From b0320a42f6869ce369fab28787508b467aa0e154 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 13:46:31 -0400 Subject: [PATCH 01/12] MAINT: Update fsaverage --- .circleci/config.yml | 33 +++++++++++++++------------------ .travis.yml | 22 +++++++--------------- 2 files changed, 22 insertions(+), 33 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index bbb755d..d4647b8 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -25,12 +25,6 @@ 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 +37,18 @@ 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 "https://api.github.com/repos/mne-tools/mne-python/zipball/master" - save_cache: key: pip-cache paths: @@ -59,17 +60,18 @@ jobs: 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; + mkdir -p $SUBJECTS_DIR; + python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)" ls $SUBJECTS_DIR + - save_cache: + key: data-cache-0 + paths: + - "~/subjects" + - run: name: Install PySurfer command: | @@ -85,10 +87,6 @@ jobs: path: doc/_build/html/ destination: html - - save_cache: - key: data-cache-0 - paths: - - "~/subjects" workflows: version: 2 @@ -96,4 +94,3 @@ workflows: default: jobs: - build_docs - diff --git a/.travis.yml b/.travis.yml index ed5c16c..f907eae 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,11 +1,14 @@ language: c sudo: false - +dist: xenial +services: + - xvfb env: global: PYTHON_VERSION=3.7 CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface" PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg" DISPLAY=:99.0 + SUBJECTS_DIR=~/subjects matrix: include: @@ -32,32 +35,21 @@ before_install: - if [ "${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; + - 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 ${SRC_DIR} - pytest surfer --cov=surfer -v From 5abd069de28f42a0c0649f41b71b1c09755b0702 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 13:56:44 -0400 Subject: [PATCH 02/12] FIX: Bump to 3.5 --- .travis.yml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index f907eae..b19dda2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,10 +19,10 @@ matrix: packages: - mencoder - # 2.7, no mencoder + # 3.5, no mencoder - os: linux - env: PYTHON_VERSION=2.7 - CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8 mayavi" + env: PYTHON_VERSION=3.5 + CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8" PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio" # OSX @@ -37,10 +37,8 @@ before_install: fi; - git clone https://github.com/astropy/ci-helpers.git - source ci-helpers/travis/setup_conda.sh - - if [ "$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)" From d497e2071930e4db0ad937c76506d1165771fa6d Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 14:06:05 -0400 Subject: [PATCH 03/12] ENH: Run more on CircleCI --- .circleci/config.yml | 2 +- .travis.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index d4647b8..156d5b9 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -81,7 +81,7 @@ 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 + sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html - store_artifacts: path: doc/_build/html/ diff --git a/.travis.yml b/.travis.yml index b19dda2..434b5d4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,7 +23,7 @@ matrix: - os: linux env: PYTHON_VERSION=3.5 CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8" - PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio" + PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio" # OSX - os: osx From fcad3d0fccec390f951ea0ca5989b5cfa6bc71b1 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 14:18:55 -0400 Subject: [PATCH 04/12] MAINT: CI --- .circleci/config.yml | 2 +- .travis.yml | 2 +- doc/documentation/command_line.rst | 3 --- examples/plot_label.py | 16 ++++++++-------- 4 files changed, 10 insertions(+), 13 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 156d5b9..1c7f9c4 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -81,7 +81,7 @@ jobs: name: Build docs command: | cd doc - sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html + sphinx-build -nWT --keep-going -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html - store_artifacts: path: doc/_build/html/ diff --git a/.travis.yml b/.travis.yml index 434b5d4..657efe8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,7 +23,7 @@ matrix: - os: linux env: PYTHON_VERSION=3.5 CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8" - PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio" + PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio" # OSX - os: osx diff --git a/doc/documentation/command_line.rst b/doc/documentation/command_line.rst index cd21a64..6015a13 100644 --- a/doc/documentation/command_line.rst +++ b/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 diff --git a/examples/plot_label.py b/examples/plot_label.py index 8083347..8b602d7 100644 --- a/examples/plot_label.py +++ b/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) From d2a5eb27a4f93cf444a3c32c7b23482483a55391 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 14:25:00 -0400 Subject: [PATCH 05/12] MAINT: CI --- examples/plot_probabilistic_label.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/examples/plot_probabilistic_label.py b/examples/plot_probabilistic_label.py index 30ba576..213445b 100644 --- a/examples/plot_probabilistic_label.py +++ b/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) From 5184984e74e06e5dc330dcbe2cb8129946c541f7 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 14:25:44 -0400 Subject: [PATCH 06/12] MAINT: CI --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 657efe8..523612e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -23,7 +23,7 @@ matrix: - os: linux env: PYTHON_VERSION=3.5 CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8" - PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio" + PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio imageio-ffmpeg" # OSX - os: osx From 0f5049cfba140dde8ec72d21c5b4baefff151b79 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 14:37:57 -0400 Subject: [PATCH 07/12] MAINT: Circle --- .circleci/config.yml | 2 +- doc/Makefile | 2 +- doc/conf.py | 26 ++++++++++---------------- 3 files changed, 12 insertions(+), 18 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1c7f9c4..53dfcfa 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -81,7 +81,7 @@ jobs: name: Build docs command: | cd doc - sphinx-build -nWT --keep-going -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html + PATTERN="^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$" make html_dev-pattern - store_artifacts: path: doc/_build/html/ diff --git a/doc/Makefile b/doc/Makefile index 96649d1..054b415 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -2,7 +2,7 @@ # # You can set these variables from the command line. -SPHINXOPTS = +SPHINXOPTS = -nWT --keep-going SPHINXBUILD = sphinx-build PAPER = BUILDDIR = _build diff --git a/doc/conf.py b/doc/conf.py index 5e60d4c..83feed8 100644 --- a/doc/conf.py +++ b/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 From aef59c2f13b23e93b0b739f0c52ecc2839f0f614 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 14:55:49 -0400 Subject: [PATCH 08/12] FIX: Pattern --- .circleci/config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 53dfcfa..64d985c 100644 --- a/.circleci/config.yml +++ b/.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=\"^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$\"" >> $BASH_ENV; - run: name: Merge with upstream command: | @@ -81,7 +82,8 @@ jobs: name: Build docs command: | cd doc - PATTERN="^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$" make html_dev-pattern + echo $PATTERN + make html_dev-pattern - store_artifacts: path: doc/_build/html/ From 766099151f08a089432a4b7a0ea950c747288129 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 15:21:51 -0400 Subject: [PATCH 09/12] FIX: Circle --- .circleci/config.yml | 9 +++++---- doc/Makefile | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 64d985c..a747b12 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,7 +13,8 @@ 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=\"^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$\"" >> $BASH_ENV; + echo "export PATTERN=/plot_" >> $BASH_ENV; + echo "export IGNORE_PATTERN=\"\(plot_fmri_activation_volume\|plot_resting_correlations\)\"" >> $BASH_ENV; - run: name: Merge with upstream command: | @@ -48,7 +49,7 @@ jobs: 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 mayavi pip install --user -q --upgrade "https://api.github.com/repos/mne-tools/mne-python/zipball/master" - save_cache: key: pip-cache @@ -60,12 +61,12 @@ 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: | - mkdir -p $SUBJECTS_DIR; + echo $SUBJECTS_DIR + mkdir -p $SUBJECTS_DIR python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)" ls $SUBJECTS_DIR - save_cache: diff --git a/doc/Makefile b/doc/Makefile index 054b415..a49af30 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -50,7 +50,7 @@ html_dev: @echo "Build finished. The HTML pages are in $(BUILDDIR)/html" html_dev-pattern: - BUILD_DEV_HTML=1 $(SPHINXBUILD) -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=$(PATTERN) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + BUILD_DEV_HTML=1 $(SPHINXBUILD) -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=$(PATTERN) -D sphinx_gallery_conf.ignore_pattern=$(IGNORE_PATTERN) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html" From bbc1d801ae2bdf38d02f3e801ee5eedeb6d8df24 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 15:29:56 -0400 Subject: [PATCH 10/12] FIX: Try again --- .circleci/config.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a747b12..47a97f1 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,8 +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_" >> $BASH_ENV; - echo "export IGNORE_PATTERN=\"\(plot_fmri_activation_volume\|plot_resting_correlations\)\"" >> $BASH_ENV; + echo "export PATTERN=\"^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$\"" >> $BASH_ENV; - run: name: Merge with upstream command: | From aa52d5a3aacf15a5fa7e4566fa10bfbcfadcc1eb Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 15:31:56 -0400 Subject: [PATCH 11/12] FIX: Better --- .circleci/config.yml | 6 +++--- doc/Makefile | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 47a97f1..ac40d89 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,7 +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=\"^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\$\"" >> $BASH_ENV; + echo "export PATTERN=\"^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\\$\"" >> $BASH_ENV; - run: name: Merge with upstream command: | @@ -48,8 +48,8 @@ jobs: 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 sphinx-gallery mayavi - pip install --user -q --upgrade "https://api.github.com/repos/mne-tools/mne-python/zipball/master" + 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: diff --git a/doc/Makefile b/doc/Makefile index a49af30..77929cb 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -4,7 +4,7 @@ # You can set these variables from the command line. SPHINXOPTS = -nWT --keep-going SPHINXBUILD = sphinx-build -PAPER = +GPAPER = BUILDDIR = _build # Internal variables. @@ -50,7 +50,7 @@ html_dev: @echo "Build finished. The HTML pages are in $(BUILDDIR)/html" html_dev-pattern: - BUILD_DEV_HTML=1 $(SPHINXBUILD) -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=$(PATTERN) -D sphinx_gallery_conf.ignore_pattern=$(IGNORE_PATTERN) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + BUILD_DEV_HTML=1 $(SPHINXBUILD) -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=$(PATTERN) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html" From a287741444cd1b5cc47a181ff8ee189132ba4b19 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Tue, 25 Jun 2019 15:42:23 -0400 Subject: [PATCH 12/12] FIX: One more --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index ac40d89..dd7ca25 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,7 +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=\"^\(\(?\!plot_fmri_activation_volume\|plot_resting_correlations\|rotate_animation\|save_movie\|save_views\).\)*\\$\"" >> $BASH_ENV; + echo "export PATTERN=\"plot_\(?\!fmri_activation_volume\|resting_correlations\)\"" >> $BASH_ENV; - run: name: Merge with upstream command: |