', position=-1, ), + resource_monitor=dict(nohash=True, + usedefault=True, + ), terminal_output=dict(nohash=True, ), ) diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 622003f8a2..c5ee3f28f3 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -46,8 +46,7 @@ from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined, TraitedSpec, DynamicTraitedSpec, Bunch, InterfaceResult, md5, Interface, - TraitDictObject, TraitListObject, isdefined, - runtime_profile) + TraitDictObject, TraitListObject, isdefined) from .utils import (generate_expanded_graph, modify_paths, export_graph, make_output_dir, write_workflow_prov, clean_working_directory, format_dot, topological_sort, @@ -690,6 +689,7 @@ def update(self, **opts): self.inputs.update(**opts) def write_report(self, report_type=None, cwd=None): + from ...utils.profiler import resource_monitor if not str2bool(self.config['execution']['create_report']): return report_dir = op.join(cwd, '_report') @@ -724,15 +724,13 @@ def write_report(self, report_type=None, cwd=None): return fp.writelines(write_rst_header('Runtime info', level=1)) # Init rst dictionary of runtime stats - rst_dict = {'hostname' : self.result.runtime.hostname, - 'duration' : self.result.runtime.duration} + rst_dict = {'hostname': self.result.runtime.hostname, + 'duration': self.result.runtime.duration} # Try and insert memory/threads usage if available - if runtime_profile: - try: - rst_dict['runtime_memory_gb'] = self.result.runtime.runtime_memory_gb - rst_dict['runtime_threads'] = self.result.runtime.runtime_threads - except AttributeError: - logger.info('Runtime memory and threads stats unavailable') + if resource_monitor: + rst_dict['runtime_memory_gb'] = getattr(self.result.runtime, 'mem_peak_gb') + rst_dict['runtime_threads'] = getattr(self.result.runtime, 'nthreads_max') + if hasattr(self.result.runtime, 'cmdline'): rst_dict['command'] = self.result.runtime.cmdline fp.writelines(write_rst_dict(rst_dict)) diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py index 90d566ddf9..adaf506122 100644 --- a/nipype/pipeline/engine/tests/test_engine.py +++ b/nipype/pipeline/engine/tests/test_engine.py @@ -475,7 +475,7 @@ def double_func(x): def test_mapnode_nested(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() from nipype import MapNode, Function def func1(in1): @@ -505,7 +505,7 @@ def func1(in1): def test_mapnode_expansion(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() from nipype import MapNode, Function def func1(in1): @@ -527,9 +527,8 @@ def func1(in1): def test_node_hash(tmpdir): - wd = str(tmpdir) - os.chdir(wd) from nipype.interfaces.utility import Function + tmpdir.chdir() def func1(): return 1 @@ -548,13 +547,13 @@ def func2(a): modify = lambda x: x + 1 n1.inputs.a = 1 w1.connect(n1, ('a', modify), n2, 'a') - w1.base_dir = wd + w1.base_dir = os.getcwd() # generate outputs w1.run(plugin='Linear') # ensure plugin is being called w1.config['execution'] = {'stop_on_first_crash': 'true', 'local_hash_check': 'false', - 'crashdump_dir': wd} + 'crashdump_dir': os.getcwd()} # create dummy distributed plugin class from nipype.pipeline.plugins.base import DistributedPluginBase @@ -576,14 +575,14 @@ def _submit_job(self, node, updatehash=False): # set local check w1.config['execution'] = {'stop_on_first_crash': 'true', 'local_hash_check': 'true', - 'crashdump_dir': wd} + 'crashdump_dir': os.getcwd()} w1.run(plugin=RaiseError()) def test_old_config(tmpdir): - wd = str(tmpdir) - os.chdir(wd) + tmpdir.chdir() + wd = os.getcwd() from nipype.interfaces.utility import Function def func1(): @@ -614,8 +613,8 @@ def func2(a): def test_mapnode_json(tmpdir): """Tests that mapnodes don't generate excess jsons """ - wd = str(tmpdir) - os.chdir(wd) + tmpdir.chdir() + wd = os.getcwd() from nipype import MapNode, Function, Workflow def func1(in1): @@ -671,8 +670,8 @@ def test_parameterize_dirs_false(tmpdir): def test_serial_input(tmpdir): - wd = str(tmpdir) - os.chdir(wd) + tmpdir.chdir() + wd = os.getcwd() from nipype import MapNode, Function, Workflow def func1(in1): @@ -708,7 +707,7 @@ def func1(in1): def test_write_graph_runs(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() for graph in ('orig', 'flat', 'exec', 'hierarchical', 'colored'): for simple in (True, False): @@ -736,7 +735,7 @@ def test_write_graph_runs(tmpdir): def test_deep_nested_write_graph_runs(tmpdir): - os.chdir(str(tmpdir)) + tmpdir.chdir() for graph in ('orig', 'flat', 'exec', 'hierarchical', 'colored'): for simple in (True, False): diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py index f677d6c253..bedd3c0c63 100644 --- a/nipype/pipeline/engine/utils.py +++ b/nipype/pipeline/engine/utils.py @@ -1022,7 +1022,8 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False, _write_detailed_dot(graph, outfname) if format != 'dot': cmd = 'dot -T%s -O %s' % (format, outfname) - res = CommandLine(cmd, terminal_output='allatonce').run() + res = CommandLine(cmd, terminal_output='allatonce', + resource_monitor=False).run() if res.runtime.returncode: logger.warn('dot2png: %s', res.runtime.stderr) pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form) @@ -1033,7 +1034,8 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False, nx.drawing.nx_pydot.write_dot(pklgraph, simplefname) if format != 'dot': cmd = 'dot -T%s -O %s' % (format, simplefname) - res = CommandLine(cmd, terminal_output='allatonce').run() + res = CommandLine(cmd, terminal_output='allatonce', + resource_monitor=False).run() if res.runtime.returncode: logger.warn('dot2png: %s', res.runtime.stderr) if show: @@ -1053,7 +1055,7 @@ def format_dot(dotfilename, format='png'): if format != 'dot': cmd = 'dot -T%s -O \'%s\'' % (format, dotfilename) try: - CommandLine(cmd).run() + CommandLine(cmd, resource_monitor=False).run() except IOError as ioe: if "could not be found" in str(ioe): raise IOError("Cannot draw directed graph; executable 'dot' is unavailable") @@ -1294,6 +1296,51 @@ def write_workflow_prov(graph, filename=None, format='all'): return ps.g +def write_workflow_resources(graph, filename=None): + import simplejson as json + if not filename: + filename = os.path.join(os.getcwd(), 'resource_monitor.json') + + big_dict = { + 'time': [], + 'name': [], + 'interface': [], + 'mem_gb': [], + 'cpus': [], + 'mapnode': [], + 'params': [], + } + + for idx, node in enumerate(graph.nodes()): + nodename = node.fullname + classname = node._interface.__class__.__name__ + + params = '' + if node.parameterization: + params = '_'.join(['{}'.format(p) + for p in node.parameterization]) + + rt_list = node.result.runtime + if not isinstance(rt_list, list): + rt_list = [rt_list] + + for subidx, runtime in enumerate(rt_list): + nsamples = len(runtime.prof_dict['time']) + + for key in ['time', 'mem_gb', 'cpus']: + big_dict[key] += runtime.prof_dict[key] + + big_dict['interface'] += [classname] * nsamples + big_dict['name'] += [nodename] * nsamples + big_dict['mapnode'] += [subidx] * nsamples + big_dict['params'] += [params] * nsamples + + with open(filename, 'w') as rsf: + json.dump(big_dict, rsf) + + return filename + + def topological_sort(graph, depth_first=False): """Returns a depth first sorted order if depth_first is True """ diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py index 17d49b046a..936881dd0f 100644 --- a/nipype/pipeline/engine/workflows.py +++ b/nipype/pipeline/engine/workflows.py @@ -51,6 +51,7 @@ write_rst_list, to_str) from .utils import (generate_expanded_graph, modify_paths, export_graph, make_output_dir, write_workflow_prov, + write_workflow_resources, clean_working_directory, format_dot, topological_sort, get_print_name, merge_dict, evaluate_connect_function, _write_inputs, format_node) @@ -593,6 +594,9 @@ def run(self, plugin=None, plugin_args=None, updatehash=False): 'workflow_provenance_%s' % datestr) logger.info('Provenance file prefix: %s' % prov_base) write_workflow_prov(execgraph, prov_base, format='all') + + if str2bool(self.config['execution'].get('resource_monitor', 'false')): + write_workflow_resources(execgraph) return execgraph # PRIVATE API AND FUNCTIONS diff --git a/nipype/pipeline/plugins/__init__.py b/nipype/pipeline/plugins/__init__.py index cb2c193004..34d3abdebc 100644 --- a/nipype/pipeline/plugins/__init__.py +++ b/nipype/pipeline/plugins/__init__.py @@ -1,6 +1,7 @@ # -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: +from __future__ import print_function, division, unicode_literals, absolute_import from .debug import DebugPlugin from .linear import LinearPlugin @@ -19,5 +20,4 @@ from .slurm import SLURMPlugin from .slurmgraph import SLURMGraphPlugin -from .callback_log import log_nodes_cb from . import semaphore_singleton diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index 7334e00c52..dab48b15f0 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -16,7 +16,6 @@ import uuid from time import strftime, sleep, time from traceback import format_exception, format_exc -from warnings import warn import numpy as np import scipy.sparse as ssp @@ -59,9 +58,9 @@ def report_crash(node, traceback=None, hostname=None): timeofcrash = strftime('%Y%m%d-%H%M%S') login_name = getpass.getuser() crashfile = 'crash-%s-%s-%s-%s' % (timeofcrash, - login_name, - name, - str(uuid.uuid4())) + login_name, + name, + str(uuid.uuid4())) crashdir = node.config['execution']['crashdump_dir'] if crashdir is None: crashdir = os.getcwd() @@ -143,7 +142,8 @@ def create_pyscript(node, updatehash=False, store_exception=True): from collections import OrderedDict config_dict=%s config.update_config(config_dict) - ## Only configure matplotlib if it was successfully imported, matplotlib is an optional component to nipype + ## Only configure matplotlib if it was successfully imported, + ## matplotlib is an optional component to nipype if can_import_matplotlib: config.update_matplotlib() logging.update_logging(config) @@ -188,10 +188,11 @@ class PluginBase(object): """Base class for plugins""" def __init__(self, plugin_args=None): - if plugin_args and 'status_callback' in plugin_args: - self._status_callback = plugin_args['status_callback'] - else: - self._status_callback = None + if plugin_args is None: + plugin_args = {} + self.plugin_args = plugin_args + + self._status_callback = plugin_args.get('status_callback') return def run(self, graph, config, updatehash=False): @@ -223,9 +224,7 @@ def __init__(self, plugin_args=None): self.mapnodesubids = None self.proc_done = None self.proc_pending = None - self.max_jobs = np.inf - if plugin_args and 'max_jobs' in plugin_args: - self.max_jobs = plugin_args['max_jobs'] + self.max_jobs = self.plugin_args.get('max_jobs', np.inf) def run(self, graph, config, updatehash=False): """Executes a pre-defined pipeline using distributed approaches @@ -240,12 +239,12 @@ def run(self, graph, config, updatehash=False): self.mapnodesubids = {} # setup polling - TODO: change to threaded model notrun = [] - while np.any(self.proc_done == False) | \ - np.any(self.proc_pending == True): + while not np.all(self.proc_done) or np.any(self.proc_pending): toappend = [] # trigger callbacks for any pending results while self.pending_tasks: + logger.info('Processing %d pending tasks.', len(self.pending_tasks)) taskid, jobid = self.pending_tasks.pop() try: result = self._get_result(taskid) @@ -264,6 +263,8 @@ def run(self, graph, config, updatehash=False): 'traceback': format_exc()} notrun.append(self._clean_queue(jobid, graph, result=result)) + + logger.debug('Appending %d new tasks.' % len(toappend)) if toappend: self.pending_tasks.extend(toappend) num_jobs = len(self.pending_tasks) @@ -349,7 +350,7 @@ def _submit_mapnode(self, jobid): def _send_procs_to_workers(self, updatehash=False, graph=None): """ Sends jobs to workers """ - while np.any(self.proc_done == False): + while not np.all(self.proc_done): num_jobs = len(self.pending_tasks) if np.isinf(self.max_jobs): slots = None @@ -601,8 +602,8 @@ class GraphPluginBase(PluginBase): """ def __init__(self, plugin_args=None): - if plugin_args and 'status_callback' in plugin_args: - warn('status_callback not supported for Graph submission plugins') + if plugin_args and plugin_args.get('status_callback'): + logger.warning('status_callback not supported for Graph submission plugins') super(GraphPluginBase, self).__init__(plugin_args=plugin_args) def run(self, graph, config, updatehash=False): diff --git a/nipype/pipeline/plugins/callback_log.py b/nipype/pipeline/plugins/callback_log.py deleted file mode 100644 index 5ddc9eedd5..0000000000 --- a/nipype/pipeline/plugins/callback_log.py +++ /dev/null @@ -1,67 +0,0 @@ -# -*- coding: utf-8 -*- -# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: -"""Callback logger for recording workflow and node run stats -""" -from __future__ import print_function, division, unicode_literals, absolute_import - - -# Log node stats function -def log_nodes_cb(node, status): - """Function to record node run statistics to a log file as json - dictionaries - - Parameters - ---------- - node : nipype.pipeline.engine.Node - the node being logged - status : string - acceptable values are 'start', 'end'; otherwise it is - considered and error - - Returns - ------- - None - this function does not return any values, it logs the node - status info to the callback logger - """ - - # Import packages - import datetime - import logging - import json - - # Check runtime profile stats - if node.result is not None: - try: - runtime = node.result.runtime - runtime_memory_gb = runtime.runtime_memory_gb - runtime_threads = runtime.runtime_threads - except AttributeError: - runtime_memory_gb = runtime_threads = 'Unknown' - else: - runtime_memory_gb = runtime_threads = 'N/A' - - # Init variables - logger = logging.getLogger('callback') - status_dict = {'name' : node.name, - 'id' : node._id, - 'estimated_memory_gb' : node._interface.estimated_memory_gb, - 'num_threads' : node._interface.num_threads} - - # Check status and write to log - # Start - if status == 'start': - status_dict['start'] = str(datetime.datetime.now()) - # End - elif status == 'end': - status_dict['finish'] = str(datetime.datetime.now()) - status_dict['runtime_threads'] = runtime_threads - status_dict['runtime_memory_gb'] = runtime_memory_gb - # Other - else: - status_dict['finish'] = str(datetime.datetime.now()) - status_dict['error'] = True - - # Dump string to log - logger.debug(json.dumps(status_dict)) diff --git a/nipype/pipeline/plugins/condor.py b/nipype/pipeline/plugins/condor.py index 9b8b5c218d..de4265e3f3 100644 --- a/nipype/pipeline/plugins/condor.py +++ b/nipype/pipeline/plugins/condor.py @@ -46,6 +46,7 @@ def __init__(self, **kwargs): def _is_pending(self, taskid): cmd = CommandLine('condor_q', + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%d' % taskid # check condor cluster @@ -59,6 +60,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('condor_qsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) qsubargs = '' diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py index 1001ab5dac..61aa44229e 100644 --- a/nipype/pipeline/plugins/dagman.py +++ b/nipype/pipeline/plugins/dagman.py @@ -154,6 +154,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes): child)) # hand over DAG to condor_dagman cmd = CommandLine('condor_submit_dag', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') # needs -update_submit or re-running a workflow will fail cmd.inputs.args = '%s -update_submit %s' % (self._dagman_args, diff --git a/nipype/pipeline/plugins/lsf.py b/nipype/pipeline/plugins/lsf.py index 6e27b3ab95..d065b521d8 100644 --- a/nipype/pipeline/plugins/lsf.py +++ b/nipype/pipeline/plugins/lsf.py @@ -45,6 +45,7 @@ def _is_pending(self, taskid): finished and is ready to be checked for completeness. So return True if status is either 'PEND' or 'RUN'""" cmd = CommandLine('bjobs', + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%d' % taskid # check lsf task @@ -60,6 +61,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('bsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) bsubargs = '' diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 3994f2e1cd..4f25a3f286 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -7,7 +7,6 @@ http://stackoverflow.com/a/8963618/1183453 """ from __future__ import print_function, division, unicode_literals, absolute_import -from builtins import open # Import packages from multiprocessing import Process, Pool, cpu_count, pool @@ -20,12 +19,14 @@ from ... import logging, config from ...utils.misc import str2bool +from ...utils.profiler import get_system_total_memory_gb from ..engine import MapNode from .base import (DistributedPluginBase, report_crash) # Init logger logger = logging.getLogger('workflow') + # Run node def run_node(node, updatehash, taskid): """Function to execute node.run(), catch and log any errors and @@ -44,6 +45,10 @@ def run_node(node, updatehash, taskid): dictionary containing the node runtime results and stats """ + from nipype import logging + logger = logging.getLogger('workflow') + + logger.debug('run_node called on %s', node.name) # Init variables result = dict(result=None, traceback=None, taskid=taskid) @@ -77,34 +82,6 @@ class NonDaemonPool(pool.Pool): Process = NonDaemonProcess -# Get total system RAM -def get_system_total_memory_gb(): - """Function to get the total RAM of the running system in GB - """ - - # Import packages - import os - import sys - - # Get memory - if 'linux' in sys.platform: - with open('/proc/meminfo', 'r') as f_in: - meminfo_lines = f_in.readlines() - mem_total_line = [line for line in meminfo_lines \ - if 'MemTotal' in line][0] - mem_total = float(mem_total_line.split()[1]) - memory_gb = mem_total/(1024.0**2) - elif 'darwin' in sys.platform: - mem_str = os.popen('sysctl hw.memsize').read().strip().split(' ')[-1] - memory_gb = float(mem_str)/(1024.0**3) - else: - err_msg = 'System platform: %s is not supported' - raise Exception(err_msg) - - # Return memory - return memory_gb - - class MultiProcPlugin(DistributedPluginBase): """Execute workflow with multiprocessing, not sending more jobs at once than the system can support. @@ -134,53 +111,36 @@ def __init__(self, plugin_args=None): self._taskresult = {} self._task_obj = {} self._taskid = 0 - non_daemon = True - self.plugin_args = plugin_args - self.processors = cpu_count() - self.memory_gb = get_system_total_memory_gb()*0.9 # 90% of system memory - - self._timeout=2.0 - self._event = threading.Event() - - + self._timeout = 2.0 + # self._event = threading.Event() - # Check plugin args - if self.plugin_args: - if 'non_daemon' in self.plugin_args: - non_daemon = plugin_args['non_daemon'] - if 'n_procs' in self.plugin_args: - self.processors = self.plugin_args['n_procs'] - if 'memory_gb' in self.plugin_args: - self.memory_gb = self.plugin_args['memory_gb'] - - logger.debug("MultiProcPlugin starting %d threads in pool"%(self.processors)) + # Read in options or set defaults. + non_daemon = self.plugin_args.get('non_daemon', True) + self.processors = self.plugin_args.get('n_procs', cpu_count()) + self.memory_gb = self.plugin_args.get('memory_gb', # Allocate 90% of system memory + get_system_total_memory_gb() * 0.9) + self.raise_insufficient = self.plugin_args.get('raise_insufficient', True) # Instantiate different thread pools for non-daemon processes - if non_daemon: - # run the execution using the non-daemon pool subclass - self.pool = NonDaemonPool(processes=self.processors) - else: - self.pool = Pool(processes=self.processors) - - def _wait(self): - if len(self.pending_tasks) > 0: - if self._config['execution']['poll_sleep_duration']: - self._timeout = float(self._config['execution']['poll_sleep_duration']) - sig_received=self._event.wait(self._timeout) - if not sig_received: - logger.debug('MultiProcPlugin timeout before signal received. Deadlock averted??') - self._event.clear() + logger.debug('MultiProcPlugin starting in "%sdaemon" mode (n_procs=%d, mem_gb=%0.2f)', + 'non' if non_daemon else '', self.processors, self.memory_gb) + self.pool = (NonDaemonPool if non_daemon else Pool)(processes=self.processors) + + # def _wait(self): + # if len(self.pending_tasks) > 0: + # if self._config['execution']['poll_sleep_duration']: + # self._timeout = float(self._config['execution']['poll_sleep_duration']) + # sig_received = self._event.wait(self._timeout) + # if not sig_received: + # logger.debug('MultiProcPlugin timeout before signal received. Deadlock averted??') + # self._event.clear() def _async_callback(self, args): - self._taskresult[args['taskid']]=args - self._event.set() + self._taskresult[args['taskid']] = args + # self._event.set() def _get_result(self, taskid): - if taskid not in self._taskresult: - result=None - else: - result=self._taskresult[taskid] - return result + return self._taskresult.get(taskid) def _report_crash(self, node, result=None): if result and result['traceback']: @@ -217,32 +177,38 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): executing_now = [] # Check to see if a job is available - currently_running_jobids = np.flatnonzero((self.proc_pending == True) & \ - (self.depidx.sum(axis=0) == 0).__array__()) + currently_running_jobids = np.flatnonzero( + self.proc_pending & (self.depidx.sum(axis=0) == 0).__array__()) # Check available system resources by summing all threads and memory used busy_memory_gb = 0 busy_processors = 0 for jobid in currently_running_jobids: - if self.procs[jobid]._interface.estimated_memory_gb <= self.memory_gb and \ - self.procs[jobid]._interface.num_threads <= self.processors: - - busy_memory_gb += self.procs[jobid]._interface.estimated_memory_gb - busy_processors += self.procs[jobid]._interface.num_threads - - else: - raise ValueError( - "Resources required by jobid {0} ({3}GB, {4} threads) exceed what is " - "available on the system ({1}GB, {2} threads)".format( - jobid, self.memory_gb, self.processors, - self.procs[jobid]._interface.estimated_memory_gb, - self.procs[jobid]._interface.num_threads)) + est_mem_gb = self.procs[jobid]._interface.estimated_memory_gb + est_num_th = self.procs[jobid]._interface.num_threads + + if est_mem_gb > self.memory_gb: + logger.warning( + 'Job %s - Estimated memory (%0.2fGB) exceeds the total amount' + ' available (%0.2fGB).', self.procs[jobid].name, est_mem_gb, self.memory_gb) + if self.raise_insufficient: + raise RuntimeError('Insufficient resources available for job') + + if est_num_th > self.processors: + logger.warning( + 'Job %s - Requested %d threads, but only %d are available.', + self.procs[jobid].name, est_num_th, self.processors) + if self.raise_insufficient: + raise RuntimeError('Insufficient resources available for job') + + busy_memory_gb += min(est_mem_gb, self.memory_gb) + busy_processors += min(est_num_th, self.processors) free_memory_gb = self.memory_gb - busy_memory_gb free_processors = self.processors - busy_processors # Check all jobs without dependency not run - jobids = np.flatnonzero((self.proc_done == False) & \ + jobids = np.flatnonzero((self.proc_done == False) & (self.depidx.sum(axis=0) == 0).__array__()) # Sort jobs ready to run first by memory and then by number of threads @@ -251,14 +217,15 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): key=lambda item: (self.procs[item]._interface.estimated_memory_gb, self.procs[item]._interface.num_threads)) - if str2bool(config.get('execution', 'profile_runtime')): + resource_monitor = str2bool(config.get('execution', 'resource_monitor', 'false')) + if resource_monitor: logger.debug('Free memory (GB): %d, Free processors: %d', free_memory_gb, free_processors) # While have enough memory and processors for first job # Submit first job on the list for jobid in jobids: - if str2bool(config.get('execution', 'profile_runtime')): + if resource_monitor: logger.debug('Next Job: %d, memory (GB): %d, threads: %d' \ % (jobid, self.procs[jobid]._interface.estimated_memory_gb, @@ -266,7 +233,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): if self.procs[jobid]._interface.estimated_memory_gb <= free_memory_gb and \ self.procs[jobid]._interface.num_threads <= free_processors: - logger.info('Executing: %s ID: %d' %(self.procs[jobid]._id, jobid)) + logger.info('Executing: %s ID: %d' % (self.procs[jobid]._id, jobid)) executing_now.append(self.procs[jobid]) if isinstance(self.procs[jobid], MapNode): @@ -297,12 +264,13 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): if str2bool(self.procs[jobid].config['execution']['local_hash_check']): logger.debug('checking hash locally') try: - hash_exists, _, _, _ = self.procs[ - jobid].hash_exists() - logger.debug('Hash exists %s' % str(hash_exists)) - if (hash_exists and (self.procs[jobid].overwrite == False or - (self.procs[jobid].overwrite == None and - not self.procs[jobid]._interface.always_run))): + hash_exists, _, _, _ = self.procs[jobid].hash_exists() + overwrite = self.procs[jobid].overwrite + always_run = self.procs[jobid]._interface.always_run + if (hash_exists and (overwrite is False or + (overwrite is None and not always_run))): + logger.debug('Skipping cached node %s with ID %s.', + self.procs[jobid]._id, jobid) self._task_finished_cb(jobid) self._remove_node_dirs() continue @@ -313,22 +281,24 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): self._clean_queue(jobid, graph) self.proc_pending[jobid] = False continue - logger.debug('Finished checking hash') + finally: + logger.debug('Finished checking hash') if self.procs[jobid].run_without_submitting: - logger.debug('Running node %s on master thread' \ - % self.procs[jobid]) + logger.debug('Running node %s on master thread', + self.procs[jobid]) try: self.procs[jobid].run() except Exception: etype, eval, etr = sys.exc_info() traceback = format_exception(etype, eval, etr) report_crash(self.procs[jobid], traceback=traceback) - self._task_finished_cb(jobid) - self._remove_node_dirs() + finally: + self._task_finished_cb(jobid) + self._remove_node_dirs() else: - logger.debug('MultiProcPlugin submitting %s' % str(jobid)) + logger.debug('MultiProcPlugin submitting %s', str(jobid)) tid = self._submit_job(deepcopy(self.procs[jobid]), updatehash=updatehash) if tid is None: diff --git a/nipype/pipeline/plugins/oar.py b/nipype/pipeline/plugins/oar.py index ca77fade1e..d3a9c6f360 100644 --- a/nipype/pipeline/plugins/oar.py +++ b/nipype/pipeline/plugins/oar.py @@ -68,6 +68,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('oarsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) oarsubargs = '' diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py index 5288bb36cb..62b35fa99a 100644 --- a/nipype/pipeline/plugins/pbs.py +++ b/nipype/pipeline/plugins/pbs.py @@ -48,6 +48,7 @@ def _is_pending(self, taskid): result = CommandLine('qstat {}'.format(taskid), environ=dict(os.environ), terminal_output='allatonce', + resource_monitor=False, ignore_exception=True).run() stderr = result.runtime.stderr errmsg = 'Unknown Job Id' # %s' % taskid @@ -59,6 +60,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('qsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) qsubargs = '' diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py index 1aafd24e37..719b82578c 100644 --- a/nipype/pipeline/plugins/pbsgraph.py +++ b/nipype/pipeline/plugins/pbsgraph.py @@ -55,6 +55,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes): qsub_args, batchscriptfile)) cmd = CommandLine('sh', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%s' % submitjobsfile cmd.run() diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index 268fecf2a9..d337ebb961 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -364,6 +364,7 @@ def _is_pending(self, taskid): def _submit_batchtask(self, scriptfile, node): cmd = CommandLine('qsub', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) qsubargs = '' diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py index dd4b8076e8..882c455450 100644 --- a/nipype/pipeline/plugins/sgegraph.py +++ b/nipype/pipeline/plugins/sgegraph.py @@ -147,6 +147,7 @@ def make_job_name(jobnumber, nodeslist): batchscript=batchscriptfile) fp.writelines(full_line) cmd = CommandLine('bash', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%s' % submitjobsfile cmd.run() diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index 3f83772f6a..083f804a75 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -62,6 +62,7 @@ def _is_pending(self, taskid): # subprocess.Popen requires taskid to be a string res = CommandLine('squeue', args=' '.join(['-j', '%s' % taskid]), + resource_monitor=False, terminal_output='allatonce').run() return res.runtime.stdout.find(str(taskid)) > -1 @@ -72,6 +73,7 @@ def _submit_batchtask(self, scriptfile, node): formatting/processing """ cmd = CommandLine('sbatch', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') path = os.path.dirname(scriptfile) diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py index 794a35bc84..ed571ecffe 100644 --- a/nipype/pipeline/plugins/slurmgraph.py +++ b/nipype/pipeline/plugins/slurmgraph.py @@ -146,6 +146,7 @@ def make_job_name(jobnumber, nodeslist): batchscript=batchscriptfile) fp.writelines(full_line) cmd = CommandLine('bash', environ=dict(os.environ), + resource_monitor=False, terminal_output='allatonce') cmd.inputs.args = '%s' % submitjobsfile cmd.run() diff --git a/nipype/pipeline/plugins/tests/test_multiproc.py b/nipype/pipeline/plugins/tests/test_multiproc.py index 6dab555a11..20718feda6 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc.py +++ b/nipype/pipeline/plugins/tests/test_multiproc.py @@ -1,14 +1,13 @@ # -*- coding: utf-8 -*- import logging -import os, sys +import os from multiprocessing import cpu_count import nipype.interfaces.base as nib from nipype.utils import draw_gantt_chart -import pytest import nipype.pipeline.engine as pe -from nipype.pipeline.plugins.callback_log import log_nodes_cb -from nipype.pipeline.plugins.multiproc import get_system_total_memory_gb +from nipype.utils.profiler import log_nodes_cb, get_system_total_memory_gb + class InputSpec(nib.TraitedSpec): input1 = nib.traits.Int(desc='a random int') @@ -32,6 +31,7 @@ def _list_outputs(self): outputs['output1'] = [1, self.inputs.input1] return outputs + def test_run_multiproc(tmpdir): os.chdir(str(tmpdir)) @@ -82,8 +82,8 @@ def find_metrics(nodes, last_node): from dateutil.parser import parse import datetime - start = nodes[0]['start'] - total_duration = int((last_node['finish'] - start).total_seconds()) + start = parse(nodes[0]['start']) + total_duration = max(int((parse(last_node['finish']) - start).total_seconds()), 1) total_memory = [] total_threads = [] @@ -100,8 +100,8 @@ def find_metrics(nodes, last_node): x = now for j in range(start_index, len(nodes)): - node_start = nodes[j]['start'] - node_finish = nodes[j]['finish'] + node_start = parse(nodes[j]['start']) + node_finish = parse(nodes[j]['finish']) if node_start < x and node_finish > x: total_memory[i] += float(nodes[j]['estimated_memory_gb']) @@ -115,8 +115,10 @@ def find_metrics(nodes, last_node): return total_memory, total_threads -def test_no_more_memory_than_specified(): - LOG_FILENAME = 'callback.log' + +def test_no_more_memory_than_specified(tmpdir): + tmpdir.chdir() + LOG_FILENAME = tmpdir.join('callback.log').strpath my_logger = logging.getLogger('callback') my_logger.setLevel(logging.DEBUG) @@ -146,10 +148,9 @@ def test_no_more_memory_than_specified(): plugin_args={'memory_gb': max_memory, 'status_callback': log_nodes_cb}) - nodes = draw_gantt_chart.log_to_dict(LOG_FILENAME) last_node = nodes[-1] - #usage in every second + # usage in every second memory, threads = find_metrics(nodes, last_node) result = True @@ -173,6 +174,7 @@ def test_no_more_memory_than_specified(): os.remove(LOG_FILENAME) + def test_no_more_threads_than_specified(): LOG_FILENAME = 'callback.log' my_logger = logging.getLogger('callback') @@ -205,7 +207,7 @@ def test_no_more_threads_than_specified(): nodes = draw_gantt_chart.log_to_dict(LOG_FILENAME) last_node = nodes[-1] - #usage in every second + # usage in every second memory, threads = find_metrics(nodes, last_node) result = True diff --git a/nipype/utils/config.py b/nipype/utils/config.py index ebea9e5816..241f2de8ee 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -11,21 +11,24 @@ ''' from __future__ import print_function, division, unicode_literals, absolute_import import os -import shutil import errno from warnings import warn from io import StringIO from distutils.version import LooseVersion -from simplejson import load, dump +import configparser import numpy as np from builtins import str, object, open + +from simplejson import load, dump +from ..external import portalocker from future import standard_library standard_library.install_aliases() -import configparser -from ..external import portalocker +CONFIG_DEPRECATIONS = { + 'profile_runtime': ('resource_monitor', '1.13.2'), +} NUMPY_MMAP = LooseVersion(np.__version__) >= LooseVersion('1.12.0') @@ -34,7 +37,7 @@ default_cfg = """ [logging] workflow_level = INFO -filemanip_level = INFO +utils_level = INFO interface_level = INFO log_to_file = false log_directory = %s @@ -64,7 +67,6 @@ parameterize_dirs = true poll_sleep_duration = 2 xvfb_max_wait = 10 -profile_runtime = false [check] interval = 1209600 @@ -114,13 +116,29 @@ def set_log_dir(self, log_dir): """ self._config.set('logging', 'log_directory', log_dir) - def get(self, section, option): - return self._config.get(section, option) + def get(self, section, option, default=None): + if option in CONFIG_DEPRECATIONS: + msg = ('Config option "%s" has been deprecated as of nipype %s. Please use ' + '"%s" instead.') % (option, CONFIG_DEPRECATIONS[option][1], + CONFIG_DEPRECATIONS[option][0]) + warn(msg) + option = CONFIG_DEPRECATIONS[option][0] + + if self._config.has_option(section, option): + return self._config.get(section, option) + return default def set(self, section, option, value): if isinstance(value, bool): value = str(value) + if option in CONFIG_DEPRECATIONS: + msg = ('Config option "%s" has been deprecated as of nipype %s. Please use ' + '"%s" instead.') % (option, CONFIG_DEPRECATIONS[option][1], + CONFIG_DEPRECATIONS[option][0]) + warn(msg) + option = CONFIG_DEPRECATIONS[option][0] + return self._config.set(section, option, value) def getboolean(self, section, option): @@ -172,3 +190,6 @@ def update_matplotlib(self): def enable_provenance(self): self._config.set('execution', 'write_provenance', 'true') self._config.set('execution', 'hash_method', 'content') + + def enable_resource_monitor(self): + self._config.set('execution', 'resource_monitor', 'true') diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index ebf52d06d3..0d6bce7d45 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -254,6 +254,7 @@ def get_doc(cmd, opt_map, help_flag=None, trap_error=True): """ res = CommandLine('which %s' % cmd.split(' ')[0], + resource_monitor=False, terminal_output='allatonce').run() cmd_path = res.runtime.stdout.strip() if cmd_path == '': @@ -330,6 +331,7 @@ def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True): """ res = CommandLine('which %s' % cmd.split(' ')[0], + resource_monitor=False, terminal_output='allatonce').run() cmd_path = res.runtime.stdout.strip() if cmd_path == '': diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py index 4c18a66f8f..c91acf662c 100644 --- a/nipype/utils/draw_gantt_chart.py +++ b/nipype/utils/draw_gantt_chart.py @@ -11,7 +11,6 @@ import random import datetime import simplejson as json -from dateutil import parser from builtins import str, range, open # Py2 compat: http://python-future.org/compatible_idioms.html#collections-counter-and-ordereddict from future import standard_library @@ -102,61 +101,14 @@ def log_to_dict(logfile): ''' # Init variables - #keep track of important vars - nodes_list = [] #all the parsed nodes - unifinished_nodes = [] #all start nodes that dont have a finish yet - with open(logfile, 'r') as content: - #read file separating each line - content = content.read() - lines = content.split('\n') - - for l in lines: - #try to parse each line and transform in a json dict. - #if the line has a bad format, just skip - node = None - try: - node = json.loads(l) - except ValueError: - pass - - if not node: - continue - - #if it is a start node, add to unifinished nodes - if 'start' in node: - node['start'] = parser.parse(node['start']) - unifinished_nodes.append(node) - - #if it is end node, look in uninished nodes for matching start - #remove from unifinished list and add to node list - elif 'finish' in node: - node['finish'] = parser.parse(node['finish']) - #because most nodes are small, we look backwards in the unfinished list - for s in range(len(unifinished_nodes)): - aux = unifinished_nodes[s] - #found the end for node start, copy over info - if aux['id'] == node['id'] and aux['name'] == node['name'] \ - and aux['start'] < node['finish']: - node['start'] = aux['start'] - node['duration'] = \ - (node['finish'] - node['start']).total_seconds() - - unifinished_nodes.remove(aux) - nodes_list.append(node) - break - - #finished parsing - #assume nodes without finish didn't finish running. - #set their finish to last node run - last_node = nodes_list[-1] - for n in unifinished_nodes: - n['finish'] = last_node['finish'] - n['duration'] = (n['finish'] - n['start']).total_seconds() - nodes_list.append(n) - - # Return list of nodes - return nodes_list + # read file separating each line + lines = content.readlines() + + nodes_list = [json.loads(l) for l in lines] + + # Return list of nodes + return nodes_list def calculate_resource_timeseries(events, resource): @@ -453,7 +405,7 @@ def generate_gantt_chart(logfile, cores, minute_scale=10, ----- # import logging # import logging.handlers - # from nipype.pipeline.plugins.callback_log import log_nodes_cb + # from nipype.utils.profiler import log_nodes_cb # log_filename = 'callback.log' # logger = logging.getLogger('callback') diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index 59b269e943..e321a597a6 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -27,7 +27,7 @@ from .misc import is_container from ..interfaces.traits_extension import isdefined -fmlogger = logging.getLogger("filemanip") +fmlogger = logging.getLogger('utils') related_filetype_sets = [ diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index b30b50bc72..f07d2f8cd0 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -6,6 +6,7 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: import logging +from warnings import warn import os import sys from .misc import str2bool @@ -15,7 +16,6 @@ RFHandler except ImportError: # Next 2 lines are optional: issue a warning to the user - from warnings import warn warn("ConcurrentLogHandler not installed. Using builtin log handler") from logging.handlers import RotatingFileHandler as RFHandler @@ -33,10 +33,12 @@ def __init__(self, config): stream=sys.stdout) # logging.basicConfig(stream=sys.stdout) self._logger = logging.getLogger('workflow') + self._utlogger = logging.getLogger('utils') self._fmlogger = logging.getLogger('filemanip') self._iflogger = logging.getLogger('interface') self.loggers = {'workflow': self._logger, + 'utils': self._utlogger, 'filemanip': self._fmlogger, 'interface': self._iflogger} self._hdlr = None @@ -53,15 +55,17 @@ def enable_file_logging(self): formatter = logging.Formatter(fmt=self.fmt, datefmt=self.datefmt) hdlr.setFormatter(formatter) self._logger.addHandler(hdlr) - self._fmlogger.addHandler(hdlr) + self._utlogger.addHandler(hdlr) self._iflogger.addHandler(hdlr) + self._fmlogger.addHandler(hdlr) self._hdlr = hdlr def disable_file_logging(self): if self._hdlr: self._logger.removeHandler(self._hdlr) - self._fmlogger.removeHandler(self._hdlr) + self._utlogger.removeHandler(self._hdlr) self._iflogger.removeHandler(self._hdlr) + self._fmlogger.removeHandler(self._hdlr) self._hdlr = None def update_logging(self, config): @@ -69,14 +73,17 @@ def update_logging(self, config): self.disable_file_logging() self._logger.setLevel(logging.getLevelName(config.get('logging', 'workflow_level'))) - self._fmlogger.setLevel(logging.getLevelName(config.get('logging', - 'filemanip_level'))) + self._utlogger.setLevel(logging.getLevelName(config.get('logging', + 'utils_level'))) self._iflogger.setLevel(logging.getLevelName(config.get('logging', 'interface_level'))) if str2bool(config.get('logging', 'log_to_file')): self.enable_file_logging() def getLogger(self, name): + if name == 'filemanip': + warn('The "filemanip" logger has been deprecated and replaced by ' + 'the "utils" logger as of nipype 1.13.2') if name in self.loggers: return self.loggers[name] return None diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py new file mode 100644 index 0000000000..75bb19a611 --- /dev/null +++ b/nipype/utils/profiler.py @@ -0,0 +1,286 @@ +# -*- coding: utf-8 -*- +# @Author: oesteban +# @Date: 2017-09-21 15:50:37 +# @Last Modified by: oesteban +# @Last Modified time: 2017-09-27 12:57:50 +""" +Utilities to keep track of performance +""" +from __future__ import print_function, division, unicode_literals, absolute_import + +import threading +from time import time +try: + import psutil +except ImportError as exc: + psutil = None + +from .. import config, logging +from .misc import str2bool +from builtins import open + +proflogger = logging.getLogger('utils') + +resource_monitor = str2bool(config.get('execution', 'resource_monitor', 'false')) +if resource_monitor and psutil is None: + proflogger.warn('Switching "resource_monitor" off: the option was on, but the ' + 'necessary package "psutil" could not be imported.') + resource_monitor = False + +# Init variables +_MB = 1024.0**2 + + +class ResourceMonitor(threading.Thread): + def __init__(self, pid, freq=5, fname=None): + if freq <= 0: + raise RuntimeError('Frequency (%0.2fs) cannot be lower than zero' % freq) + + if fname is None: + fname = '.nipype.prof' + + self._pid = pid + self._fname = fname + self._freq = freq + + self._log = open(self._fname, 'w') + print('%s,0.0,0' % time(), file=self._log) + self._log.flush() + threading.Thread.__init__(self) + self._event = threading.Event() + + def stop(self): + if not self._event.is_set(): + self._event.set() + self.join() + ram = _get_ram_mb(self._pid) or 0 + cpus = _get_num_threads(self._pid) or 0 + print('%s,%f,%d' % (time(), ram, cpus), + file=self._log) + self._log.flush() + self._log.close() + + def run(self): + while not self._event.is_set(): + ram = _get_ram_mb(self._pid) + cpus = _get_num_threads(self._pid) + if ram is not None and cpus is not None: + print('%s,%f,%d' % (time(), ram, cpus), + file=self._log) + self._log.flush() + self._event.wait(self._freq) + + +# Log node stats function +def log_nodes_cb(node, status): + """Function to record node run statistics to a log file as json + dictionaries + + Parameters + ---------- + node : nipype.pipeline.engine.Node + the node being logged + status : string + acceptable values are 'start', 'end'; otherwise it is + considered and error + + Returns + ------- + None + this function does not return any values, it logs the node + status info to the callback logger + """ + + if status != 'end': + return + + # Import packages + import logging + import json + + status_dict = { + 'name': node.name, + 'id': node._id, + 'start': getattr(node.result.runtime, 'startTime'), + 'finish': getattr(node.result.runtime, 'endTime'), + 'duration': getattr(node.result.runtime, 'duration'), + 'runtime_threads': getattr( + node.result.runtime, 'nthreads_max', 'N/A'), + 'runtime_memory_gb': getattr( + node.result.runtime, 'mem_peak_gb', 'N/A'), + 'estimated_memory_gb': node._interface.estimated_memory_gb, + 'num_threads': node._interface.num_threads, + } + + if status_dict['start'] is None or status_dict['finish'] is None: + status_dict['error'] = True + + # Dump string to log + logging.getLogger('callback').debug(json.dumps(status_dict)) + + +# Get total system RAM +def get_system_total_memory_gb(): + """ + Function to get the total RAM of the running system in GB + """ + + # Import packages + import os + import sys + + # Get memory + if 'linux' in sys.platform: + with open('/proc/meminfo', 'r') as f_in: + meminfo_lines = f_in.readlines() + mem_total_line = [line for line in meminfo_lines + if 'MemTotal' in line][0] + mem_total = float(mem_total_line.split()[1]) + memory_gb = mem_total / (1024.0**2) + elif 'darwin' in sys.platform: + mem_str = os.popen('sysctl hw.memsize').read().strip().split(' ')[-1] + memory_gb = float(mem_str) / (1024.0**3) + else: + err_msg = 'System platform: %s is not supported' + raise Exception(err_msg) + + # Return memory + return memory_gb + + +# Get max resources used for process +def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False): + """ + Function to get the RAM and threads utilized by a given process + + Parameters + ---------- + pid : integer + the process ID of process to profile + mem_mb : float + the high memory watermark so far during process execution (in MB) + num_threads: int + the high thread watermark so far during process execution + + Returns + ------- + mem_mb : float + the new high memory watermark of process (MB) + num_threads : float + the new high thread watermark of process + """ + + if not resource_monitor: + raise RuntimeError('Attempted to measure resources with ' + '"resource_monitor" set off.') + + try: + mem_mb = max(mem_mb, _get_ram_mb(pid, pyfunc=pyfunc)) + num_threads = max(num_threads, _get_num_threads(pid)) + except Exception as exc: + proflogger = logging.getLogger('profiler') + proflogger.info('Could not get resources used by process. Error: %s', exc) + + return mem_mb, num_threads + + +# Get number of threads for process +def _get_num_threads(pid): + """ + Function to get the number of threads a process is using + + Parameters + ---------- + pid : integer + the process ID of process to profile + + Returns + ------- + num_threads : int + the number of threads that the process is using + + """ + + try: + proc = psutil.Process(pid) + # If process is running + if proc.status() == psutil.STATUS_RUNNING: + num_threads = proc.num_threads() + elif proc.num_threads() > 1: + tprocs = [psutil.Process(thr.id) for thr in proc.threads()] + alive_tprocs = [tproc for tproc in tprocs if tproc.status() == psutil.STATUS_RUNNING] + num_threads = len(alive_tprocs) + else: + num_threads = 1 + + child_threads = 0 + # Iterate through child processes and get number of their threads + for child in proc.children(recursive=True): + # Leaf process + if len(child.children()) == 0: + # If process is running, get its number of threads + if child.status() == psutil.STATUS_RUNNING: + child_thr = child.num_threads() + # If its not necessarily running, but still multi-threaded + elif child.num_threads() > 1: + # Cast each thread as a process and check for only running + tprocs = [psutil.Process(thr.id) for thr in child.threads()] + alive_tprocs = [tproc for tproc in tprocs + if tproc.status() == psutil.STATUS_RUNNING] + child_thr = len(alive_tprocs) + # Otherwise, no threads are running + else: + child_thr = 0 + # Increment child threads + child_threads += child_thr + except psutil.NoSuchProcess: + return None + + # Number of threads is max between found active children and parent + num_threads = max(child_threads, num_threads) + + # Return number of threads found + return num_threads + + +# Get ram usage of process +def _get_ram_mb(pid, pyfunc=False): + """ + Function to get the RAM usage of a process and its children + Reference: http://ftp.dev411.com/t/python/python-list/095thexx8g/\ +multiprocessing-forking-memory-usage + + Parameters + ---------- + pid : integer + the PID of the process to get RAM usage of + pyfunc : boolean (optional); default=False + a flag to indicate if the process is a python function; + when Pythons are multithreaded via multiprocess or threading, + children functions include their own memory + parents. if this + is set, the parent memory will removed from children memories + + + Returns + ------- + mem_mb : float + the memory RAM in MB utilized by the process PID + + """ + try: + # Init parent + parent = psutil.Process(pid) + # Get memory of parent + parent_mem = parent.memory_info().rss + mem_mb = parent_mem / _MB + # Iterate through child processes + for child in parent.children(recursive=True): + child_mem = child.memory_info().rss + if pyfunc: + child_mem -= parent_mem + mem_mb += child_mem / _MB + except psutil.NoSuchProcess: + return None + + # Return memory + return mem_mb diff --git a/nipype/utils/provenance.py b/nipype/utils/provenance.py index 066cbb9a57..c316f67272 100644 --- a/nipype/utils/provenance.py +++ b/nipype/utils/provenance.py @@ -21,7 +21,7 @@ from .. import get_info, logging, __version__ from .filemanip import (md5, hashlib, hash_infile) -iflogger = logging.getLogger('interface') +logger = logging.getLogger('utils') foaf = pm.Namespace("foaf", "http://xmlns.com/foaf/0.1/") dcterms = pm.Namespace("dcterms", "http://purl.org/dc/terms/") nipype_ns = pm.Namespace("nipype", "http://nipy.org/nipype/terms/") @@ -173,7 +173,7 @@ def safe_encode(x, as_literal=True): jsonstr = json.dumps(outdict) except UnicodeDecodeError as excp: jsonstr = "Could not encode dictionary. {}".format(excp) - iflogger.warn('Prov: %s', jsonstr) + logger.warning('Prov: %s', jsonstr) if not as_literal: return jsonstr @@ -203,7 +203,7 @@ def safe_encode(x, as_literal=True): jsonstr = json.dumps(x) except UnicodeDecodeError as excp: jsonstr = "Could not encode list/tuple. {}".format(excp) - iflogger.warn('Prov: %s', jsonstr) + logger.warning('Prov: %s', jsonstr) if not as_literal: return jsonstr @@ -285,9 +285,20 @@ def prov_encode(graph, value, create_container=True): def write_provenance(results, filename='provenance', format='all'): - ps = ProvStore() - ps.add_results(results) - return ps.write_provenance(filename=filename, format=format) + prov = None + try: + ps = ProvStore() + ps.add_results(results) + prov = ps.write_provenance(filename=filename, format=format) + except Exception as e: + import traceback + err_msg = traceback.format_exc() + if getattr(e, 'args'): + err_msg += '\n\nException arguments:\n' + ', '.join(['"%s"' % arg for arg in e.args]) + logger.warning('Writing provenance failed - Exception details:\n%s', err_msg) + + return prov + class ProvStore(object): diff --git a/nipype/utils/spm_docs.py b/nipype/utils/spm_docs.py index 1b7a1a1dc4..89869c1e87 100644 --- a/nipype/utils/spm_docs.py +++ b/nipype/utils/spm_docs.py @@ -27,7 +27,7 @@ def grab_doc(task_name): """ - cmd = matlab.MatlabCommandLine() + cmd = matlab.MatlabCommandLine(resource_monitor=False) # We need to tell Matlab where to find our spm_get_doc.m file. cwd = os.path.dirname(__file__) # Build matlab command diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py index 315d55441f..b590ecb351 100644 --- a/nipype/utils/tests/test_cmd.py +++ b/nipype/utils/tests/test_cmd.py @@ -104,6 +104,7 @@ def test_run_4d_realign_without_arguments(self): [--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]] [--ignore_exception] [--loops [LOOPS [LOOPS ...]]] + [--resource_monitor] [--slice_order SLICE_ORDER] [--speedup [SPEEDUP [SPEEDUP ...]]] [--start START] diff --git a/nipype/interfaces/tests/test_runtime_profiler.py b/nipype/utils/tests/test_profiler.py similarity index 87% rename from nipype/interfaces/tests/test_runtime_profiler.py rename to nipype/utils/tests/test_profiler.py index 400b2728ae..7c08330d13 100644 --- a/nipype/interfaces/tests/test_runtime_profiler.py +++ b/nipype/utils/tests/test_profiler.py @@ -1,33 +1,20 @@ # -*- coding: utf-8 -*- -# test_runtime_profiler.py +# test_profiler.py # # Author: Daniel Clark, 2016 """ -Module to unit test the runtime_profiler in nipype +Module to unit test the resource_monitor in nipype """ from __future__ import print_function, division, unicode_literals, absolute_import from builtins import open, str # Import packages -from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec, - runtime_profile) import pytest -import sys +from nipype.utils.profiler import resource_monitor as run_profile +from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec) -run_profile = runtime_profile - -if run_profile: - try: - import psutil - skip_profile_msg = 'Run profiler tests' - except ImportError as exc: - skip_profile_msg = 'Missing python packages for runtime profiling, skipping...\n'\ - 'Error: %s' % exc - run_profile = False -else: - skip_profile_msg = 'Not running profiler' # UseResources inputspec class UseResourcesInputSpec(CommandLineInputSpec): @@ -39,7 +26,7 @@ class UseResourcesInputSpec(CommandLineInputSpec): num_gb = traits.Float(desc='Number of GB of RAM to use', argstr='-g %f') num_threads = traits.Int(desc='Number of threads to use', - argstr='-p %d') + argstr='-p %d') # UseResources interface @@ -163,17 +150,17 @@ def _collect_range_runtime_stats(self, num_threads): # Iterate through all combos for num_gb in np.arange(0.25, ram_gb_range+ram_gb_step, ram_gb_step): # Cmd-level - cmd_start_str, cmd_fin_str = self._run_cmdline_workflow(num_gb, num_threads) - cmd_start_ts = json.loads(cmd_start_str)['start'] - cmd_node_stats = json.loads(cmd_fin_str) + cmd_node_str = self._run_cmdline_workflow(num_gb, num_threads) + cmd_node_stats = json.loads(cmd_node_str) + cmd_start_ts = cmd_node_stats['start'] cmd_runtime_threads = int(cmd_node_stats['runtime_threads']) cmd_runtime_gb = float(cmd_node_stats['runtime_memory_gb']) cmd_finish_ts = cmd_node_stats['finish'] # Func-level - func_start_str, func_fin_str = self._run_function_workflow(num_gb, num_threads) - func_start_ts = json.loads(func_start_str)['start'] - func_node_stats = json.loads(func_fin_str) + func_node_str = self._run_function_workflow(num_gb, num_threads) + func_node_stats = json.loads(func_node_str) + func_start_ts = func_node_stats['start'] func_runtime_threads = int(func_node_stats['runtime_threads']) func_runtime_gb = float(func_node_stats['runtime_memory_gb']) func_finish_ts = func_node_stats['finish'] @@ -233,7 +220,7 @@ def _run_cmdline_workflow(self, num_gb, num_threads): import nipype.pipeline.engine as pe import nipype.interfaces.utility as util - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb # Init variables base_dir = tempfile.mkdtemp() @@ -241,6 +228,7 @@ def _run_cmdline_workflow(self, num_gb, num_threads): # Init logger logger = logging.getLogger('callback') + logger.propagate = False logger.setLevel(logging.DEBUG) handler = logging.FileHandler(log_file) logger.addHandler(handler) @@ -274,14 +262,14 @@ def _run_cmdline_workflow(self, num_gb, num_threads): # Get runtime stats from log file with open(log_file, 'r') as log_handle: lines = log_handle.readlines() - start_str = lines[0].rstrip('\n') - finish_str = lines[1].rstrip('\n') + + node_str = lines[0].rstrip('\n') # Delete wf base dir shutil.rmtree(base_dir) # Return runtime stats - return start_str, finish_str + return node_str # Test node def _run_function_workflow(self, num_gb, num_threads): @@ -308,7 +296,7 @@ def _run_function_workflow(self, num_gb, num_threads): import nipype.pipeline.engine as pe import nipype.interfaces.utility as util - from nipype.pipeline.plugins.callback_log import log_nodes_cb + from nipype.utils.profiler import log_nodes_cb # Init variables base_dir = tempfile.mkdtemp() @@ -353,17 +341,15 @@ def _run_function_workflow(self, num_gb, num_threads): # Get runtime stats from log file with open(log_file, 'r') as log_handle: lines = log_handle.readlines() - start_str = lines[0].rstrip('\n') - finish_str = lines[1].rstrip('\n') # Delete wf base dir shutil.rmtree(base_dir) # Return runtime stats - return start_str, finish_str + return lines[0].rstrip('\n') # Test resources were used as expected in cmdline interface - @pytest.mark.skipif(run_profile == False, reason=skip_profile_msg) + @pytest.mark.skipif(run_profile is False, reason='resources monitor is disabled') def test_cmdline_profiling(self): ''' Test runtime profiler correctly records workflow RAM/CPUs consumption @@ -379,9 +365,9 @@ def test_cmdline_profiling(self): num_threads = self.num_threads # Run workflow and get stats - start_str, finish_str = self._run_cmdline_workflow(num_gb, num_threads) + node_str = self._run_cmdline_workflow(num_gb, num_threads) # Get runtime stats as dictionary - node_stats = json.loads(finish_str) + node_stats = json.loads(node_str) # Read out runtime stats runtime_gb = float(node_stats['runtime_memory_gb']) @@ -404,8 +390,8 @@ def test_cmdline_profiling(self): assert abs(expected_runtime_threads - runtime_threads) <= 1, threads_err # Test resources were used as expected - @pytest.mark.skipif(True, reason="https://github.com/nipy/nipype/issues/1663") - @pytest.mark.skipif(run_profile == False, reason=skip_profile_msg) + # @pytest.mark.skipif(True, reason="https://github.com/nipy/nipype/issues/1663") + @pytest.mark.skipif(run_profile is False, reason='resources monitor is disabled') def test_function_profiling(self): ''' Test runtime profiler correctly records workflow RAM/CPUs consumption @@ -421,9 +407,9 @@ def test_function_profiling(self): num_threads = self.num_threads # Run workflow and get stats - start_str, finish_str = self._run_function_workflow(num_gb, num_threads) + node_str = self._run_function_workflow(num_gb, num_threads) # Get runtime stats as dictionary - node_stats = json.loads(finish_str) + node_stats = json.loads(node_str) # Read out runtime stats runtime_gb = float(node_stats['runtime_memory_gb']) @@ -444,5 +430,3 @@ def test_function_profiling(self): # Assert runtime stats are what was input assert runtime_gb_err <= allowed_gb_err, mem_err assert abs(expected_runtime_threads - runtime_threads) <= 1, threads_err - - diff --git a/nipype/interfaces/tests/use_resources b/nipype/utils/tests/use_resources similarity index 100% rename from nipype/interfaces/tests/use_resources rename to nipype/utils/tests/use_resources