Merge branch 'main' of https://github.com/mne-tools/mne-python into e…

…dflibpytest
withmywoessner · Nov 9, 2023 · 4823ddc · 4823ddc
2 parents 8e73352 + fd53fc4
commit 4823ddc
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -223,13 +223,16 @@ jobs:
             - data-cache-fsaverage
       - restore_cache:
           keys:
-            - data-cache-bst-phantom-ctf
+            - data-cache-bst-raw
       - restore_cache:
           keys:
-            - data-cache-bst-raw
+            - data-cache-bst-phantom-ctf
       - restore_cache:
           keys:
             - data-cache-bst-phantom-elekta
+      - restore_cache:
+          keys:
+            - data-cache-bst-phantom-kernel
       - restore_cache:
           keys:
             - data-cache-bst-auditory
@@ -368,18 +371,22 @@ jobs:
           key: data-cache-fsaverage
           paths:
             - ~/mne_data/MNE-fsaverage-data  # (762 M)
-      - save_cache:
-          key: data-cache-bst-phantom-ctf
-          paths:
-            - ~/mne_data/MNE-brainstorm-data/bst_phantom_ctf  # (177 M)
       - save_cache:
           key: data-cache-bst-raw
           paths:
             - ~/mne_data/MNE-brainstorm-data/bst_raw  # (830 M)
+      - save_cache:
+          key: data-cache-bst-phantom-ctf
+          paths:
+            - ~/mne_data/MNE-brainstorm-data/bst_phantom_ctf  # (177 M)
       - save_cache:
           key: data-cache-bst-phantom-elekta
           paths:
             - ~/mne_data/MNE-brainstorm-data/bst_phantom_elekta  # (1.4 G)
+      - save_cache:
+          key: data-cache-bst-phantom-kernel
+          paths:
+            - ~/mne_data/MNE-phantom-kernel-data  # (362 M)
       - save_cache:
           key: data-cache-bst-auditory
           paths:

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,3 +1,3 @@
 e81ec528a42ac687f3d961ed5cf8e25f236925b0  # black
-20737c0bd7c0dafee0a00caa1dba8ce573fd0f53  # move SetChannelsMixin between files
 12395f9d9cf6ea3c72b225b62e052dd0d17d9889  # YAML indentation
+d6d2f8c6a2ed4a0b27357da9ddf8e0cd14931b59  # isort
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -24,7 +24,7 @@
 #################################################
 
 # Artifact regression
-/mne/preprocessing/_regress.py @wmvanvliet @cbrnr
+/mne/preprocessing/_regress.py @wmvanvliet
 /mne/preprocessing/tests/test_regress.py @wmvanvliet
 
 # Beamforming
@@ -33,25 +33,26 @@
 *lcmv*.py @britta-wstnr
 
 # Channels
-/mne/channels @cbrnr @agramfort @mscheltienne
+/mne/channels @agramfort @mscheltienne @dengemann @jasmainak
 
 # Core sensor-space classes
-/mne/epochs.py @drammock @agramfort @mscheltienne
-/mne/evoked.py @drammock @agramfort @mscheltienne
-/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne
+/mne/epochs.py @drammock @agramfort @mscheltienne @dengemann
+/mne/evoked.py @drammock @agramfort @mscheltienne @dengemann
+/mne/io/*.* @drammock @cbrnr @agramfort @mscheltienne @dengemann
 
 # Current-source density
-/mne/preprocessing/_csd.py  @alexrockhill
+/mne/preprocessing/_csd.py  @alexrockhill @dengemann
 
 # Decoding
-/mne/decoding/csp.py @cbrnr @agramfort
+/mne/decoding/csp.py @cbrnr @agramfort @dengemann
+/mne/decoding/*.py @jasmainak
 
 # fNIRS
 /mne/preprocessing/nirs @rob-luke
 *fnirs*.py @rob-luke
 
 # forward
-/mne/forward/ @agramfort
+/mne/forward/ @agramfort @jasmainak
 *forward*.py @agramfort
 
 # Intracranial
@@ -69,19 +70,21 @@
 /mne/io/nirx @rob-luke
 /mne/io/snirf @rob-luke
 /mne/export @sappelhoff @cbrnr
+/mne/io/eeglab.py @jasmainak
+/mne/io/eeglab/tests/test_eeglab.py @jasmainak
 
 # Minimum Norm
 /mne/minimum_norm @agramfort
 
 # Preprocessing
-/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne
-/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne
+/mne/preprocessing/ica.py @cbrnr @adam2392 @agramfort @mscheltienne @dengemann
+/mne/preprocessing/infomax_.py @cbrnr @adam2392 @mscheltienne @dengemann
 /mne/preprocessing/*annotate*.py @mscheltienne
 /mne/preprocessing/bads.py @mscheltienne
 /mne/preprocessing/e*g.py @mscheltienne
 
 # Report
-/mne/report @hoechenberger
+/mne/report @hoechenberger @dengemann @jasmainak
 
 # Simulation
 /mne/simulation/ @agramfort
@@ -93,25 +96,28 @@
 /mne/_freesurfer.py @alexrockhill @larsoner
 
 # TFR
-/mne/time_frequency @drammock @cbrnr @adam2392 @mscheltienne
+/mne/time_frequency @drammock @adam2392 @mscheltienne
 
 # Viz
-/mne/viz @drammock @cbrnr
+/mne/viz @drammock @dengemann
 /mne/viz/_brain @larsoner @wmvanvliet
 /mne/viz/ui_events.py @wmvanvliet
-/tutorials/visualization @larsoner @wmvanvliet
-/examples/visualization @larsoner
+/tutorials/visualization @larsoner @wmvanvliet @dengemann
+/examples/visualization @larsoner @dengemann
+
+# Datasets
+/mne/datasets/brainstorm @jasmainak
 
 #########################
 # Project-level / other #
 #########################
 
 # Examples and tutorials
-/examples @drammock @agramfort
-/tutorials @drammock @agramfort
+/examples @drammock @agramfort @dengemann
+/tutorials @drammock @agramfort @dengemann
 
 # Non-tutorial documentation text and infrastructure
-/doc @larsoner @drammock @agramfort
+/doc @larsoner @drammock @agramfort @dengemann
 /logo @drammock
 
 # Installation documentation
@@ -120,5 +126,5 @@
 # Project infrastructure and CIs
 /*.* @larsoner @drammock  # files in the root directory
 /.circleci @larsoner
-/.github @larsoner @cbrnr
+/.github @larsoner
 /tools @larsoner @drammock
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -18,7 +18,7 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -106,7 +106,7 @@ jobs:
       - name: 'Install OSMesa VTK variant'
         run: |
           # TODO: As of 2023/02/28, notebook tests need a pinned mesalib
-          mamba install -c conda-forge "vtk>=9.2=*osmesa*" "vtk-base>=9.2=*osmesa*" "mesalib=23.1.4"
+          mamba install -c conda-forge "vtk>=9.2=*osmesa*" "vtk-base>=9.2=*osmesa*" "mesalib=23.1.4" "numpy=1.24.4" "numba=0.57.1"
           mamba list
         if: matrix.kind == 'notebook'
       - run: ./tools/github_actions_dependencies.sh

diff --git a/.lgtm.yml b/.lgtm.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,21 +1,22 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.10.1
     hooks:
       - id: black
         args: [--quiet]
 
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.1.4
     hooks:
       - id: ruff
         name: ruff mne
+        args: ["--fix"]
         files: ^mne/
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.291
+    rev: v0.1.4
     hooks:
       - id: ruff
         name: ruff tutorials and examples
@@ -26,7 +27,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         additional_dependencies:
@@ -40,3 +41,13 @@ repos:
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]
+
+  # rstcheck
+  - repo: https://github.com/rstcheck/rstcheck.git
+    rev: v6.2.0
+    hooks:
+      - id: rstcheck
+        files: ^doc/.*\.(rst|inc)$
+        # https://github.com/rstcheck/rstcheck/issues/199
+        # https://github.com/rstcheck/rstcheck/issues/200
+        exclude: ^doc/(help/faq|install/manual_install|install/mne_c|install/advanced|install/updating|_includes/channel_interpolation|_includes/inverse|_includes/ssp)\.rst$
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -15,6 +15,7 @@ recursive-include tutorials *.py
 recursive-include tutorials *.txt
 
 recursive-include mne *.py
+recursive-include mne *.pyi
 recursive-include mne/data *
 recursive-include mne/icons *
 recursive-include mne/data/helmets *