Merge branch 'master' of https://github.com/nipy/nipype into enh/eddy

Author: mgxd

.coveragerc

@@ -4,6 +4,5 @@ source = nipype
 include = */nipype/*
 omit =
     */nipype/external/*
-    */nipype/workflows/*
     */nipype/fixes/*
     */setup.py

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,10 @@
+### Summary
+
+### Actual behavior
+
+### Expected behavior
+
+### How to replicate the behavior
+
+### Platform details:
+please paste the output of: `python -c "import nipype; print(nipype.get_info())"`

.travis.yml

@@ -19,12 +19,12 @@ before_install:
   if $INSTALL_DEB_DEPENDECIES; then sudo ln -s /run/shm /dev/shm; fi &&
   bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) &&
   sudo apt-get -y update &&
-  sudo apt-get -y install xvfb fusefat &&
+  sudo apt-get -y install xvfb fusefat graphviz &&
   if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -y -qq
   fsl afni elastix fsl-atlases; fi &&
   if $INSTALL_DEB_DEPENDECIES; then
     source /etc/fsl/fsl.sh;
-    source /etc/afni/afni.sh; 
+    source /etc/afni/afni.sh;
     export FSLOUTPUTTYPE=NIFTI_GZ; fi }
 - travis_retry bef_inst
 install:
@@ -36,15 +36,10 @@ install:
   conda install -y nipype &&
   rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
   pip install -r requirements.txt &&
-  pip install -e .[$NIPYPE_EXTRAS] &&
-  export COVERAGE_PROCESS_START=$(pwd)/.coveragerc &&
-  export COVERAGE_DATA_FILE=$(pwd)/.coverage &&
-  echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; }
+  pip install -e .[$NIPYPE_EXTRAS]; }
 - travis_retry inst
 script:
-- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3
-after_success:
-- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+- py.test --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra

Makefile

@@ -5,7 +5,7 @@
 PYTHON ?= python
 NOSETESTS=`which nosetests`
 
-.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-doc test-coverage test html specs check-before-commit check
+.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check
 
 zipdoc: html
 	zip documentation.zip doc/_build/html
@@ -56,16 +56,11 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	python -W once:FSL:UserWarning:nipype $(NOSETESTS) --with-doctest --with-doctest-ignore-unicode --logging-level=DEBUG --verbosity=3 nipype
-
-test-doc:
-	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --doctest-tests --doctest-extension=rst \
-	--doctest-fixtures=_fixture doc/
+	py.test --doctest-module nipype
 
 test-coverage: clean-tests in
-	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --with-coverage --cover-package=nipype \
-	--config=.coveragerc
-
+	py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype
+	
 test: tests # just another name
 tests: clean test-code
 

README.rst

@@ -77,18 +77,21 @@ Information specific to Nipype is located here::
 Support and Communication
 -------------------------
 
-If you have a problem or would like to ask a question about how to do something in Nipype please submit a question
-to `NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a platform similar to StackOverflow but dedicated to neuroinformatics. All previous Nipype questions are available here::
-
-       http://neurostars.org/t/nipype/
-
+If you have a problem or would like to ask a question about how to do something in Nipype please open an issue
+in this GitHub repository.
 
 To participate in the Nipype development related discussions please use the following mailing list::
 
        http://mail.python.org/mailman/listinfo/neuroimaging
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
 
+  .. warning ::
+
+    As of `Nov 23, 2016 <https://twitter.com/neuroquestion/status/801453442132754432>`_,
+    `NeuroStars <http://neurostars.org>`_ is down. We used to have all previous Nipype
+    questions available under the `nipype <http://neurostars.org/t/nipype/>`_ label.
+
 
 Nipype structure
 ----------------

circle.yml

@@ -20,7 +20,7 @@ dependencies:
     - sudo apt-get -y update && sudo apt-get install -y wget bzip2
 
   override:
-    - mkdir -p ~/examples ~/scratch/nose ~/scratch/logs
+    - mkdir -p ~/examples ~/scratch/pytest ~/scratch/logs
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
     - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
     - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
@@ -35,10 +35,10 @@ dependencies:
 test:
   override:
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
-    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35 :
+        timeout: 2600
+    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27 :
         timeout: 2600
-    - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
-        timeout: 5200
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
     - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
@@ -55,8 +55,8 @@ test:
 
   post:
     - bash docker/circleci/teardown.sh
-    - for xml_f in ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests; done
-    - for xml_f in ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests; done
+    - for xml_f in ${CIRCLE_TEST_REPORTS}/pytest/coverage*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests; done
+    - for xml_f in ${CIRCLE_TEST_REPORTS}/pytest/smoketest*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests; done
 
 general:
   artifacts:

doc/devel/testing_nipype.rst

@@ -40,7 +40,7 @@ or::
 Test implementation
 -------------------
 
-Nipype testing framework is built upon `nose <http://nose.readthedocs.io/en/latest/>`_.
+Nipype testing framework is built upon `pytest <http://doc.pytest.org/en/latest/>`_.
 By the time these guidelines are written, Nipype implements 17638 tests.
 
 After installation in developer mode, the tests can be run with the
@@ -50,20 +50,18 @@ following simple command at the root folder of the project ::
 
 If ``make`` is not installed in the system, it is possible to run the tests using::
 
-    python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest \
-           --with-doctest-ignore-unicode --logging-level=DEBUG --verbosity=3 nipype
+     py.test --doctest-modules --cov=nipype nipype
 
 
-A successful test run should complete in a few minutes and end with
+A successful test run should complete in 10-30 minutes and end with
 something like::
 
     ----------------------------------------------------------------------
-    Ran 17922 tests in 107.254s
+    2445 passed, 41 skipped, 7 xfailed in 1277.66 seconds
 
-    OK (SKIP=27)
 
 
-All tests should pass (unless you're missing a dependency). If the ``SUBJECTS_DIR```
+No test should fail (unless you're missing a dependency). If the ``SUBJECTS_DIR```
 environment variable is not set, some FreeSurfer related tests will fail.
 If any of the tests failed, please report them on our `bug tracker
 <http://github.com/nipy/nipype/issues>`_.
@@ -90,6 +88,11 @@ Some tests in Nipype make use of some images distributed within the `FSL course
 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.
 
+Xfail tests
+~~~~~~~~~~
+
+Some tests are expect to fail until the code will be changed or for other reasons.
+
 
 Avoiding any MATLAB calls from testing
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -115,7 +118,7 @@ Nipype is as easy as follows::
                       -v ~/examples:/root/examples:ro \
                       -v ~/scratch:/scratch \
                       -w /root/src/nipype \
-                      nipype/nipype_test:py27 /usr/bin/run_nosetests.sh
+                      nipype/nipype_test:py27 /usr/bin/run_pytest.sh
 
 For running nipype in Python 3.5::
 
@@ -126,4 +129,4 @@ For running nipype in Python 3.5::
                       -v ~/examples:/root/examples:ro \
                       -v ~/scratch:/scratch \
                       -w /root/src/nipype \
-                      nipype/nipype_test:py35 /usr/bin/run_nosetests.sh
+                      nipype/nipype_test:py35 /usr/bin/run_pytest.sh

doc/users/config_file.rst

@@ -134,7 +134,7 @@ Execution
 *poll_sleep_duration*
     This controls how long the job submission loop will sleep between submitting
     all pending jobs and checking for job completion. To be nice to cluster
-    schedulers the default is set to 60 seconds.
+    schedulers the default is set to 2 seconds.
 
 *xvfb_max_wait*
     Maximum time (in seconds) to wait for Xvfb to start, if the _redirect_x parameter of an Interface is True.

docker/circleci/run_nosetests.sh renamed to docker/circleci/run_pytests.sh

@@ -6,7 +6,7 @@ set -u
 PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
 
 # Create necessary directories
-mkdir -p /scratch/nose /scratch/crashfiles /scratch/logs/py${PYTHON_VERSION}
+mkdir -p /scratch/pytest /scratch/crashfiles /scratch/logs/py${PYTHON_VERSION}
 
 # Create a nipype config file
 mkdir -p /root/.nipype
@@ -20,17 +20,18 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then
     echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
 fi
 
-# Run tests
+# Run tests using pytest
 cd /root/src/nipype/
 make clean
-nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml"
+py.test --doctest-modules --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}.xml --cov=nipype nipype
+
 
 # Workaround: run here the profiler tests in python 3
 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
     echo '[execution]' >> /root/.nipype/nipype.cfg
     echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
-    nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml"
-    nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml"
+    py.test --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}_profiler.xml --cov=nipype nipype/interfaces/tests/test_runtime_profiler.py 
+    py.test --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml --cov=nipype nipype/pipeline/plugins/tests/test_multiproc*.py 
 fi
 
 # Copy crashfiles to scratch

docker/circleci/teardown.sh

@@ -6,8 +6,8 @@
 set -u
 set -e
 
-mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
+mkdir -p ${CIRCLE_TEST_REPORTS}/pytest
+sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/pytest
 mkdir -p ~/docs
 sudo mv ~/scratch/docs/* ~/docs/
 mkdir -p ~/logs