Merge branch 'main' into deno

mne-tools · Sep 20, 2024 · a039428 · a039428
2 parents 51064f3 + 1cbcfdd
commit a039428
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Showing 3 changed files with 17 additions and 11 deletions.
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -219,8 +219,9 @@ jobs:
 
     - name: Install BIDS validator (stable)
       if: matrix.bids-validator-version == 'validator-stable'
+      # XXX: Remove pin once this is solved: https://github.com/bids-standard/bids-validator/issues/2124
       run: |
-        npm install -g bids-validator
+        npm install -g bids-validator@1.14.10
 
     - name: Install BIDS validator (main-schema)
       if: matrix.bids-validator-version == 'validator-main-schema'
@@ -305,6 +306,8 @@ jobs:
       uses: codecov/codecov-action@v4
       with:
         files: ./coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true
 
   build_docs:
     runs-on: ubuntu-latest

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.2
+    rev: v0.6.5
     hooks:
       - id: ruff
         name: ruff mne_bids/

diff --git a/mne_bids/tests/test_dig.py b/mne_bids/tests/test_dig.py
@@ -142,26 +142,30 @@ def test_dig_template(tmp_path):
     for datatype in ("eeg", "ieeg"):
         (bids_root / "sub-01" / "ses-01" / datatype).mkdir(parents=True)
 
+    raw = _load_raw()
+    raw.pick(["eeg"])
+    montage = raw.get_montage()
+    pos = montage.get_positions()
+
     for datatype in ("eeg", "ieeg"):
         bids_path = _bids_path.copy().update(root=bids_root, datatype=datatype)
         for coord_frame in BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS:
-            raw = _load_raw()
-            raw.pick(["eeg"])
             bids_path.update(space=coord_frame)
-            montage = raw.get_montage()
-            pos = montage.get_positions()
+            raw.set_montage(None)
+            _montage = montage.copy()
             mne_coord_frame = BIDS_TO_MNE_FRAMES.get(coord_frame, None)
             if mne_coord_frame is None:
-                montage.apply_trans(mne.transforms.Transform("head", "unknown"))
+                _montage.apply_trans(mne.transforms.Transform("head", "unknown"))
             else:
-                montage.apply_trans(mne.transforms.Transform("head", mne_coord_frame))
-            _write_dig_bids(bids_path, raw, montage, acpc_aligned=True)
+                _montage.apply_trans(mne.transforms.Transform("head", mne_coord_frame))
+            _write_dig_bids(bids_path, raw, _montage, acpc_aligned=True)
             electrodes_path = bids_path.copy().update(
                 task=None, run=None, suffix="electrodes", extension=".tsv"
             )
             coordsystem_path = bids_path.copy().update(
                 task=None, run=None, suffix="coordsystem", extension=".json"
             )
+            # _read_dig_bids updates raw inplace
             if mne_coord_frame is None:
                 with pytest.warns(
                     RuntimeWarning, match="not an MNE-Python coordinate frame"
@@ -172,8 +176,7 @@ def test_dig_template(tmp_path):
                     electrodes_path.update(space="fsaverage")
                     coordsystem_path.update(space="fsaverage")
                 _read_dig_bids(electrodes_path, coordsystem_path, datatype, raw)
-            montage2 = raw.get_montage()
-            pos2 = montage2.get_positions()
+            pos2 = raw.get_montage().get_positions()
             np.testing.assert_array_almost_equal(
                 np.array(list(pos["ch_pos"].values())),
                 np.array(list(pos2["ch_pos"].values())),