Merge branch 'main' into speed

.circleci/config.yml

@@ -42,7 +42,8 @@ jobs:
         - run:
             name: Get Python running
             command: |
-              pip install --upgrade PyQt6!=6.6.1 "PyQt6-Qt6!=6.6.1" sphinx-gallery pydata-sphinx-theme numpydoc scikit-learn nilearn mne-bids autoreject git+https://github.com/pyvista/pyvista@main memory_profiler sphinxcontrib.bibtex sphinxcontrib.youtube darkdetect qdarkstyle
+              # TO DO: sphinx-gallery main -> stable on 0.17 release
+              pip install --upgrade PyQt6!=6.6.0 "PyQt6-Qt6!=6.6.0,!=6.7.0" git+https://github.com/sphinx-gallery/sphinx-gallery.git pydata-sphinx-theme numpydoc scikit-learn nilearn mne-bids autoreject pyvista memory_profiler sphinxcontrib.bibtex sphinxcontrib.youtube darkdetect qdarkstyle
               pip install -ve ./mne-python .
         - run:
             name: Check Qt
@@ -58,13 +59,19 @@ jobs:
         - run:
             name: List packages
             command: python -m pip list
+        - restore_cache:
+            keys:
+              - data-cache-sample
+        - restore_cache:
+            keys:
+              - data-cache-misc
         - restore_cache:
             keys:
               - data-cache-somato
         - run:
             name: Get data
             command: |
-              python -c "import mne; mne.datasets.somato.data_path(update_path=True, verbose=True); mne.datasets.misc.data_path(update_path=True, verbose=True);"
+              python -c "import mne; mne.datasets.somato.data_path(update_path=True, verbose=True); mne.datasets.misc.data_path(update_path=True, verbose=True); sample_path = mne.datasets.sample.data_path(update_path=True, verbose=True); mne.datasets.fetch_fsaverage(subjects_dir=sample_path / 'subjects', verbose=True)"
               ls -al ~/mne_data;
         - run:
             name: make html
@@ -83,6 +90,10 @@ jobs:
             root: doc/_build
             paths:
               - html
+        - save_cache:
+            key: data-cache-sample
+            paths:
+              - ~/mne_data/MNE-sample-data
         - save_cache:
             key: data-cache-somato
             paths:

.github/workflows/tests.yml

@@ -62,12 +62,12 @@ jobs:
       if: "matrix.mne-version == 'mne-main'"
       run: git clone --single-branch --branch main https://github.com/mne-tools/mne-python.git
     - run: pip install -ve ./mne-python
-    - run: pip install -v ${{ matrix.qt }}!=6.6.1 "PyQt6-Qt6!=6.6.1"
+    - run: pip install -v ${{ matrix.qt }}!=6.6.0 "PyQt6-Qt6!=6.6.0,!=6.7.0"
     - run: pip install -ve .[tests]
     - run: mne sys_info
-    - run: |
-        set -eo pipefail
-        mne sys_info -pd | grep "qtpy:\? .*${{ matrix.qt }}=.*$"
+    # Check Qt
+    - run: ./tools/check_qt_import.sh $MNE_QT_BACKEND
+      if: ${{ env.MNE_QT_BACKEND != '' }}
       name: Check Qt
       shell: bash
     - run: python -c "import mne_gui_addons; print(mne_gui_addons.__version__)"

doc/conf.py

@@ -1,6 +1,7 @@
 import faulthandler
 import os
 import sys
+from pathlib import Path
 
 import pyvista
 import mne_gui_addons
@@ -11,6 +12,14 @@
 os.environ["MNE_BROWSER_THEME"] = "light"
 os.environ["MNE_3D_OPTION_THEME"] = "light"
 
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+curpath = Path(__file__).parent.resolve(strict=True)
+sys.path.append(str(curpath / "sphinxext"))
+
 project = "MNE-GUI-Addons"
 release = mne_gui_addons.__version__
 version = ".".join(release.split(".")[:2])
@@ -35,10 +44,7 @@
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
     "matplotlib": ("https://matplotlib.org/stable", None),
     "nibabel": ("https://nipy.org/nibabel", None),
-    "dipy": (
-        "https://dipy.org/documentation/latest/",
-        "https://dipy.org/documentation/latest/objects.inv/",
-    ),
+    "dipy": ("https://docs.dipy.org/stable", None),
     "mne": ("https://mne.tools/stable", None),
     "mne_bids": ("https://mne.tools/mne-bids/stable", None),
 }
@@ -53,8 +59,6 @@
     "AverageTFR": "mne.time_frequency.AverageTFR",
     "EpochsTFR": "mne.time_frequency.EpochsTFR",
     "Transform": "mne.transforms.Transform",
-    # MNE-GUI-Addons
-    # 'IntracranialElectrodeLocator': 'mne_gui_addons.IntracranialElectrodeLocator',  # Many doc errors!
 }
 numpydoc_xref_ignore = {
     # words
@@ -108,7 +112,7 @@
     "remove_config_comments": True,
     "min_reported_time": 1.0,
     "abort_on_example_error": False,
-    "image_scrapers": ("matplotlib", mne_gui_addons._GUIScraper(), "pyvista"),
+    "image_scrapers": ("matplotlib", "mne_gui_addons_doc_utils.gui_scraper", "pyvista"),
     "show_memory": not sys.platform.startswith(("win", "darwin")),
     "line_numbers": False,  # messes with style
     "capture_repr": ("_repr_html_",),

doc/sphinxext/mne_gui_addons_doc_utils.py

@@ -0,0 +1,5 @@
+"""Doc building utils."""
+
+import mne_gui_addons
+
+gui_scraper = mne_gui_addons._GUIScraper()

mne_gui_addons/_ieeg_locate.py

@@ -103,7 +103,8 @@ def __init__(
             )
 
         self._ch_names = info.ch_names
-        # load channels, leave in "head" coordinate frame until transforms are loaded in super
+        # load channels, leave in "head" coordinate frame
+        # until transforms are loaded in super
         self._chs = {
             name: ch["loc"][:3] for name, ch in zip(info.ch_names, info["chs"])
         }
@@ -133,7 +134,8 @@ def __init__(
             self._update_lines(group)
 
         # ready for user
-        # set current position as (0, 0, 0) surface RAS (center of mass roughly) if no positions
+        # set current position as (0, 0, 0) surface RAS
+        # (center of mass roughly) if no positions
         if np.isnan(self._chs[self._ch_names[self._ch_index]]).any():
             self._set_ras(
                 apply_trans(
@@ -572,7 +574,8 @@ def _auto_find_line(self, tv, r, max_search_radius=50, voxel_tol=2):
                     if np.min(
                         [np.linalg.norm(next_loc - loc) for loc in locs]
                     ) > np.sqrt(3):
-                        # update the direction to account for bent electrodes and grids contoured to the brain
+                        # update the direction to account for bent electrodes
+                        # and grids contoured to the brain
                         rr_tmp = next_loc - np.array(
                             locs[-1] if direction == 1 else locs[0]
                         )
@@ -714,7 +717,8 @@ def auto_find_contacts(
                 )
                 v /= np.linalg.norm(v)
             for i, tv in enumerate(local_maxima):  # try neartest sequentially
-                # only try entry if given, otherwise try other local maxima as direction vectors
+                # only try entry if given,
+                # otherwise try other local maxima as direction vectors
                 for tv2 in local_maxima[i + 1 :] if entry is None else [tv + v]:
                     # find specified direction vector/direction vector to next contact
                     r = (tv2 - tv) / np.linalg.norm(tv2 - tv)

mne_gui_addons/tests/test_ieeg_locate.py

@@ -83,8 +83,7 @@ def test_ieeg_elec_locate_io(renderer_interactive_pyvistaqt):
     with pytest.warns(RuntimeWarning, match="nasion not found"):
         info.set_montage(montage)
     with pytest.raises(RuntimeError, match='must be in the "head" coordinate frame'):
-        with pytest.warns(RuntimeWarning, match="`pial` surface not found"):
-            mne_gui.locate_ieeg(info, trans, aligned_ct, subject, subjects_dir)
+        mne_gui.locate_ieeg(info, trans, aligned_ct, subject, subjects_dir)
 
 
 @pytest.mark.allow_unclosed_pyside2

pyproject.toml

@@ -16,6 +16,8 @@ classifiers = [
 dependencies = [
     "packaging",
     "qtpy",
+    "PyQt6!=6.6.0",
+    "PyQt6-Qt6!=6.6.0,!=6.7.0",
     "pyvista",
     "pyvistaqt",
     "mne",