[dependabot]: Bump github/codeql-action from 4.35.2 to 4.35.3 in the actions group (#13897)

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: mne[bot] <50266005+mne-bot@users.noreply.github.com>
Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

Author: 3 people

.github/workflows/codeql-analysis.yml

@@ -44,7 +44,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v4.35.2
+      uses: github/codeql-action/init@v4.35.3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -58,7 +58,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v4.35.2
+      uses: github/codeql-action/autobuild@v4.35.3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -71,4 +71,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v4.35.2
+      uses: github/codeql-action/analyze@v4.35.3

environment.yml

@@ -62,6 +62,7 @@ dependencies:
   - tqdm >=4.66
   - traitlets
   - trame
+  - trame-pyvista
   - trame-vtk
   - trame-vuetify
   - vtk ==9.6.0

mne/beamformer/tests/test_lcmv.py

@@ -564,6 +564,20 @@ def test_make_lcmv_bem(tmp_path, reg, proj, kind):
     make_lcmv(epochs.info, forward_fixed, data_cov_grad, reg=0.01, noise_cov=noise_cov)
 
 
+@pytest.fixture(scope="module")
+def evoked_fwd_noise_data():
+    """Fixture to supply reusable data."""
+    _, _, evoked, data_cov, noise_cov, _, _, _, _, _ = _get_data(proj=True)
+    assert "eeg" not in evoked
+    assert "meg" in evoked
+    sphere = mne.make_sphere_model(r0=(0.0, 0.0, 0.0), head_radius=0.080)
+    src = mne.setup_volume_source_space(
+        pos=25.0, sphere=sphere, mindist=5.0, exclude=2.0
+    )
+    fwd_sphere = mne.make_forward_solution(evoked.info, None, src, sphere)
+    return evoked, fwd_sphere, noise_cov, data_cov
+
+
 @testing.requires_testing_data
 @pytest.mark.slowtest
 @pytest.mark.parametrize(
@@ -576,24 +590,16 @@ def test_make_lcmv_bem(tmp_path, reg, proj, kind):
         (None, "max-power"),
     ],
 )
-def test_make_lcmv_sphere(pick_ori, weight_norm):
+def test_make_lcmv_sphere(pick_ori, weight_norm, evoked_fwd_noise_data):
     """Test LCMV with sphere head model."""
     # unit-noise gain beamformer and orientation
     # selection and rank reduction of the leadfield
-    _, _, evoked, data_cov, noise_cov, _, _, _, _, _ = _get_data(proj=True)
-    assert "eeg" not in evoked
-    assert "meg" in evoked
-    sphere = mne.make_sphere_model(r0=(0.0, 0.0, 0.0), head_radius=0.080)
-    src = mne.setup_volume_source_space(
-        pos=25.0, sphere=sphere, mindist=5.0, exclude=2.0
-    )
-    fwd_sphere = mne.make_forward_solution(evoked.info, None, src, sphere)
-
+    evoked, fwd_sphere, noise_cov, data_cov = evoked_fwd_noise_data
     # Test that we get an error if not reducing rank
     with (
         pytest.raises(ValueError, match="Singular matrix detected"),
         _record_warnings(),
-        pytest.warns(RuntimeWarning, match="positive semidefinite"),
+        pytest.warns(RuntimeWarning, match="(positive semidefinite|largest eigenvalu)"),
     ):
         make_lcmv(
             evoked.info,

mne/source_estimate.py

@@ -3219,18 +3219,21 @@ def spatio_temporal_dist_adjacency(src, n_times, dist, verbose=None):
         vertices are time 1, the nodes from 2 to 2N are the vertices
         during time 2, etc.
     """
+    from scipy import sparse
+
     if src[0]["dist"] is None:
         raise RuntimeError(
             "src must have distances included, consider using "
             "setup_source_space with add_dist=True"
         )
     blocks = [s["dist"][s["vertno"], :][:, s["vertno"]] for s in src]
     # Ensure we keep explicit zeros; deal with changes in SciPy
-    for block in blocks:
+    for bi, block in enumerate(blocks):
         if isinstance(block, np.ndarray):
             block[block == 0] = -np.inf
         else:
             block.data[block.data == 0] == -1
+        blocks[bi] = sparse.csr_array(block)  # avoid SciPy dep warning about mat->arr
     edges = sparse.block_diag(blocks)
     edges.data[:] = np.less_equal(edges.data, dist)
     # clean it up and put it in coo format

mne/utils/config.py

@@ -823,6 +823,7 @@ def sys_info(
         # "trame",  # no version, see https://github.com/Kitware/trame/issues/183
         "trame_client",
         "trame_server",
+        "trame_pyvista",
         "trame_vtk",
         "trame_vuetify",
         "",

pyproject.toml

@@ -185,6 +185,7 @@ full-no-qt = [
   "threadpoolctl",
   "traitlets",
   "trame",
+  "trame-pyvista",
   "trame-vtk",
   "trame-vuetify",
   "vtk >= 9.2",

tools/install_pre_requirements.sh

@@ -61,9 +61,8 @@ python -m pip install $STD_ARGS \
 	git+https://github.com/BUNPC/pysnirf2 \
 	git+https://github.com/the-siesta-group/edfio \
 	git+https://github.com/python-quantities/python-quantities \
-	trame trame-vtk trame-vuetify nest-asyncio2 jupyter ipyevents ipympl openmeeg \
-	imageio-ffmpeg xlrd mffpy traitlets pybv eeglabio defusedxml \
-	antio curryreader
+	trame trame-vtk trame-vuetify trame-pyvista nest-asyncio2 jupyter ipyevents ipympl \
+	openmeeg imageio-ffmpeg xlrd mffpy traitlets pybv eeglabio defusedxml antio curryreader
 echo "::endgroup::"
 
 echo "::group::Make sure we're on a NumPy 2.0 variant"