Merge branch 'master' of github.com:nipy/nipype into fix/retroicor

Author: mgxd

.travis.yml

@@ -6,9 +6,9 @@ python:
 - 3.4
 - 3.5
 env:
-- INSTALL_DEB_DEPENDECIES=true
-- INSTALL_DEB_DEPENDECIES=false
-- INSTALL_DEB_DEPENDECIES=true DUECREDIT_ENABLE=yes
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
 before_install:
 - function bef_inst {
   wget http://repo.continuum.io/miniconda/Miniconda${TRAVIS_PYTHON_VERSION:0:1}-latest-Linux-x86_64.sh
@@ -28,16 +28,15 @@ before_install:
   export FSLOUTPUTTYPE=NIFTI_GZ; }
 - travis_retry bef_inst
 install:
+#  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&
 - function inst {
   conda config --add channels conda-forge &&
   conda update --yes conda &&
   conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
-  conda install -y nipype matplotlib nitime &&
-  pip install python-coveralls coverage doctest-ignore-unicode &&
-  if [ ! -z "$DUECREDIT_ENABLE"]; then pip install duecredit; fi &&
+  conda install -y nipype &&
   rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
   pip install -r requirements.txt &&
-  pip install -e . &&
+  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}; }

CHANGES

@@ -1,6 +1,7 @@
 Upcoming release 0.13
 =====================
 
+* ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
 * FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
 * ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606)
 * ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399)

Makefile

@@ -3,7 +3,7 @@
 # rsync -e ssh nipype-0.1-py2.5.egg cburns,[email protected]:/home/frs/project/n/ni/nipy/nipype/nipype-0.1/
 
 PYTHON ?= python
-NOSETESTS ?= nosetests
+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
 
@@ -56,7 +56,7 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	$(NOSETESTS) -s nipype --with-doctest --with-doctest-ignore-unicode
+	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 \
@@ -66,7 +66,8 @@ test-coverage: clean-tests in
 	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --with-coverage --cover-package=nipype \
 	--config=.coveragerc
 
-test: clean test-code
+test: tests # just another name
+tests: clean test-code
 
 html:
 	@echo "building docs"

circle.yml

@@ -1,4 +1,10 @@
 machine:
+  environment:
+    OSF_NIPYPE_URL: "https://files.osf.io/v1/resources/nefdp/providers/osfstorage"
+    DATA_NIPYPE_TUTORIAL_URL: "${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21"
+    DATA_NIPYPE_FSL_COURSE: "${OSF_NIPYPE_URL}/57f472cf9ad5a101f977ecfe"
+    DATA_NIPYPE_FSL_FEEDS: "${OSF_NIPYPE_URL}/57f473066c613b01f113e7af"
+
   services:
     - docker
 
@@ -15,9 +21,9 @@ dependencies:
 
   override:
     - mkdir -p ~/examples ~/scratch/nose ~/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 https://dl.dropbox.com/s/jzgq2nupxyz36bp/nipype-tutorial.tar.bz2 && 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 https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz && 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 https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/fsl-5.0.9-feeds.tar.gz && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
+    - 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
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600

doc/devel/testing_nipype.rst

@@ -1,3 +1,5 @@
+.. _dev_testing_nipype:
+
 ==============
 Testing nipype
 ==============
@@ -14,37 +16,91 @@ If both batteries of tests are passing, the following badges should be shown in
   :target: https://circleci.com/gh/nipy/nipype/tree/master
 
 
-Tests implementation
---------------------
+Installation for developers
+---------------------------
+
+To check out the latest development version::
+
+    git clone https://github.com/nipy/nipype.git
+
+After cloning::
+
+    cd nipype
+    pip install -r requirements.txt
+    python setup.py develop
+
+or::
+
+    cd nipype
+    pip install -r requirements.txt
+    pip install -e .[tests]
+
+
+
+Test implementation
+-------------------
 
 Nipype testing framework is built upon `nose <http://nose.readthedocs.io/en/latest/>`_.
 By the time these guidelines are written, Nipype implements 17638 tests.
 
-To run the tests locally, first get nose installed::
+After installation in developer mode, the tests can be run with the
+following simple command at the root folder of the project ::
+
+    make tests
 
-  pip install nose
+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
 
-Then, after nipype is `installed in developer mode <../users/install.html#nipype-for-developers>`_,
-the tests can be run with the following simple command::
 
-  make tests
+A successful test run should complete in a few minutes and end with
+something like::
 
+    ----------------------------------------------------------------------
+    Ran 17922 tests in 107.254s
+
+    OK (SKIP=27)
+
+
+All tests should pass (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>`_.
+
+On Debian systems, set the following environment variable before running
+tests::
+
+       export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB
+
+where ``$pathtomatlabdir`` is the path to your matlab installation and
+``$platform`` is the directory referring to x86 or x64 installations
+(typically ``glnxa64`` on 64-bit installations).
 
 Skip tests
-----------
+~~~~~~~~~~
 
 Nipype will skip some tests depending on the currently available software and data
 dependencies. Installing software dependencies and downloading the necessary data
 will reduce the number of skip tests.
 
 Some tests in Nipype make use of some images distributed within the `FSL course data
 <http://fsl.fmrib.ox.ac.uk/fslcourse/>`_. This reduced version of the package can be downloaded `here
-<https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz>`_.
+<https://files.osf.io/v1/resources/nefdp/providers/osfstorage/57f472cf9ad5a101f977ecfe>`_.
 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.
 
 
+Avoiding any MATLAB calls from testing
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+On unix systems, set an empty environment variable::
+
+    export NIPYPE_NO_MATLAB=
+
+This will skip any tests that require matlab.
+
+
 Testing Nipype using Docker
 ---------------------------
 

doc/users/install.rst

@@ -43,6 +43,12 @@ or::
   pip install nipype
 
 
+If you want to install all the optional features of ``nipype``,
+use the following command (only for ``nipype>=0.13``)::
+
+  pip install nipype[all]
+
+
 Debian and Ubuntu
 ~~~~~~~~~~~~~~~~~
 
@@ -73,77 +79,24 @@ If you downloaded the source distribution named something
 like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the
 ``nipype-x.y`` directory and install nipype using::
 
-    pip install -r requirements.txt
     python setup.py install
 
 **Note:** Depending on permissions you may need to use ``sudo``.
 
 
-Nipype for developers
----------------------
-
-To check out the latest development version::
-
-        git clone git://github.com/nipy/nipype.git
-
-or::
-
-        git clone https://github.com/nipy/nipype.git
-
-After cloning::
-
-        pip install -r requirements.txt
-        python setup.py develop
-
-
-Check out the list of nipype's `current dependencies <https://github.com/nipy/nipype/blob/master/requirements.txt>`_.
-
-
 Testing the install
 -------------------
 
-The best way to test the install is to run the test suite.  If you have
-nose_ installed, then do the following::
-
-    python -c "import nipype; nipype.test()"
-
-you can also test with nosetests::
-
-    nosetests --with-doctest <installation filepath>/nipype  --exclude=external --exclude=testing
-
-or::
-
-    nosetests --with-doctest nipype
-
-A successful test run should complete in a few minutes and end with
-something like::
-
-    Ran 13053 tests in 126.618s
-
-    OK (SKIP=66)
-
-All tests should pass (unless you're missing a dependency). If SUBJECTS_DIR
-variable is not set some FreeSurfer related tests will fail. If any tests
-fail, please report them on our `bug tracker
-<http://github.com/nipy/nipype/issues>`_.
-
-On Debian systems, set the following environment variable before running
-tests::
-
-       export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB
+The best way to test the install is checking nipype's version ::
 
-where ``$pathtomatlabdir`` is the path to your matlab installation and
-``$platform`` is the directory referring to x86 or x64 installations
-(typically ``glnxa64`` on 64-bit installations).
+    python -c "import nipype; print(nipype.__version__)"
 
-Avoiding any MATLAB calls from testing
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-On unix systems, set an empty environment variable::
+Installation for developers
+---------------------------
 
-    export NIPYPE_NO_MATLAB=
+Developers should start `here <../devel/testing_nipype.html>`_.
 
-This will skip any tests that require matlab.
 
 Recommended Software
 ------------

docker/nipype_test/Dockerfile_py27

@@ -40,12 +40,13 @@ RUN chmod +x /usr/bin/run_*
 # Speed up building
 RUN mkdir -p /root/src/nipype
 COPY requirements.txt /root/src/nipype/requirements.txt
-RUN pip install -r /root/src/nipype/requirements.txt
+RUN pip install -r /root/src/nipype/requirements.txt && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
 
 # Re-install nipype
 COPY . /root/src/nipype
 RUN rm -r /usr/local/miniconda/lib/python2.7/site-packages/nipype* && \
     cd /root/src/nipype && \
-    pip install -e .
+    pip install -e .[all]
 
 CMD ["/bin/bash"]

docker/nipype_test/Dockerfile_py34

@@ -45,12 +45,13 @@ RUN rm -r ${FSLDIR}/bin/imglob && \
 # Speed up building
 RUN mkdir -p /root/src/nipype
 COPY requirements.txt /root/src/nipype/requirements.txt
-RUN pip install -r /root/src/nipype/requirements.txt
+RUN pip install -r /root/src/nipype/requirements.txt && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.4/site-packages/matplotlib/mpl-data/matplotlibrc
 
 # Re-install nipype
 COPY . /root/src/nipype
 RUN rm -r /usr/local/miniconda/lib/python3.4/site-packages/nipype* && \
     cd /root/src/nipype && \
-    pip install -e . 
+    pip install -e .[all]
 
 CMD ["/bin/bash"]

docker/nipype_test/Dockerfile_py35

@@ -30,7 +30,7 @@ FROM nipype/nipype_test:base-0.0.2
 MAINTAINER The nipype developers https://github.com/nipy/nipype
 
 WORKDIR /root
-   
+
 COPY docker/circleci/run_* /usr/bin/
 RUN chmod +x /usr/bin/run_*
 
@@ -43,12 +43,13 @@ RUN rm -r ${FSLDIR}/bin/imglob && \
 # Speed up building
 RUN mkdir -p /root/src/nipype
 COPY requirements.txt /root/src/nipype/requirements.txt
-RUN pip install -r /root/src/nipype/requirements.txt
+RUN pip install -r /root/src/nipype/requirements.txt && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python3.5/site-packages/matplotlib/mpl-data/matplotlibrc
 
 # Re-install nipype
 COPY . /root/src/nipype
 RUN rm -r /usr/local/miniconda/lib/python3.5/site-packages/nipype* && \
     cd /root/src/nipype && \
-    pip install -e . 
+    pip install -e .[all]
 
 CMD ["/bin/bash"]