MAINT: Update fsaverage (#270)

* MAINT: Update fsaverage

* FIX: Bump to 3.5

* ENH: Run more on CircleCI

* MAINT: CI

* MAINT: CI

* MAINT: CI

* MAINT: Circle

* FIX: Pattern

* FIX: Circle

* FIX: Try again

* FIX: Better

* FIX: One more

Author: larsoner

.circleci/config.yml

@@ -13,6 +13,7 @@ jobs:
               echo "export DISPLAY=:99" >> $BASH_ENV;
               echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV;
               echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV;
+              echo "export PATTERN=\"plot_\(?\!fmri_activation_volume\|resting_correlations\)\"" >> $BASH_ENV;
         - run:
             name: Merge with upstream
             command: |
@@ -25,12 +26,6 @@ jobs:
                 git fetch upstream master;
               fi
 
-        # Load our data
-        - restore_cache:
-            keys:
-              - data-cache-0
-              - pip-cache
-
         - run:
             name: Spin up Xvfb
             command: |
@@ -43,11 +38,18 @@ jobs:
             command: |
               sudo apt-get install qt5-default
 
+        # Load our data
+        - restore_cache:
+            keys:
+              - data-cache-0
+              - pip-cache
+
         - run:
             name: Get Python running
             command: |
               pip install --user -q --upgrade pip numpy
-              pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi
+              pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg sphinx-gallery
+              pip install --user -q --upgrade mayavi "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
         - save_cache:
             key: pip-cache
             paths:
@@ -58,18 +60,19 @@ jobs:
             name: Check installation
             command: |
               LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
-              echo $SUBJECTS_DIR
+
         - run:
             name: Get data
             command: |
-              if [ ! -d $SUBJECTS_DIR ]; then
-                mkdir $SUBJECTS_DIR;
-                cd $SUBJECTS_DIR;
-                wget http://faculty.washington.edu/larsoner/fsaverage_min.zip;
-                unzip fsaverage_min.zip;
-                rm fsaverage_min.zip;
-              fi;
+              echo $SUBJECTS_DIR
+              mkdir -p $SUBJECTS_DIR
+              python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
               ls $SUBJECTS_DIR
+        - save_cache:
+            key: data-cache-0
+            paths:
+              - "~/subjects"
+
         - run:
             name: Install PySurfer
             command: |
@@ -79,21 +82,17 @@ jobs:
             name: Build docs
             command: |
               cd doc
-              sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_morphometry\|plot_label\.py\|plot_probabilistic_label\|plot_resting_correlations\|plot_transparent_brain\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html
+              echo $PATTERN
+              make html_dev-pattern
 
         - store_artifacts:
             path: doc/_build/html/
             destination: html
 
-        - save_cache:
-            key: data-cache-0
-            paths:
-              - "~/subjects"
 
 workflows:
   version: 2
 
   default:
     jobs:
       - build_docs
-

.travis.yml

@@ -1,11 +1,14 @@
 language: c
 sudo: false
-
+dist: xenial
+services:
+    - xvfb
 env:
     global: PYTHON_VERSION=3.7
             CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface"
             PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg"
             DISPLAY=:99.0
+            SUBJECTS_DIR=~/subjects
 
 matrix:
     include:
@@ -16,11 +19,11 @@ matrix:
               packages:
                 - mencoder
 
-        # 2.7, no mencoder
+        # 3.5, no mencoder
         - os: linux
-          env: PYTHON_VERSION=2.7
-               CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8 mayavi"
-               PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio"
+          env: PYTHON_VERSION=3.5
+               CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8"
+               PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio imageio-ffmpeg"
 
         # OSX
         - os: osx
@@ -32,32 +35,19 @@ before_install:
     - if [ "${TRAVIS_OS_NAME}" == "osx" ]; then
         unset -f cd;
       fi;
-    - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
-        echo "Starting Xvfb...";
-        /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;
-      fi;
     - git clone https://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda.sh
-    - if [ "$PYTHON_VERSION" != "2.7" ]; then
-        pip install vtk;
-        pip install mayavi;
-      fi;
+    - pip install vtk
+    - pip install mayavi
+    - mkdir -p $SUBJECTS_DIR
+    - pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
+    - python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
 
 install:
     - python setup.py build
     - python setup.py install
     - SRC_DIR=$(pwd)
 
-before_script:
-    # Let's create a (fake) display on Travis, and let's use a funny resolution
-    - cd ~
-    - wget --quiet http://faculty.washington.edu/larsoner/fsaverage_min.zip
-    - mkdir subjects
-    - cd subjects
-    - unzip ../fsaverage_min.zip
-    - cd ..
-    - export SUBJECTS_DIR="${PWD}/subjects"
-
 script:
     - cd ${SRC_DIR}
     - pytest surfer --cov=surfer -v

doc/Makefile

@@ -2,9 +2,9 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -nWT --keep-going
 SPHINXBUILD   = sphinx-build
-PAPER         =
+GPAPER         =
 BUILDDIR      = _build
 
 # Internal variables.

doc/conf.py

@@ -51,7 +51,7 @@
 ]
 
 autosummary_generate = True
-autodoc_default_flags = ['inherited-members']
+autodoc_default_options = {'inherited-members': None}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -250,10 +250,10 @@
     # 'python': ('http://docs.python.org/', None),
     # 'numpy': ('http://docs.scipy.org/doc/numpy-dev/', None),
     # 'scipy': ('http://scipy.github.io/devdocs/', None),
-    'matplotlib': ('http://matplotlib.org', None),
-    'imageio': ('http://imageio.readthedocs.io/en/latest', None),
-    'mayavi': ('http://docs.enthought.com/mayavi/mayavi', None),
-    'nibabel': ('http://nipy.org/nibabel', None),
+    'matplotlib': ('https://matplotlib.org', None),
+    'imageio': ('https://imageio.readthedocs.io/en/latest', None),
+    'mayavi': ('https://docs.enthought.com/mayavi/mayavi', None),
+    'nibabel': ('https://nipy.org/nibabel', None),
 }
 
 # One entry per manual page. List of tuples
@@ -268,31 +268,25 @@
 
 try:
     from mayavi import mlab
-    find_mayavi_figures = True
     # Do not pop up any mayavi windows while running the
     # examples. These are very annoying since they steal the focus.
     mlab.options.offscreen = True
+    scrapers = ('matplotlib', 'mayavi')
 except Exception:
-    find_mayavi_figures = False
+    scrapers = ('matplotlib',)
 
 sphinx_gallery_conf = {
     'doc_module': ('surfer',),
-    'reference_url': {
-        'surfer': None,
-        'matplotlib': 'http://matplotlib.org',
-        'numpy': 'http://docs.scipy.org/doc/numpy',
-        'scipy': 'http://docs.scipy.org/doc/scipy/reference',
-        'mayavi': 'http://docs.enthought.com/mayavi/mayavi',
-        },
+    'reference_url': {'surfer': None},
     'examples_dirs': examples_dirs,
     'gallery_dirs': gallery_dirs,
     'within_subsection_order': FileNameSortKey,
-    'find_mayavi_figures': find_mayavi_figures,
+    'image_scrapers': scrapers,
     'default_thumb_file': os.path.join('_static', 'pysurfer_logo_small.png'),
     'backreferences_dir': 'generated',
     'download_section_examples': False,
     'thumbnail_size': (250, 250),
-    }
+}
 
 numpydoc_class_members_toctree = False
 numpydoc_show_inherited_class_members = False

doc/documentation/command_line.rst

@@ -50,6 +50,3 @@ Other command-line options
 As in tksurfer, most aspects of the visualization can be initialized
 from the command-line. To get a full documentation of the command-line
 interface, simply type ``pysurfer`` at a terminal prompt and hit enter.
-For convenience, this usage message is reproduced below.
-
-.. literalinclude:: pysurfer_usage.txt

examples/plot_label.py

@@ -18,31 +18,31 @@
 
 # If the label lives in the normal place in the subjects directory,
 # you can plot it by just using the name
-brain.add_label("BA1_exvivo")
+brain.add_label("BA1")
 
 # Some labels have an associated scalar value at each ID in the label.
 # For example, they may be probabilistically defined. You can threshold
 # what vertices show up in the label using this scalar data
-brain.add_label("BA1_exvivo", color="blue", scalar_thresh=.5)
+brain.add_label("BA1", color="blue", scalar_thresh=.5)
 
 # Or you can give a path to a label in an arbitrary location
 subj_dir = brain.subjects_dir
 label_file = os.path.join(subj_dir, subject_id,
-                          "label", "%s.MT_exvivo.label" % hemi)
+                          "label", "%s.MT.label" % hemi)
 brain.add_label(label_file)
 
 # By default the label is 'filled-in', but you can
 # plot just the label boundaries
-brain.add_label("BA44_exvivo", borders=True)
+brain.add_label("BA44", borders=True)
 
 # You can also control the opacity of the label color
-brain.add_label("BA6_exvivo", alpha=.7)
+brain.add_label("BA6", alpha=.7)
 
 # Finally, you can plot the label in any color you want.
 brain.show_view(dict(azimuth=-42, elevation=105, distance=225,
                      focalpoint=[-30, -20, 15]))
 
 # Use any valid matplotlib color.
-brain.add_label("V1_exvivo", color="steelblue", alpha=.6)
-brain.add_label("V2_exvivo", color="#FF6347", alpha=.6)
-brain.add_label("entorhinal_exvivo", color=(.2, 1, .5), alpha=.6)
+brain.add_label("V1", color="steelblue", alpha=.6)
+brain.add_label("V2", color="#FF6347", alpha=.6)
+brain.add_label("entorhinal", color=(.2, 1, .5), alpha=.6)

examples/plot_probabilistic_label.py

@@ -28,27 +28,27 @@
 The easiest way to label any vertex that could be in the region is with
 add_label.
 """
-brain.add_label("BA1_exvivo", color="#A6BDDB")
+brain.add_label("BA1", color="#A6BDDB")
 
 """
 You can also threshold based on the probability of that region being at each
 vertex.
 """
-brain.add_label("BA1_exvivo", color="#2B8CBE", scalar_thresh=.5)
+brain.add_label("BA1", color="#2B8CBE", scalar_thresh=.5)
 
 """
 It's also possible to plot just the label boundary, in case you wanted to
 overlay the label on an activation plot to asses whether it falls within that
 region.
 """
-brain.add_label("BA45_exvivo", color="#F0F8FF", borders=3, scalar_thresh=.5)
-brain.add_label("BA45_exvivo", color="#F0F8FF", alpha=.3, scalar_thresh=.5)
+brain.add_label("BA45", color="#F0F8FF", borders=3, scalar_thresh=.5)
+brain.add_label("BA45", color="#F0F8FF", alpha=.3, scalar_thresh=.5)
 
 """
 Finally, with a few tricks, you can display the whole probabilistic map.
 """
 subjects_dir = environ["SUBJECTS_DIR"]
-label_file = join(subjects_dir, "fsaverage", "label", "lh.BA6_exvivo.label")
+label_file = join(subjects_dir, "fsaverage", "label", "lh.BA6.label")
 
 prob_field = np.zeros_like(brain.geo['lh'].x)
 ids, probs = read_label(label_file, read_scalars=True)