From dbbe24bfc5f0c1ce5ea46103131f2a7e76e19107 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 12:45:00 +1100 Subject: [PATCH 1/8] FIX: width/height in offscreen mode --- surfer/viz.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/surfer/viz.py b/surfer/viz.py index 75eab52..4fcde5d 100644 --- a/surfer/viz.py +++ b/surfer/viz.py @@ -208,7 +208,7 @@ def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen, try: mlab.options.offscreen = True with warnings.catch_warnings(record=True): # traits - figures = [[mlab.figure(size=(h / n_row, w / n_col)) + figures = [[mlab.figure(size=(w / n_col, h / n_row)) for _ in range(n_col)] for __ in range(n_row)] finally: mlab.options.offscreen = orig_val From 544082aa6b28e0e23ccc88b4aab9b724e86ac1cd Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 13:11:11 +1100 Subject: [PATCH 2/8] MAINT: Sisyphus --- .circleci/config.yml | 7 ++----- .travis.yml | 7 ++----- appveyor.yml | 3 +-- 3 files changed, 5 insertions(+), 12 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 849d72a..286a081 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -23,17 +23,14 @@ jobs: # 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: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 - 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" >> $BASH_ENV - run: /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset; # Python env - - run: pip install -U --user --progress-bar off numpy scipy matplotlib vtk PyQt5 sip PyQt5-sip nibabel sphinx numpydoc pillow imageio https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master - - run: pip install -U --user --progress-bar off mayavi + - run: pip install -U --user --progress-bar off numpy scipy matplotlib vtk "PyQt5<5.12" nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi - save_cache: key: pip-cache paths: diff --git a/.travis.yml b/.travis.yml index f44bb7c..c112564 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,7 +4,7 @@ sudo: false env: global: PYTHON_VERSION=3.6 CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface" - PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio" + PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg" DISPLAY=:99.0 matrix: @@ -20,7 +20,7 @@ matrix: - os: linux env: PYTHON_VERSION=2.7 CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8 mayavi" - PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio" + PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio imageio-ffmpeg" # OSX - os: osx @@ -57,9 +57,6 @@ before_script: - unzip ../fsaverage_min.zip - cd .. - export SUBJECTS_DIR="${PWD}/subjects" - - if [[ $PIP_DEPENDENCIES == *"imageio"* ]] || [ ! -z "$CONDA_ENVIRONMENT" ]; then - python -c "import imageio; imageio.plugins.ffmpeg.download()"; - fi script: - cd ${SRC_DIR} diff --git a/appveyor.yml b/appveyor.yml index 4a79ae0..39520c5 100644 --- a/appveyor.yml +++ b/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 numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9" - "pip install traits traitsui pyface vtk mayavi nibabel" - - "python -c \"import imageio; imageio.plugins.ffmpeg.download()\"" - "powershell make/get_fsaverage.ps1" - "python setup.py develop" - "SET SUBJECTS_DIR=%CD%\\subjects" From a0820213c6c38fe8ebdd9c3af622d5369157eff2 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 13:39:07 +1100 Subject: [PATCH 3/8] BUG: Modernize labels --- .circleci/config.yml | 38 +++++++++++++++++++------------- setup.cfg | 3 ++- surfer/tests/test_utils.py | 4 ++-- surfer/tests/test_viz.py | 45 +++++++++++++++++++------------------- surfer/utils.py | 7 ++++++ 5 files changed, 57 insertions(+), 40 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 286a081..bb410a9 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -6,14 +6,15 @@ jobs: 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: Merge with master + 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 $(cat merge.txt)"; + git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge"; + fi # Load our data - restore_cache: @@ -23,14 +24,21 @@ jobs: # Fix libgcc_s.so.1 pthread_cancel bug: # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136 - - run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 - - run: echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV - - run: echo "export PATH=~/.local/bin:$PATH" >> $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<5.12" nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi + - run: + name: Fix libgcc_s.so.1 pthread_cancel bug + command: | + sudo apt-get install qt5-default + - run: + name: Set up environment + command: | + echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV + echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV + echo "export DISPLAY=:99" >> $BASH_ENV + /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; + - run: + name: Python env + command: | + pip install -U --user --progress-bar off numpy scipy matplotlib vtk "PyQt5<5.12" nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi - save_cache: key: pip-cache paths: diff --git a/setup.cfg b/setup.cfg index 133852e..709ecec 100644 --- a/setup.cfg +++ b/setup.cfg @@ -8,4 +8,5 @@ filterwarnings = ignore:can't resolve package from __spec__ or __package__, falling back on __name__ and __path__:ImportWarning ignore:The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead:DeprecationWarning ignore:elementwise == comparison failed:DeprecationWarning - ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning \ No newline at end of file + ignore:Importing from numpy:DeprecationWarning + ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning diff --git a/surfer/tests/test_utils.py b/surfer/tests/test_utils.py index 8d71382..d9a6d72 100644 --- a/surfer/tests/test_utils.py +++ b/surfer/tests/test_utils.py @@ -32,12 +32,12 @@ def _slow_compute_normals(rr, tris): @utils.requires_fsaverage() def test_surface(): """Test IO for Surface class""" - subj_dir = utils._get_subjects_dir() + extra, subj_dir = utils._get_extra() for subjects_dir in [None, subj_dir]: surface = utils.Surface('fsaverage', 'lh', 'inflated', subjects_dir=subjects_dir) surface.load_geometry() - surface.load_label('BA1') + surface.load_label('BA1' + extra) surface.load_curvature() xfm = np.eye(4) xfm[:3, -1] += 2 # translation diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py index 5d534a2..5666c14 100644 --- a/surfer/tests/test_viz.py +++ b/surfer/tests/test_viz.py @@ -13,7 +13,8 @@ from unittest import SkipTest from surfer import Brain, io, utils -from surfer.utils import requires_fsaverage, requires_imageio, requires_fs +from surfer.utils import (requires_fsaverage, requires_imageio, requires_fs, + _get_extra) warnings.simplefilter('always') @@ -247,30 +248,30 @@ def test_label(): brain = Brain(subject_id, hemi, surf) view = get_view(brain) - brain.add_label("BA1") + extra, subj_dir = _get_extra() + brain.add_label("BA1" + extra) check_view(brain, view) - brain.add_label("BA1", color="blue", scalar_thresh=.5) - subj_dir = utils._get_subjects_dir() + brain.add_label("BA1" + extra, color="blue", scalar_thresh=.5) label_file = pjoin(subj_dir, subject_id, - "label", "%s.MT.label" % hemi) + "label", "%s.MT%s.label" % (hemi, extra)) brain.add_label(label_file) - brain.add_label("BA44", borders=True) - brain.add_label("BA6", alpha=.7) + brain.add_label("BA44" + extra, borders=True) + brain.add_label("BA6" + extra, alpha=.7) brain.show_view("medial") - 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) + brain.add_label("V1" + extra, color="steelblue", alpha=.6) + brain.add_label("V2" + extra, color="#FF6347", alpha=.6) + brain.add_label("entorhinal" + extra, color=(.2, 1, .5), alpha=.6) brain.set_surf('white') brain.show_view(dict(elevation=40, distance=430), distance=430) with pytest.raises(ValueError, match='!='): brain.show_view(dict(elevation=40, distance=430), distance=431) # remove labels - brain.remove_labels('V1') - assert 'V2' in brain.labels_dict - assert 'V1' not in brain.labels_dict + brain.remove_labels('V1' + extra) + assert 'V2' + extra in brain.labels_dict + assert 'V1' + extra not in brain.labels_dict brain.remove_labels() - assert 'V2' not in brain.labels_dict + assert 'V2' + extra not in brain.labels_dict brain.close() @@ -432,15 +433,15 @@ def test_probabilistic_labels(): brain = Brain("fsaverage", "lh", "inflated", cortex="low_contrast") - brain.add_label("BA1", color="darkblue") - - brain.add_label("BA1", color="dodgerblue", scalar_thresh=.5) + extra, subj_dir = _get_extra() + brain.add_label("BA1" + extra, color="darkblue") + brain.add_label("BA1" + extra, color="dodgerblue", scalar_thresh=.5) + brain.add_label("BA45" + extra, color="firebrick", borders=True) + brain.add_label("BA45" + extra, color="salmon", borders=True, + scalar_thresh=.5) - brain.add_label("BA45", color="firebrick", borders=True) - brain.add_label("BA45", color="salmon", borders=True, scalar_thresh=.5) - - subj_dir = utils._get_subjects_dir() - label_file = pjoin(subj_dir, "fsaverage", "label", "lh.BA6.label") + label_file = pjoin(subj_dir, "fsaverage", "label", + "lh.BA6%s.label" % (extra,)) prob_field = np.zeros_like(brain.geo['lh'].x) ids, probs = nib.freesurfer.read_label(label_file, read_scalars=True) prob_field[ids] = probs diff --git a/surfer/utils.py b/surfer/utils.py index cd2b9f3..8e3e22c 100644 --- a/surfer/utils.py +++ b/surfer/utils.py @@ -745,3 +745,10 @@ def requires_fs(): has = ('FREESURFER_HOME' in os.environ) return pytest.mark.skipif( not has, reason='Requires FreeSurfer command line tools') + + +def _get_extra(): + # Get extra label for newer freesurfer + subj_dir = _get_subjects_dir() + fname = op.join(subj_dir, 'fsaverage', 'label', 'lh.BA1.label') + return '_exvivo' if not op.isfile(fname) else '', subj_dir From 6bd55f911554740e5d16ced58747c6e19b742f0d Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 13:41:28 +1100 Subject: [PATCH 4/8] FIX: Circle --- .circleci/config.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index bb410a9..76cec3c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -7,14 +7,14 @@ jobs: # Get our data and merge with upstream - checkout - run: - name: Merge with master - 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 $(cat merge.txt)"; - git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge"; - fi + name: Merge with master + 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 $(cat merge.txt)"; + git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge"; + fi # Load our data - restore_cache: From eb705f43d26706b62dae866a85d9a29a34f9d5bb Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 13:44:40 +1100 Subject: [PATCH 5/8] FIX: Stretch --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 76cec3c..631ac9a 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,7 +2,7 @@ version: 2 jobs: build: docker: - - image: circleci/python:3.6-jessie + - image: circleci/python:3.7-stretch steps: # Get our data and merge with upstream - checkout From 507d4192e78c66ac5f9dbaa434fe57037b49b9e1 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 14:03:18 +1100 Subject: [PATCH 6/8] FIX: More --- .circleci/config.yml | 76 ++++++++++++++++++++++++++++++-------------- .travis.yml | 2 +- setup.cfg | 1 + 3 files changed, 55 insertions(+), 24 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 631ac9a..9e1542a 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,53 +1,66 @@ version: 2 jobs: - build: + build_docs: docker: - image: circleci/python:3.7-stretch steps: - # Get our data and merge with upstream - checkout - run: - name: Merge with master + 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; + - 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 $(cat merge.txt)"; - git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge"; + git remote add upstream git://github.com/mne-tools/mne-python.git; + git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge"; + git fetch upstream master; fi # Load our data - restore_cache: keys: - - data-cache + - data-cache-0 - pip-cache - # Fix libgcc_s.so.1 pthread_cancel bug: + - 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 + - run: - name: Set up environment - command: | - echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV - echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV - echo "export DISPLAY=:99" >> $BASH_ENV - /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; - - run: - name: Python env + name: Get Python running command: | - pip install -U --user --progress-bar off numpy scipy matplotlib vtk "PyQt5<5.12" nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi + 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 - 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: | + 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; @@ -56,14 +69,31 @@ jobs: 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 + ls $SUBJECTS_DIR + - run: + name: Install PySurfer + command: | + python setup.py develop --user + + - run: + 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 - store_artifacts: path: doc/_build/html/ destination: html - save_cache: - key: data-cache + key: data-cache-0 paths: - "~/subjects" + +workflows: + version: 2 + + default: + jobs: + - build_docs + diff --git a/.travis.yml b/.travis.yml index c112564..4331acf 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,7 +2,7 @@ language: c sudo: false env: - global: PYTHON_VERSION=3.6 + 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 diff --git a/setup.cfg b/setup.cfg index 709ecec..15e1d8c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -9,4 +9,5 @@ filterwarnings = ignore:The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead:DeprecationWarning ignore:elementwise == comparison failed:DeprecationWarning ignore:Importing from numpy:DeprecationWarning + ignore:.*ufunc size changed.*:RuntimeWarning ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning From f75bdb461d184e6936507b5c3d53fb43d48f62f9 Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 14:14:08 +1100 Subject: [PATCH 7/8] MAINT: Push the rock --- .circleci/config.yml | 2 +- .travis.yml | 2 +- setup.cfg | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 9e1542a..bbb755d 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -20,7 +20,7 @@ jobs: echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt if [[ $(cat merge.txt) != "" ]]; then echo "Merging $(cat merge.txt)"; - git remote add upstream git://github.com/mne-tools/mne-python.git; + git remote add upstream git://github.com/nipy/PySurfer.git; git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge"; git fetch upstream master; fi diff --git a/.travis.yml b/.travis.yml index 4331acf..ed5c16c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -20,7 +20,7 @@ matrix: - 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 imageio-ffmpeg" + PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio" # OSX - os: osx diff --git a/setup.cfg b/setup.cfg index 15e1d8c..d9bfc29 100644 --- a/setup.cfg +++ b/setup.cfg @@ -10,4 +10,5 @@ filterwarnings = ignore:elementwise == comparison failed:DeprecationWarning ignore:Importing from numpy:DeprecationWarning ignore:.*ufunc size changed.*:RuntimeWarning + ignore:Using or importing the ABCs:DeprecationWarning ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning From 6a8c3f4f304cbb183bfb62db84420205c4c8547b Mon Sep 17 00:00:00 2001 From: Eric Larson Date: Fri, 22 Mar 2019 16:18:37 +1100 Subject: [PATCH 8/8] FIX: Skip for 3 --- surfer/tests/test_viz.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py index 5666c14..158518d 100644 --- a/surfer/tests/test_viz.py +++ b/surfer/tests/test_viz.py @@ -355,7 +355,8 @@ def test_morphometry(): def test_movie(tmpdir): """Test saving a movie of an MEG inverse solution.""" import imageio - + if sys.version_info < (3,): + raise SkipTest('imageio ffmpeg requires Python 3') # create and setup the Brain instance _set_backend() brain = Brain(*std_args)