From ff67fa2e5db9ac0fbc19afe02e77f71fd10960ed Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Tue, 26 Apr 2016 22:09:24 -0400 Subject: [PATCH 1/2] cleaning up a few build and test elements --- .gitignore | 4 ++++ .travis.yml | 1 + doc/conf.py | 6 ++++-- nipype/info.py | 1 + nipype/workflows/smri/freesurfer/recon.py | 8 ++++---- 5 files changed, 14 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index b6098e8c05..8d472e7389 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,7 @@ nipype/testing/data/von_errmap.nii.gz crash*.pklz .coverage htmlcov/ +__pycache__/ +*~ +.ipynb_checkpoints/ +.ruby-version \ No newline at end of file diff --git a/.travis.yml b/.travis.yml index 82e9e1cf59..0ffdfb3642 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,6 +4,7 @@ language: python python: - 2.7 - 3.4 +- 3.5 env: - INSTALL_DEB_DEPENDECIES=true - INSTALL_DEB_DEPENDECIES=false diff --git a/doc/conf.py b/doc/conf.py index 1a0d7e9cca..d786e44682 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -41,8 +41,7 @@ # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['readthedocs_ext.readthedocs', - 'sphinx.ext.todo', +extensions = ['sphinx.ext.todo', 'sphinx.ext.pngmath', 'sphinx.ext.inheritance_diagram', 'sphinx.ext.graphviz', @@ -56,6 +55,9 @@ #'IPython.sphinxext.ipython_directive', #'IPython.sphinxext.ipython_console_highlighting' ] +on_rtd = os.environ.get('READTHEDOCS') == 'True' +if on_rtd: + extensions.append('readthedocs_ext.readthedocs') # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/nipype/info.py b/nipype/info.py index 08aba268a2..75ef29e9c6 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -61,6 +61,7 @@ def get_nipype_gitversion(): "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.5", "Topic :: Scientific/Engineering"] description = 'Neuroimaging in Python: Pipelines and Interfaces' diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py index 454321ff83..a388cb6bfd 100644 --- a/nipype/workflows/smri/freesurfer/recon.py +++ b/nipype/workflows/smri/freesurfer/recon.py @@ -107,14 +107,14 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None): Note: The input subject_id is not passed to the commands in the workflow. Commands - that require subject_id are reading implicit inputs from + that require subject_id are reading implicit inputs from {SUBJECTS_DIR}/{subject_id}. For those commands the subject_id is set to the default value and SUBJECTS_DIR is set to the node directory. The implicit inputs are then copied to the node directory in order to mimic a SUBJECTS_DIR structure. For example, if the command implicitly reads in brainmask.mgz, the - interface would copy that input file to - {node_dir}/{subject_id}/mri/brainmask.mgz and set SUBJECTS_DIR to node_dir. - The workflow only uses the input subject_id to datasink the outputs to + interface would copy that input file to + {node_dir}/{subject_id}/mri/brainmask.mgz and set SUBJECTS_DIR to node_dir. + The workflow only uses the input subject_id to datasink the outputs to {subjects_dir}/{subject_id}. """ reconall = pe.Workflow(name=name) From 002b836cbda88fb882d79a3f6302f96a33638949 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Tue, 26 Apr 2016 22:44:20 -0400 Subject: [PATCH 2/2] fix: travis environment --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 0ffdfb3642..4a49e0778d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -40,7 +40,7 @@ install: - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION - source activate testenv - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then pip install ordereddict; fi -- conda install --yes numpy scipy nose networkx dateutil +- conda install --yes numpy scipy nose networkx python-dateutil - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes traits; else pip install traits; fi - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi - pip install python-coveralls