MRG: width/height in offscreen mode

.circleci/config.yml

@@ -1,48 +1,66 @@
 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;
+        - 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
 
         # 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: 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: Fix libgcc_s.so.1 pthread_cancel bug
+            command: |
+              sudo apt-get install qt5-default
+
+        - 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
         - 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;
@@ -51,14 +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
+

.travis.yml

@@ -2,9 +2,9 @@ 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"
+            PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg"
             DISPLAY=:99.0
 
 matrix:
@@ -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}

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"

setup.cfg

@@ -8,4 +8,7 @@ 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
+    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

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

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()
 
@@ -354,7 +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)
@@ -432,15 +434,15 @@ 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

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

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