Merge branch 'main' into ruff

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.13
+    rev: v0.1.14
     hooks:
       - id: ruff
         name: ruff lint mne

environment.yml

@@ -14,6 +14,7 @@ dependencies:
   - packaging
   - numba
   - pandas
+  - pyarrow
   - xlrd
   - scikit-learn
   - h5py

mne/annotations.py

@@ -1616,9 +1616,7 @@ def events_from_annotations(
         inds = values = np.array([]).astype(int)
         for annot in annotations[event_sel]:
             annot_offset = annot["onset"] + annot["duration"]
-            _onsets = np.arange(
-                start=annot["onset"], stop=annot_offset, step=chunk_duration
-            )
+            _onsets = np.arange(annot["onset"], annot_offset, chunk_duration)
             good_events = annot_offset - _onsets >= chunk_duration
             if good_events.any():
                 _onsets = _onsets[good_events]

mne/conftest.py

@@ -196,6 +196,10 @@ def pytest_configure(config):
     ignore:ast\.NameConstant is deprecated and will be removed in Python 3\.14.*:DeprecationWarning
     # pooch
     ignore:Python 3\.14 will, by default, filter extracted tar archives.*:DeprecationWarning
+    # pandas
+    ignore:\n*Pyarrow will become a required dependency of pandas.*:DeprecationWarning
+    # pyvista <-> NumPy 2.0
+    ignore:__array_wrap__ must accept context and return_scalar arguments.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

pyproject.toml

@@ -72,6 +72,7 @@ full = [
     "numba",
     "h5py",
     "pandas",
+    "pyarrow",  # only needed to avoid a deprecation warning in pandas
     "numexpr",
     "jupyter",
     "python-picard",
@@ -109,7 +110,7 @@ full = [
 
 # Dependencies for running the test infrastructure
 test = [
-    "pytest!=8.0.0rc1",
+    "pytest!=8.0.0rc1,!=8.0.0rc2",
     "pytest-cov",
     "pytest-timeout",
     "pytest-harvest",

tools/azure_dependencies.sh

@@ -8,12 +8,7 @@ elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	STD_ARGS="$STD_ARGS --pre"
 	python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://www.riverbankcomputing.com/pypi/simple" "PyQt6!=6.6.1" PyQt6-sip PyQt6-Qt6 "PyQt6-Qt6!=6.6.1"
 	echo "Numpy etc."
-	# See github_actions_dependencies.sh for comments
-	# Until https://github.com/scipy/scipy/issues/19605 and
-	# https://github.com/scipy/scipy/issues/19713 are resolved, we can't use the NumPy
-	# 2.0 wheels :(
-	python -m pip install $STD_ARGS --only-binary numpy scipy h5py
-	python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" scikit-learn matplotlib statsmodels
+	python -m pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" "scikit-learn>=1.5.dev0" matplotlib pillow statsmodels pyarrow
 	# echo "dipy"
 	# python -m pip install $STD_ARGS --only-binary ":all:" --extra-index-url "https://pypi.anaconda.org/scipy-wheels-nightly/simple" dipy
 	# echo "OpenMEEG"

tools/github_actions_dependencies.sh

@@ -28,7 +28,7 @@ else
 	echo "PyQt6"
 	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url https://www.riverbankcomputing.com/pypi/simple "PyQt6!=6.6.1" "PyQt6-Qt6!=6.6.1"
 	echo "NumPy/SciPy/pandas etc."
-	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" "scikit-learn==1.4.dev0" matplotlib pillow statsmodels
+	pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" "numpy>=2.0.0.dev0" "scipy>=1.12.0.dev0" "scikit-learn>=1.5.dev0" matplotlib pillow statsmodels pyarrow
 	# No pandas, dipy, h5py, openmeeg, python-picard (needs numexpr) until they update to NumPy 2.0 compat
 	INSTALL_KIND="test_extra"
 	# echo "dipy"