From d2301f7916d0e3dda4e404a9f2afc19615f7cc67 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 28 Mar 2018 19:54:01 -0400 Subject: [PATCH 1/2] TEST: Rename test_dcm2nii to avoid clobbering auto test on OS X --- .../interfaces/tests/{test_dcm2nii.py => test_extra_dcm2nii.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename nipype/interfaces/tests/{test_dcm2nii.py => test_extra_dcm2nii.py} (100%) diff --git a/nipype/interfaces/tests/test_dcm2nii.py b/nipype/interfaces/tests/test_extra_dcm2nii.py similarity index 100% rename from nipype/interfaces/tests/test_dcm2nii.py rename to nipype/interfaces/tests/test_extra_dcm2nii.py From 15274fb8c532d719e0b5f2d525fc6eb14eef926b Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 28 Mar 2018 19:54:49 -0400 Subject: [PATCH 2/2] STY: Whitespace cleanup --- doc/devel/testing_nipype.rst | 12 ++++++------ nipype/interfaces/afni/preprocess.py | 24 ++++++++++++------------ 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/doc/devel/testing_nipype.rst b/doc/devel/testing_nipype.rst index 03d063f2e5..0cce8b4671 100644 --- a/doc/devel/testing_nipype.rst +++ b/doc/devel/testing_nipype.rst @@ -54,7 +54,7 @@ environment variable is not set, some FreeSurfer related tests will fail. If any of the tests failed, please report them on our `bug tracker `_. -On Debian systems with a local copy of MATLAB installed, set the following +On Debian systems with a local copy of MATLAB installed, set the following environment variable before running tests:: export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB @@ -74,8 +74,8 @@ A few tests in Nipype make use of some images distributed within the `FSL course `_. This reduced version of the package can be downloaded `here `_. To enable the tests depending on these data, just unpack the targz file and set the :code:`FSL_COURSE_DATA` environment -variable to point to that folder. -Note, that the test execution time can increase significantly with these additional tests. +variable to point to that folder. +Note, that the test execution time can increase significantly with these additional tests. Xfailed tests @@ -87,14 +87,14 @@ Some tests are expect to fail until the code will be changed or for other reason Testing Nipype using Docker --------------------------- -Nipype is tested inside Docker containers and users can use nipype images to test local versions. +Nipype is tested inside Docker containers and users can use nipype images to test local versions. First, install the `Docker Engine `_. Nipype has one base docker image called nipype/nipype:base, that contains several useful tools (FreeSurfer, AFNI, FSL, ANTs, etc.), and additional test images for specific Python versions: py27 for Python 2.7 and py36 for Python 3.6. Users can pull the nipype image for Python 3.6 as follows:: - + docker pull nipype/nipype:py36 In order to test a local version of nipype you can run test within container as follows:: @@ -105,5 +105,5 @@ In order to test a local version of nipype you can run test within container as Additional comments ------------------- -If the project is tested both on your local OS and within a Docker container, you might have to remove all +If the project is tested both on your local OS and within a Docker container, you might have to remove all ``__pycache__`` directories before switching between your OS and a container. diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index 13a065c27c..1d26bef587 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -2423,19 +2423,19 @@ class TProjectInputSpec(AFNICommandInputSpec): exists=True) censortr = traits.List( traits.Str(), - desc="""list of strings that specify time indexes + desc="""list of strings that specify time indexes to be removed from the analysis. Each string is - of one of the following forms: - 37 => remove global time index #37 - 2:37 => remove time index #37 in run #2 - 37..47 => remove global time indexes #37-47 - 37-47 => same as above - 2:37..47 => remove time indexes #37-47 in run #2 - *:0-2 => remove time indexes #0-2 in all runs - +Time indexes within each run start at 0. - +Run indexes start at 1 (just be to confusing). - +N.B.: 2:37,47 means index #37 in run #2 and - global time index 47; it does NOT mean + of one of the following forms: + 37 => remove global time index #37 + 2:37 => remove time index #37 in run #2 + 37..47 => remove global time indexes #37-47 + 37-47 => same as above + 2:37..47 => remove time indexes #37-47 in run #2 + *:0-2 => remove time indexes #0-2 in all runs + +Time indexes within each run start at 0. + +Run indexes start at 1 (just be to confusing). + +N.B.: 2:37,47 means index #37 in run #2 and + global time index 47; it does NOT mean index #37 in run #2 AND index #47 in run #2.""", argstr="-CENSORTR %s") cenmode = traits.Enum(