refactor documentation about installation and tests

Author: oesteban

doc/devel/testing_nipype.rst

@@ -1,3 +1,5 @@
+.. _dev_testing_nipype:
+
 ==============
 Testing nipype
 ==============
@@ -14,25 +16,69 @@ 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
@@ -45,6 +91,16 @@ To enable the tests depending on these data, just unpack the targz file and set
 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
 ~~~~~~~~~~~~~~~~~
 
@@ -73,72 +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 at the root folder of the repository ::
-
-    make test
-
-
-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 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
 ------------