merge with master

Author: Shoshana Berleant

CHANGES

@@ -1,10 +1,24 @@
 Upcoming release 0.13
 =====================
 
+* REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678)
+* ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
+* FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
+* FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671)
 * ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637)
+* ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627)
 * FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656)
+* TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files)
+* ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647)
 * 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)
+* ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599)
+* ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466)
+* FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572)
+* REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597)
+* REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593)
+* TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609)
+* ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554)
 * ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591)
 * ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604)
 * FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572)

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"

bin/nipype2boutiques

@@ -6,7 +6,7 @@ <h3>{{ _('Links') }}</h3>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li><a href="about.html#funding">Funding</a> · <a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a></li>
-    <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://coveralls.io/r/nipy/nipype'><img src='https://coveralls.io/repos/nipy/nipype/badge.png' alt='Coverage Status' /></a></li>
+    <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://codecov.io/gh/nipy/nipype'><img src='https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg' alt='Coverage Status' /></a></li>
     <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>
 

bin/nipype_cmd

@@ -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
 ---------------------------