[pull] main from mne-tools:main

.github/workflows/check_changelog.yml

@@ -13,7 +13,10 @@ jobs:
     name: Check towncrier entry in doc/changes/dev/
     runs-on: ubuntu-latest
     steps:
-      - uses: scientific-python/action-towncrier-changelog@v1
+      - uses: actions/checkout@v5
+        with:
+          persist-credentials: false
+      - uses: scientific-python/action-towncrier-changelog@v2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           BOT_USERNAME: changelog-bot

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.1
+    rev: v0.14.2
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.15.2
+    rev: v1.16.0
     hooks:
       - id: zizmor
 

doc/changes/dev/13466.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with :func:`mne.add_reference_channels` not working correctly when passing more than one channel name, by `Michael Straube`_.

mne/_fiff/reference.py

@@ -316,7 +316,7 @@ def add_reference_channels(inst, ref_channels, copy=True):
             "unit_mul": FIFF.FIFF_UNITM_NONE,
             "unit": FIFF.FIFF_UNIT_V,
             "coord_frame": FIFF.FIFFV_COORD_HEAD,
-            "loc": ref_dig_array,
+            "loc": ref_dig_array.copy(),
         }
         inst.info["chs"].append(chan_info)
         inst.info._update_redundant()

mne/_fiff/tests/test_reference.py

@@ -744,6 +744,10 @@ def test_add_reference():
     ref_data, _ = raw[[ref_idx, ref_idy]]
     assert_array_equal(ref_data, 0)
 
+    loc1 = raw.info["chs"][ref_idx]["loc"]
+    loc2 = raw.info["chs"][ref_idy]["loc"]
+    assert loc1 is not loc2
+
     # add reference channel to epochs
     raw = read_raw_fif(fif_fname, preload=True)
     events = read_events(eve_fname)

mne/datasets/tests/test_datasets.py

@@ -10,7 +10,6 @@
 
 import pooch
 import pytest
-from flaky import flaky
 
 import mne.datasets._fsaverage.base
 from mne import datasets, read_labels_from_annot, write_labels_to_annot
@@ -174,10 +173,11 @@ def _error_download_2(self, fname, downloader, processor):
         datasets._fake.data_path(download=True, force_update=True, **kwargs)
 
 
-@flaky(max_runs=3)
+# Okay to xfail this one because CircleCI downloads + uses the parcellations,
+# so we'll know if they break
+@pytest.mark.xfail(reason="Figshare blocks access from CIs sometimes")
 @pytest.mark.ultraslowtest  # not really ultraslow, but flakes out a lot
 @testing.requires_testing_data
-@requires_good_network
 def test_fetch_parcellations(tmp_path):
     """Test fetching parcellations."""
     pytest.importorskip("nibabel")

mne/surface.py

@@ -7,7 +7,6 @@
 
 import json
 import time
-import warnings
 from collections import OrderedDict
 from copy import deepcopy
 from functools import lru_cache, partial
@@ -1472,16 +1471,12 @@ def _decimate_surface_vtk(points, triangles, n_triangles):
         )
     src = vtkPolyData()
     vtkpoints = vtkPoints()
-    with warnings.catch_warnings(record=True):
-        warnings.simplefilter("ignore")
-        vtkpoints.SetData(numpy_to_vtk(points.astype(np.float64)))
+    vtkpoints.SetData(numpy_to_vtk(points.astype(np.float64)))
     src.SetPoints(vtkpoints)
     vtkcells = vtkCellArray()
     triangles_ = np.pad(triangles, ((0, 0), (1, 0)), "constant", constant_values=3)
-    with warnings.catch_warnings(record=True):
-        warnings.simplefilter("ignore")
-        idarr = numpy_to_vtkIdTypeArray(triangles_.ravel().astype(np.int64))
-    vtkcells.SetCells(triangles.shape[0], idarr)
+    idarr = numpy_to_vtkIdTypeArray(triangles_.ravel().astype(np.int64))
+    vtkcells.ImportLegacyFormat(idarr)
     src.SetPolys(vtkcells)
     # vtkDecimatePro was not very good, even with SplittingOff and
     # PreserveTopologyOn

tools/install_pre_requirements.sh

@@ -38,13 +38,7 @@ echo "::endgroup::"
 # No Numba because it forces an old NumPy version
 
 echo "::group::VTK"
-if [[ "$PLATFORM" == "Linux" ]]; then
-	# Segfault trying to load libx11.so.6
-	VTK_ARGS=""
-else
-	VTK_ARGS="--extra-index-url \"https://wheels.vtk.org\""
-fi
-python -m pip install $STD_ARGS --only-binary ":all:" vtk $VTK_ARGS
+python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://wheels.vtk.org" vtk
 python -c "import vtk"
 echo "::endgroup::"