MRG: Try envs (mne-tools#4641)

* ENH: Try envs * FIX: Fix AppVeyor * FIX: Fix GUIs * w * FIX: Skip problematic tests for OSX * FIX: Put PySurfer back * FIX: Fix doc * FIX: Switch to 3.6 * FIX: Fix Travis * STY: Fix naming [ci skip] * FIX: Fix instructions
jordandc1 · Oct 9, 2017 · 2a98e81 · 2a98e81
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commit 2a98e81
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Showing 21 changed files with 318 additions and 188 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -8,8 +8,8 @@ cache:
   - $HOME/.ccache
 env:
     # TRAVIS_PYTHON_VERSION is only needed for neo's setup.py
-    global: PYTHON_VERSION=2.7 DISPLAY=:99.0 MNE_LOGGING_LEVEL=warning TEST_LOCATION=src
-            PIP_DEPENDENCIES="codecov pytest-faulthandler" OPTION=""
+    global: PYTHON_VERSION=3.6 DISPLAY=:99.0 MNE_LOGGING_LEVEL=warning TEST_LOCATION=src
+            PIP_DEPENDENCIES="codecov pytest-faulthandler pytest-sugar" OPTION=""
             TRAVIS_PYTHON_VERSION=3.6
 
 matrix:
@@ -21,7 +21,7 @@ matrix:
                PIP_DEPENDENCIES="flake8 numpydoc codespell git+git://github.com/PyCQA/pydocstyle.git codecov check-manifest pytest-sugar"
                OPTION="--doctest-ignore-import-errors"
 
-        # Full (Linux, 2.7)
+        # Linux
         - os: linux
           env: CONDA_ENVIRONMENT="environment.yml"
                SPLIT=0
@@ -37,42 +37,39 @@ matrix:
           env: CONDA_ENVIRONMENT="environment.yml"
                SPLIT=1
 
-        # Py3k + non-default stim channel
+        # 2.7 + non-default stim channel
         - os: linux
-          env: PYTHON_VERSION=3.6 TEST_LOCATION=install MNE_STIM_CHANNEL=STI101
-               CONDA_DEPENDENCIES="numpy scipy matplotlib pandas scikit-learn h5py pillow statsmodels nose pytest pytest-cov"
-               PIP_DEPENDENCIES="nitime joblib nibabel codecov pytest-sugar pytest-faulthandler"
+          env: CONDA_ENVIRONMENT="environment2.yml" MNE_STIM_CHANNEL=STI101
                SPLIT=0
         - os: linux
-          env: PYTHON_VERSION=3.6 TEST_LOCATION=install MNE_STIM_CHANNEL=STI101
-               CONDA_DEPENDENCIES="numpy scipy matplotlib pandas scikit-learn h5py pillow statsmodels nose pytest pytest-cov"
-               PIP_DEPENDENCIES="nitime joblib nibabel codecov pytest-sugar pytest-faulthandler"
+          env: CONDA_ENVIRONMENT="environment2.yml" MNE_STIM_CHANNEL=STI101
                SPLIT=1
 
-        # Old dependencies
+        # 2.7 Old dependencies
         - os: linux
-          env: CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.12 scikit-learn=0.14 nose pytest pytest-cov"
-               PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler"
+          env: PYTHON_VERSION=2.7
+               CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.12 scikit-learn=0.14 nose pytest pytest-cov"
                SPLIT=0
         - os: linux
-          env: CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.12 scikit-learn=0.14 nose pytest pytest-cov"
-               PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler"
+          env: PYTHON_VERSION=2.7
+               CONDA_DEPENDENCIES="numpy=1.8 scipy=0.12 matplotlib=1.3 pandas=0.12 scikit-learn=0.14 nose pytest pytest-cov"
                SPLIT=1
 
         # Minimal
         - os: linux
           env: DEPS=minimial
                CONDA_DEPENDENCIES="numpy scipy matplotlib nose pytest pytest-cov"
-               PIP_DEPENDENCIES="codecov faulthandler pytest-sugar pytest-faulthandler"
                SPLIT=0
         - os: linux
           env: DEPS=minimial
                CONDA_DEPENDENCIES="numpy scipy matplotlib nose pytest pytest-cov"
-               PIP_DEPENDENCIES="codecov faulthandler pytest-sugar pytest-faulthandler"
                SPLIT=1
 
 # Setup anaconda
 before_install:
+    - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
+        /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+      fi;
     - git clone https://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda.sh
     - if [ ! -z $CONDA_ENVIRONMENT ]; then
@@ -92,9 +89,6 @@ before_install:
         fi;
         mne_surf2bem --version;
       fi;
-    - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
-        /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
-      fi;
 
 install:
     # Suppress the parallel outputs for logging cleanliness

diff --git a/doc/_static/copybutton.js b/doc/_static/copybutton.js
@@ -0,0 +1,66 @@
+// Copyright 2014 PSF. Licensed under the PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
+// File originates from the cpython source found in Doc/tools/sphinxext/static/copybutton.js
+
+$(document).ready(function() {
+    /* Add a [>>>] button on the top-right corner of code samples to hide
+     * the >>> and ... prompts and the output and thus make the code
+     * copyable. */
+    var div = $('.highlight-python .highlight,' +
+                '.highlight-default .highlight,' +
+                '.highlight-python3 .highlight')
+    var pre = div.find('pre');
+
+    // get the styles from the current theme
+    pre.parent().parent().css('position', 'relative');
+    var hide_text = 'Hide the prompts and output';
+    var show_text = 'Show the prompts and output';
+    var border_width = pre.css('border-top-width');
+    var border_style = pre.css('border-top-style');
+    var border_color = pre.css('border-top-color');
+    var button_styles = {
+        'cursor':'pointer', 'position': 'absolute', 'top': '0', 'right': '0',
+        'border-color': border_color, 'border-style': border_style,
+        'border-width': border_width, 'color': border_color, 'text-size': '75%',
+        'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em',
+        'border-radius': '0 3px 0 0'
+    }
+
+    // create and add the button to all the code blocks that contain >>>
+    div.each(function(index) {
+        var jthis = $(this);
+        if (jthis.find('.gp').length > 0) {
+            var button = $('<span class="copybutton">&gt;&gt;&gt;</span>');
+            button.css(button_styles)
+            button.attr('title', hide_text);
+            button.data('hidden', 'false');
+            jthis.prepend(button);
+        }
+        // tracebacks (.gt) contain bare text elements that need to be
+        // wrapped in a span to work with .nextUntil() (see later)
+        jthis.find('pre:has(.gt)').contents().filter(function() {
+            return ((this.nodeType == 3) && (this.data.trim().length > 0));
+        }).wrap('<span>');
+    });
+
+    // define the behavior of the button when it's clicked
+    $('.copybutton').click(function(e){
+        e.preventDefault();
+        var button = $(this);
+        if (button.data('hidden') === 'false') {
+            // hide the code output
+            button.parent().find('.go, .gp, .gt').hide();
+            button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden');
+            button.css('text-decoration', 'line-through');
+            button.attr('title', show_text);
+            button.data('hidden', 'true');
+        } else {
+            // show the code output
+            button.parent().find('.go, .gp, .gt').show();
+            button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible');
+            button.css('text-decoration', 'none');
+            button.attr('title', hide_text);
+            button.data('hidden', 'false');
+        }
+    });
+});
+
diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
@@ -2,6 +2,8 @@
 
 {% block extrahead %}
 
+    <script type="text/javascript" src="{{ pathto('_static/copybutton.js', 1) }}"></script>
+
 {% if use_google_analytics|tobool %}
     <script type="text/javascript">
     var _gaq = _gaq || [];

diff --git a/doc/advanced_setup.rst b/doc/advanced_setup.rst
@@ -11,6 +11,46 @@ Advanced setup and troubleshooting
    :local:
    :depth: 1
 
+.. _installing_master:
+
+Using the development version of MNE
+####################################
+
+It is possible to update your version of MNE between releases for
+bugfixes or new features.
+
+.. warning:: In between releases, function and class APIs can change without
+             warning.
+
+You can use ``pip`` for a one-time update:
+
+.. code-block:: console
+
+   $ pip install --upgrade --no-deps git+https://github.com/mne-tools/mne-python.git
+
+Or, if you prefer to be set up for frequent updates, you can use ``git`` directly:
+
+.. code-block:: console
+
+   $ git clone git://github.com/mne-tools/mne-python.git
+   $ cd mne-python
+   $ python setup.py develop
+
+A feature of ``python setup.py develop`` is that any changes made to
+the files (e.g., by updating to latest ``master``) will be reflected in
+``mne`` as soon as you restart your Python interpreter. So to update to
+the latest version of the ``master`` development branch, you can do:
+
+   .. code-block:: console
+
+   $ git pull origin master
+
+and MNE will be updated to have the latest changes.
+
+
+If you plan to contribute to MNE, please continue reading how to
+:ref:`contribute_to_mne`.
+
 .. _CUDA:
 
 CUDA
@@ -28,7 +68,7 @@ If you want to use NVIDIA CUDA, you should install:
 For example, on Ubuntu 15.10, a combination of system packages and ``git``
 packages can be used to install the CUDA stack:
 
-.. code-block:: bash
+.. code-block:: console
 
     # install system packages for CUDA
     $ sudo apt-get install nvidia-cuda-dev nvidia-modprobe
@@ -49,7 +89,7 @@ To initialize mne-python cuda support, after installing these dependencies
 and running their associated unit tests (to ensure your installation is correct)
 you can run:
 
-.. code-block:: bash
+.. code-block:: console
 
     $ MNE_USE_CUDA=true MNE_LOGGING_LEVEL=info python -c "import mne; mne.cuda.init_cuda()"
     Enabling CUDA with 1.55 GB available memory
@@ -62,20 +102,20 @@ initialized on startup, you can do::
 
 You can test if MNE CUDA support is working by running the associated test:
 
-.. code-block:: bash
+.. code-block:: console
 
     $ pytest mne/tests/test_filter.py
 
 If ``MNE_USE_CUDA=true`` and all tests pass with none skipped, then
 MNE-Python CUDA support works.
 
-IPython (and notebooks)
-#######################
+IPython / Jupyter notebooks
+###########################
 
-In IPython, we strongly recommend using the Qt matplotlib backend for
+In Jupyter, we strongly recommend using the Qt matplotlib backend for
 fast and correct rendering:
 
-.. code-block:: bash
+.. code-block:: console
 
     $ ipython --matplotlib=qt
 
@@ -116,5 +156,8 @@ the interpreter to use QtGui and QtCore from pyface::
 
 This line should be added before any imports from mne-python.
 
+To avoid Qt conflicts, you can also try using the ``wx`` backend via
+``conda install wxpython`` and ``ETS_TOOLKIT=wx``.
+
 For more information, see
 http://docs.enthought.com/mayavi/mayavi/building_applications.html.
diff --git a/doc/conf.py b/doc/conf.py
@@ -304,14 +304,6 @@
     'doc_module': ('mne',),
     'reference_url': {
         'mne': None,
-        'numpy': 'http://docs.scipy.org/doc/numpy',
-        'scipy': 'http://docs.scipy.org/doc/scipy/reference',
-        'matplotlib': 'http://matplotlib.org',
-        'sklearn': 'http://scikit-learn.org/stable',
-        'mayavi': 'http://docs.enthought.com/mayavi/mayavi',
-        'nibabel': 'http://nipy.org/nibabel',
-        'nilearn': 'http://nilearn.github.io',
-        'surfer': 'https://pysurfer.github.io',
         },
     'examples_dirs': examples_dirs,
     'gallery_dirs': gallery_dirs,