Mapping values to foci.

.circleci/config.yml

@@ -1,64 +1,98 @@
 version: 2
 jobs:
-    build:
+    build_docs:
       docker:
-        - image: circleci/python:3.6-jessie
+        - image: circleci/python:3.7-stretch
       steps:
-        # Get our data and merge with upstream
         - checkout
-        - run: echo $(git log -1 --pretty=%B) | tee gitlog.txt
-        - run: echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
         - run:
-           command: |
-             if [[ $(cat merge.txt) != "" ]]; then
-               echo "Merging $(cat merge.txt)";
-               git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge";
-             fi
+            name: Set BASH_ENV
+            command: |
+              echo "set -e" >> $BASH_ENV;
+              echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV;
+              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: |
+              echo $(git log -1 --pretty=%B) | tee gitlog.txt
+              echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+              if [[ $(cat merge.txt) != "" ]]; then
+                echo "Merging $(cat merge.txt)";
+                git remote add upstream git://github.com/nipy/PySurfer.git;
+                git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+                git fetch upstream master;
+              fi
+
+        - run:
+            name: Spin up Xvfb
+            command: |
+              /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;
+
+        # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136
+        # https://github.com/golemfactory/golem/issues/1019
+        - run:
+            name: Fix libgcc_s.so.1 pthread_cancel bug
+            command: |
+              sudo apt-get install qt5-default
 
         # Load our data
         - restore_cache:
             keys:
-              - data-cache
+              - data-cache-0
               - pip-cache
 
-        # Fix libgcc_s.so.1 pthread_cancel bug:
-        # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136
-        # https://github.com/golemfactory/golem/issues/1019
-        - run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 qt5-default
-        - run: echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV
-        - run: echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV
-        - run: echo "export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0.4200.1" >> $BASH_ENV
-        # Spin up Xvfb
-        - run: echo "export DISPLAY=:99" >> $BASH_ENV
-        - run: /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;
-        # Python env
-        - run: pip install -U --user --progress-bar off numpy scipy matplotlib vtk PyQt5 sip PyQt5-sip nibabel sphinx numpydoc pillow imageio https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master
-        - run: pip install -U --user --progress-bar off mayavi
+        - run:
+            name: Get Python running
+            command: |
+              python -m pip install --user -q --upgrade pip numpy
+              python -m pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg sphinx-gallery
+              python -m pip install --user -q --upgrade mayavi "https://github.com/mne-tools/mne-python/archive/master.zip"
         - save_cache:
             key: pip-cache
             paths:
-              - "~/.cache/pip"
-        - run: python setup.py develop --user
-        # Check libs
-        - run: LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
-        - run: echo $SUBJECTS_DIR
+              - ~/.cache/pip
+
+        # Look at what we have and fail early if there is some library conflict
         - run:
+            name: Check installation
             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;
-        - run: ls $SUBJECTS_DIR
-        - run: 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
+              LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
+
+        - run:
+            name: Get data
+            command: |
+              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: |
+              python setup.py develop --user
+
+        - run:
+            name: Build docs
+            command: |
+              cd doc
+              echo $PATTERN
+              make html_dev-pattern
 
         - store_artifacts:
             path: doc/_build/html/
             destination: html
 
-        - save_cache:
-            key: data-cache
-            paths:
-              - "~/subjects"
+
+workflows:
+  version: 2
+
+  default:
+    jobs:
+      - build_docs

.gitignore

@@ -5,7 +5,9 @@
 .#*
 *.swp
 *.orig
+*.mov
 build
+.idea/
 
 dist/
 doc/_build/

.travis.yml

@@ -1,11 +1,14 @@
 language: c
 sudo: false
-
+dist: bionic
+services:
+    - xvfb
 env:
-    global: PYTHON_VERSION=3.6
-            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"
+    global: PYTHON_VERSION=3.8
+            CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt 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:
@@ -15,12 +18,17 @@ matrix:
             apt:
               packages:
                 - mencoder
+                - libosmesa6
+                - libglx-mesa0
+                - libopengl0
+                - libglx0
+                - libdbus-1-3
 
-        # 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=3.6
+               CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8"
+               PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio imageio-ffmpeg"
 
         # OSX
         - os: osx
@@ -32,35 +40,24 @@ 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 [ "$PYTHON_VERSION" != "2.7" ]; then
-        pip install vtk;
+    - if [ "${PYTHON_VERSION}" == "3.6" ]; then
+        pip install --only-binary ":all:" "vtk<9";
         pip install mayavi;
+      else
+        pip install --only-binary ":all:" -f "https://vtk.org/download" "vtk>=9";
+        pip install https://github.com/enthought/mayavi/zipball/master;
       fi;
+    - mkdir -p $SUBJECTS_DIR
+    - pip install "https://github.com/mne-tools/mne-python/archive/master.zip"
+    - 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"
-    - if [[ $PIP_DEPENDENCIES == *"imageio"* ]] || [ ! -z "$CONDA_ENVIRONMENT" ]; then
-        python -c "import imageio; imageio.plugins.ffmpeg.download()";
-      fi
-
 script:
     - cd ${SRC_DIR}
     - pytest surfer --cov=surfer -v

CHANGES

@@ -1,5 +1,36 @@
-PySurfer Changes
-================
+Changelog
+=========
+
+.. currentmodule:: surfer
+
+Version 0.11.0
+--------------
+
+- Minimum Python version increased to 3.6
+- Add support to turn off full-screen antialiasing, which can be problematic on
+  some drivers (e.g., MESA software rendering on Linux)
+- Simplification and refactoring of vector-valued data plotting
+- Removal of unnecessary ``info`` log messages about smoothing matrix and
+  colormap generation (changed to ``debug`` level)
+- Clean up of exit functions like ``__del__`` to avoid segfaults
+
+
+Version 0.10.0
+--------------
+
+- Added an option to smooth to nearest vertex in :meth:`Brain.add_data` using
+  ``smoothing_steps='nearest'``
+- Added options for using offscreen mode
+- Improved integration with Jupyter notebook
+- Avoided view changes when using :meth:`Brain.add_foci`
+
+Version 0.9
+-----------
+
+- Fixed transparency issues with colormaps with
+  :meth:`Brain.scale_data_colormap`
+- Added an example of using custom colors
+- Added options for choosing units for :class:`Brain` (``m`` or ``mm``)
 
 Version 0.8
 -----------

appveyor.yml

@@ -6,9 +6,8 @@ environment:
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
   - "python --version"
-  - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio codecov pyqt5==5.9"
-  - "pip install traits traitsui pyface vtk mayavi nibabel"
-  - "python -c \"import imageio; imageio.plugins.ffmpeg.download()\""
+  - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9"
+  - "pip install traits traitsui pyface vtk https://github.com/enthought/mayavi/archive/master.zip nibabel"
   - "powershell make/get_fsaverage.ps1"
   - "python setup.py develop"
   - "SET SUBJECTS_DIR=%CD%\\subjects"

azure-pipelines.yml

@@ -0,0 +1,57 @@
+trigger:
+  # start a new build for every push
+  batch: False
+  branches:
+    include:
+      - master
+
+jobs:
+- job: Windows
+  variables:
+    PIP_CACHE_FOLDER: $(Pipeline.Workspace)/.cache/pip
+  pool:
+    vmIMage: 'VS2017-Win2016'
+  strategy:
+    maxParallel: 4
+    matrix:
+      Python37-64bit:
+        PYTHON_VERSION: '3.7'
+        PYTHON_ARCH: 'x64'
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: $(PYTHON_VERSION)
+      architecture: $(PYTHON_ARCH)
+      addToPath: true
+  - task: Cache@2
+    inputs:
+      key: 'pip'
+      path: $(PIP_CACHE_FOLDER)
+    displayName: Cache pip packages
+  - powershell: |
+     pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9 --cache-dir $(PIP_CACHE_FOLDER)
+     pip install traits traitsui pyface vtk https://github.com/enthought/mayavi/archive/master.zip nibabel --cache-dir $(PIP_CACHE_FOLDER)
+    displayName: 'Install pip dependencies'
+  - powershell: |
+     powershell make/get_fsaverage.ps1
+     $env:SUBJECTS_DIR = '$(System.DefaultWorkingDirectory)' + '\subjects'
+     Write-Host ("##vso[task.setvariable variable=SUBJECTS_DIR]" + $env:SUBJECTS_DIR)
+    displayName: 'Get fsaverage'
+  - powershell: |
+     git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
+     powershell gl-ci-helpers/appveyor/install_opengl.ps1
+    displayName: 'Get OpenGL'
+  - script: python setup.py develop
+    displayName: 'Install'
+  - script: pytest surfer --cov=surfer -v
+    displayName: 'Run tests'
+  - script: codecov --root %BUILD_REPOSITORY_LOCALPATH% -t %CODECOV_TOKEN%
+    displayName: 'Codecov'
+    env:
+      CODECOV_TOKEN: $(CODECOV_TOKEN)
+    condition: always()
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFiles: 'junit-*.xml'
+      testRunTitle: 'Publish test results for Python $(python.version)'
+    condition: always()

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/_static/navy.css

@@ -514,9 +514,11 @@ ul.keywordmatches li.goodmatch a {
 }
 .sphx-glr-thumbcontainer .figure {
     width: 250px !important;
+    max-width: 250px !important;
 }
 .sphx-glr-thumbcontainer img {
     max-height: 250px !important;
+    max-width: 250px !important;
     width: 250px !important;
 }
 .sphx-glr-thumbcontainer a.internal {
@@ -546,4 +548,8 @@ ul.keywordmatches li.goodmatch a {
     div.sphx-glr-footer-example a code span:last-child {
 	font-size: unset;
     }
-}
+}
+
+table.longtable.align-default {
+    width: 100%;
+}

doc/changes.rst

@@ -0,0 +1 @@
+.. include:: ../CHANGES