[pull] main from mne-tools:main

.github/workflows/tests.yml

@@ -50,7 +50,7 @@ jobs:
   pytest:
     name: '${{ matrix.os }} / ${{ matrix.kind }} / ${{ matrix.python }}'
     needs: style
-    timeout-minutes: 90
+    timeout-minutes: 120
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -78,7 +78,7 @@ jobs:
           - os: macos-latest  # arm64 (Apple Silicon): Sequoia
             python: '3.13'
             kind: mamba
-          - os: macos-14  # arm64 (Apple Silicon): Sonoma
+          - os: macos-15-intel  # intel: Sequoia
             python: '3.13'
             kind: mamba
           - os: windows-latest
@@ -128,12 +128,18 @@ jobs:
           # For some reason on Linux we get crashes
           if [[ "$RUNNER_OS" == "Linux" ]]; then
             sed -i "/numba/d" environment.yml
+          fi
           # And on Windows and macOS PySide6.9.0 segfaults
-          elif [[ "$RUNNER_OS" == "macOS" ]]; then
-            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.7.3/g" environment.yml
-            sed -i "" "s/  - vtk .*/  - vtk =9.3.1/g" environment.yml
-          elif [[ "$RUNNER_OS" == "Windows" ]]; then
-            sed -i "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
+            sed -i "" "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
+
+          else
+            sed -i "s/  - PySide6 .*/  - PySide6 =6.9.2/g" environment.yml
+            sed -i "s/  - vtk .*/  - vtk =9.5.1/g" environment.yml
+            if [[ "$RUNNER_OS" == "Windows" ]]; then
+              echo "MNE_IS_OSMESA=true" | tee -a $GITHUB_ENV
+            fi
           fi
         if: matrix.kind == 'conda' || matrix.kind == 'mamba'
       - uses: mamba-org/setup-micromamba@v2

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.1
+    rev: v0.13.2
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.13.0
+    rev: v1.14.2
     hooks:
       - id: zizmor
 

doc/sphinxext/related_software.py

@@ -33,7 +33,6 @@
     "meggie",
     "niseq",
     "sesameeg",
-    "invertmeeg",
 }
 
 # If it's not available on PyPI, add it to this dict:

environment.yml

@@ -62,3 +62,5 @@ dependencies:
   - trame-vuetify
   - vtk >=9.2
   - xlrd
+  - pip:
+      - pyobjc-framework-Cocoa >=5.2.0;platform_system=='Darwin'

mne/conftest.py

@@ -199,6 +199,11 @@ def pytest_configure(config: pytest.Config):
     ignore:.*The `disp` and `iprint` options of the L-BFGS-B solver.*:DeprecationWarning
     # matplotlib<->nilearn
     ignore:[\S\s]*You are using the 'agg' matplotlib backend[\S\s]*:UserWarning
+    # matplotlib<->pyparsing
+    ignore:^'.*' argument is deprecated, use '.*'$:DeprecationWarning
+    ignore:^'.*' deprecated - use '.*'$:DeprecationWarning
+    # dipy
+    ignore:'where' used without 'out', expect .*:UserWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

mne/decoding/tests/test_receptive_field.py

@@ -238,9 +238,9 @@ def test_receptive_field_basic(n_jobs):
     rf.fit(X[:, [0]], y)
     str(rf)  # repr with one feature
     # Should only accept estimators or floats
-    with pytest.raises(ValueError, match="`estimator` must be a float or"):
+    with pytest.raises((ValueError, AttributeError)):
         ReceptiveField(tmin, tmax, 1, estimator="foo").fit(X, y)
-    with pytest.raises(ValueError, match="`estimator` must be a float or"):
+    with pytest.raises((ValueError, AttributeError)):
         ReceptiveField(tmin, tmax, 1, estimator=np.array([1, 2, 3])).fit(X, y)
     with pytest.raises(ValueError, match="tmin .* must be at most tmax"):
         ReceptiveField(5, 4, 1).fit(X, y)

mne/viz/backends/_pyvista.py

@@ -8,6 +8,7 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
+import os
 import platform
 import re
 import warnings
@@ -1331,6 +1332,8 @@ def _is_osmesa(plotter):
     # and a working Nouveau is: "Mesa 24.2.3-1ubuntu1 via NVE6"
     if platform.system() == "Darwin":  # segfaults on macOS sometimes
         return False
+    if os.getenv("MNE_IS_OSMESA", "").lower() == "true":
+        return True
     gpu_info_full = plotter.ren_win.ReportCapabilities()
     gpu_info = re.findall(
         "OpenGL (?:version|renderer) string:(.+)\n",

mne/viz/backends/tests/test_renderer.py

@@ -226,6 +226,7 @@ def test_3d_warning(renderer_pyvistaqt, monkeypatch):
     bad = f"{pre}OpenGL 3.3 (Core Profile) Mesa 18.3.4 via llvmpipe (LLVM 7.0, 256 bits)\n"  # noqa
     monkeypatch.setattr(platform, "system", lambda: "Linux")  # avoid short-circuit
     monkeypatch.setattr(plotter.ren_win, "ReportCapabilities", lambda: good)
+    monkeypatch.setenv("MNE_IS_OSMESA", "false")
     assert _is_osmesa(plotter)
     monkeypatch.setattr(plotter.ren_win, "ReportCapabilities", lambda: bad)
     with pytest.warns(RuntimeWarning, match=r"18\.3\.4 is too old"):

tools/circleci_dependencies.sh

@@ -14,6 +14,6 @@ python -m pip install --upgrade --progress-bar off \
     mne-icalabel mne-lsl mne-microstates mne-nirs mne-rsa \
     neurodsp neurokit2 niseq nitime pactools mnelab \
     plotly pycrostates pyprep pyriemann python-picard sesameeg \
-    sleepecg tensorpac yasa meegkit eeg_positions wfdb invertmeeg \
+    sleepecg tensorpac yasa meegkit eeg_positions wfdb \
     curryreader
 python -m pip install --upgrade --progress-bar off --no-deps cross-domain-saliency-maps

tools/github_actions_dependencies.sh

@@ -17,6 +17,8 @@ if [ ! -z "$CONDA_ENV" ]; then
 	if [[ "${RUNNER_OS}" != "Windows" ]] && [[ "${CONDA_ENV}" != "environment_"* ]]; then
 		INSTALL_ARGS=""
 	fi
+	# TODO: Until a PyVista release supports VTK 9.5+
+	STD_ARGS="$STD_ARGS https://github.com/pyvista/pyvista/archive/refs/heads/main.zip"
 	# If on minimal or old, just install testing deps
 	if [[ "${CONDA_ENV}" == "environment_"* ]]; then
 		INSTALL_KIND="test"

tools/hooks/update_environment_file.py

@@ -53,7 +53,8 @@ def split_dep(dep):
     # handle package name differences
     package_name = translations.get(package_name, package_name)
     # PySide6==6.7.0 only exists on PyPI, not conda-forge, so excluding it in
-    # `environment.yaml` breaks the solver
+    # `environment.yaml` breaks the solver. 6.9.1 has a bug, and 6.9.2 needs newer
+    # C deps that mean we need to upgrade VTK etc.
     if package_name == "PySide6":
         version_spec = "!=6.9.1"
     # rstrip output line in case `version_spec` == ""
@@ -64,10 +65,6 @@ def split_dep(dep):
     else:
         conda_deps.add(line)
 
-# TODO: temporary workaround while we wait for a release containing the fix for
-# https://github.com/mamba-org/mamba/issues/3467
-pip_deps.remove("      - pyobjc-framework-Cocoa >=5.2.0;platform_system=='Darwin'")
-
 # prepare the pip dependencies section
 newline = "\n"  # python < 3.12 forbids backslash in {} part of f-string
 pip_section = f"""\