Merge pull request #1671 from oesteban/fix/MinorErrorsNewInstaller

[FIX] Minor errors after migration to setuptools

Author: satra

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"

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

@@ -40,7 +40,8 @@ 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

docker/nipype_test/Dockerfile_py34

@@ -45,7 +45,8 @@ 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

docker/nipype_test/Dockerfile_py35

@@ -43,7 +43,8 @@ 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

nipype/info.py

@@ -156,7 +156,7 @@ def get_nipype_gitversion():
 ]
 
 EXTRA_REQUIRES = {
-    'doc': ['Sphinx>=0.3', 'matplotlib', 'pydotplus'],
+    'doc': ['Sphinx>=0.3', 'matplotlib', 'pydotplus', 'doctest-ignore-unicode'],
     'tests': TESTS_REQUIRES,
     'fmri': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil'],

nipype/interfaces/utility.py

@@ -25,7 +25,6 @@
                    Undefined, isdefined, OutputMultiPath, runtime_profile,
                    InputMultiPath, BaseInterface, BaseInterfaceInputSpec)
 from .io import IOBase, add_traits
-from ..testing import assert_equal
 from ..utils.filemanip import (filename_to_list, copyfile, split_filename)
 from ..utils.misc import getsource, create_function_from_source
 
@@ -530,8 +529,8 @@ def _run_interface(self, runtime):
         data1 = nb.load(self.inputs.volume1).get_data()
         data2 = nb.load(self.inputs.volume2).get_data()
 
-        assert_equal(data1, data2)
-
+        if not np.all(data1 == data2):
+            raise RuntimeError('Input images are not exactly equal')
         return runtime
 
 

requirements.txt

@@ -12,3 +12,4 @@ xvfbwrapper
 psutil
 funcsigs
 configparser
+doctest-ignore-unicode