Merge pull request #119 from coganlab/pytest-mri

Change test_mri to pytest style.

.github/workflows/Package.yml

@@ -28,24 +28,6 @@ jobs:
           name: python-package-distributions
           path: dist/
 
-  publish-to-pypi:
-    name: >-
-      Publish Python 🐍 distribution 📦 to PyPI
-    needs:
-    - build
-    runs-on: ubuntu-latest
-    environment: release
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
-    steps:
-      - name: Download all the dists
-        uses: actions/download-artifact@v3
-        with:
-          name: python-package-distributions
-          path: dist/
-      - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-
   publish-to-testpypi:
     name: Publish Python 🐍 distribution 📦 to TestPyPI
     needs:
@@ -68,4 +50,22 @@ jobs:
     - name: Publish distribution 📦 to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        repository-url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    needs:
+    - publish-to-testpypi
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v3
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

ieeg/viz/mri.py

@@ -634,8 +634,9 @@ def _group_channels(info, groups: dict = None) -> dict:
 
 
 def _add_labels(fig, info, sub, every, hemi, lr, **kwargs):
+    if len(info.ch_names) < every:
+        return
     names = info.ch_names[slice(every - 1, None, every)]
-
     if not hemi == 'both':
         for hems, pos in enumerate(lr):
             if (not pos) or \
@@ -646,7 +647,8 @@ def _add_labels(fig, info, sub, every, hemi, lr, **kwargs):
             plt_names = filter(lambda x: x.startswith(['L', 'R'][hems]), names)
             plt_names = [f'{sub}-{n}' for n in plt_names]
             positions = np.array([pos[n.split("-")[1]] for n in plt_names])
-            fig.plotter.subplot(0, hems)
+            if hemi == 'split':
+                fig.plotter.subplot(0, hems)
             fig.plotter.add_point_labels(positions, plt_names, **kwargs)
     else:
         pos = {}

setup.py

@@ -79,7 +79,7 @@ def get_file_list(path, ext):
 
 setup(
     name='ieeg',
-    version='0.5',
+    version='0.5.1',
     packages=find_packages(
         where='.',
         include=['ieeg*'],

tests/test_mri.py

@@ -1,7 +1,8 @@
 import os
-
 import mne
 import vtk
+import pytest
+from ieeg.viz.mri import plot_subj, plot_on_average
 
 misc_path = mne.datasets.misc.data_path()
 sample_path = mne.datasets.sample.data_path()
@@ -11,18 +12,55 @@
 if not os.path.exists(os.path.join(subjects_dir, "1")):
     os.symlink(os.path.join(subjects_dir, 'sample'),
                os.path.join(subjects_dir, '1'))
+
 raw = mne.io.read_raw(misc_path / "seeg" / "sample_seeg_ieeg.fif")
 
 
-def test_plot_seeg():
-    from ieeg.viz.mri import plot_subj
-    plot_subj(raw, subj_dir=subjects_dir, show=False)
+@pytest.mark.parametrize(
+    'args, expected', [
+        ({}, None),
+        ({'labels_every': 1}, None),
+        ({'hemi': 'split'}, None),
+        ({'hemi': 'lh'}, None),
+        ({'size': 0.2}, None),
+        ({'background': 'red'}, None),
+        ({'transparency': 0.2}, None),
+        ({'color': (1, 0, 0)}, None),
+        ({'picks': ['LSTG 1', 'LSTG 2', 'LSTG 3', 'LSTG 4', 'RAHP 1',
+                    'RAHP 2', 'RAHP 3', 'RAHP 4', 'RAHP 5', 'RAHP 6']}, None),
+        ({'picks': ['LSTG 1', 'LSTG 2', 'LSTG 3'], 'hemi': 'rh'}, None),
+        ({'picks': [0, 1, 2, 3, 4, 5, 6, 7, 8]}, None),
+        ({'picks': [0, 1, 2, 3, 4]}, None),
+        ({'hemi': 'rh'}, None),
+        # Fails bc no wm parcellation file
+        # ({'no_wm': True}, None),
+    ]
+)
+def test_plot_seeg_inst(args, expected):
+    plot_subj(inst=raw, subj_dir=subjects_dir, show=False, **args)
 
 
-def test_plot_avg():
-    from ieeg.viz.mri import plot_on_average
-    plot_on_average(raw, subj_dir=subjects_dir, show=False, rm_wm=False,
-                    hemi='both')
+@pytest.mark.parametrize(
+    'args, expected', [
+        ({}, None),
+        ({'label_every': 1}, None),
+        ({'hemi': 'both'}, None),
+        ({'hemi': 'split'}, None),
+        ({'hemi': 'lh'}, None),
+        ({'size': 0.2}, None),
+        ({'background': 'red'}, None),
+        ({'transparency': 0.2}, None),
+        ({'color': (1, 0, 0)}, None),
+        ({'picks': ['LSTG 1', 'LSTG 2', 'LSTG 3', 'LSTG 4', 'RAHP 1',
+                    'RAHP 2', 'RAHP 3', 'RAHP 4', 'RAHP 5', 'RAHP 6']}, None),
+        ({'picks': ['LSTG 1', 'LSTG 2', 'LSTG 3'], 'hemi': 'rh'}, None),
+        ({'picks': [0, 1, 2, 3, 4, 5, 6, 7, 8]}, None),
+        ({'picks': [0, 1, 2, 3, 4]}, None),
+        ({'hemi': 'rh'}, None),
+    ]
+)
+def test_plot_avg(args, expected):
+    plot_on_average(sigs=raw, subj_dir=subjects_dir, show=False, **args)
 
 
 # if on windows, finalize closing the vtk window