Merge remote-tracking branch 'upstream/main' into kernel

* upstream/main:
  MAINT: Add branch coverage (mne-tools#12174)
  OpenSSF (mne-tools#12175)
  fix docstring in 60_sleep.py (mne-tools#12171)
  FIX: skip empty lines in read_raw_eyelink (mne-tools#12172)
  FIX: Fix bug with coreg scalars (mne-tools#12164)
  Changed casting rule in np.clip to allow reading of raw GDF files (mne-tools#12168)

Author: larsoner

doc/changes/devel.rst

@@ -49,6 +49,7 @@ Enhancements
 
 Bugs
 ~~~~
+- Fix bug where :func:`mne.io.read_raw_gdf` would fail due to improper usage of ``np.clip`` (:gh:`12168` by :newcontrib:`Rasmus Aagaard`) 
 - Fix bugs with :func:`mne.preprocessing.realign_raw` where the start of ``other`` was incorrectly cropped; and onsets and durations in ``other.annotations`` were left unsynced with the resampled data (:gh:`11950` by :newcontrib:`Qian Chu`)
 - Fix bug where ``encoding`` argument was ignored when reading annotations from an EDF file (:gh:`11958` by :newcontrib:`Andrew Gilbert`)
 - Mark tests ``test_adjacency_matches_ft`` and ``test_fetch_uncompressed_file`` as network tests (:gh:`12041` by :newcontrib:`Maksym Balatsko`)
@@ -70,7 +71,7 @@ Bugs
 - Fix bug where :class:`mne.Info` HTML representations listed all channel counts instead of good channel counts under the heading "Good channels" (:gh:`12145` by `Eric Larson`_) 
 - Fix rendering glitches when plotting Neuromag/TRIUX sensors in :func:`mne.viz.plot_alignment` and related functions (:gh:`12098` by `Eric Larson`_)
 - Fix bug with delayed checking of :class:`info["bads"] <mne.Info>` (:gh:`12038` by `Eric Larson`_)
-- Fix bug with :ref:`mne coreg` where points inside the head surface were not shown (:gh:`12147` by `Eric Larson`_)
+- Fix bug with :ref:`mne coreg` where points inside the head surface were not shown (:gh:`12147`, :gh:`12164` by `Eric Larson`_)
 - Fix bug with :func:`mne.viz.plot_alignment` where ``sensor_colors`` were not handled properly on a per-channel-type basis (:gh:`12067` by `Eric Larson`_)
 - Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` :gh:`12017` :gh:`12044` by `Paul Roujansky`_)
 - Add missing ``overwrite`` and ``verbose`` parameters to :meth:`Transform.save() <mne.transforms.Transform.save>` (:gh:`12004` by `Marijn van Vliet`_)

doc/changes/names.inc

@@ -442,6 +442,8 @@
 
 .. _ramonapariciog: https://github.com/ramonapariciog
 
+.. _Rasmus Aagaard: https://github.com/rasgaard
+
 .. _Rasmus Zetter: https://people.aalto.fi/rasmus.zetter
 
 .. _Reza Nasri: https://github.com/rznas

mne/io/edf/edf.py

@@ -1443,7 +1443,7 @@ def _read_gdf_header(fname, exclude, include=None):
                 else:
                     chn = np.zeros(n_events, dtype=np.uint32)
                     dur = np.ones(n_events, dtype=np.uint32)
-                np.clip(dur, 1, np.inf, out=dur)
+                np.maximum(dur, 1, out=dur)
                 events = [n_events, pos, typ, chn, dur]
                 edf_info["event_sfreq"] = event_sr
 
@@ -1878,7 +1878,7 @@ def read_raw_gdf(
     input_fname = os.path.abspath(input_fname)
     ext = os.path.splitext(input_fname)[1][1:].lower()
     if ext != "gdf":
-        raise NotImplementedError(f"Only BDF files are supported, got {ext}.")
+        raise NotImplementedError(f"Only GDF files are supported, got {ext}.")
     return RawGDF(
         input_fname=input_fname,
         eog=eog,

mne/io/eyelink/_utils.py

@@ -122,6 +122,8 @@ def _parse_recording_blocks(fname):
                 is_recording_block = True
             if is_recording_block:
                 tokens = line.split()
+                if not tokens:
+                    continue  # skip empty lines
                 if tokens[0][0].isnumeric():  # Samples
                     data_dict["sample_lines"].append(tokens)
                 elif tokens[0] in data_dict["event_lines"].keys():

mne/viz/backends/_pyvista.py

@@ -655,6 +655,9 @@ def quiver3d(
         clim=None,
     ):
         _check_option("mode", mode, ALLOWED_QUIVER_MODES)
+        _validate_type(scale_mode, str, "scale_mode")
+        scale_map = dict(none=False, scalar="scalars", vector="vec")
+        _check_option("scale_mode", scale_mode, list(scale_map))
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", category=FutureWarning)
             factor = scale
@@ -667,7 +670,10 @@ def quiver3d(
             grid = UnstructuredGrid(*args)
             if scalars is None:
                 scalars = np.ones((n_points,))
-            grid.point_data["scalars"] = np.array(scalars)
+                mesh_scalars = None
+            else:
+                mesh_scalars = "scalars"
+            grid.point_data["scalars"] = np.array(scalars, float)
             grid.point_data["vec"] = vectors
             if mode == "2darrow":
                 return _arrow_glyph(grid, factor), grid
@@ -715,14 +721,17 @@ def quiver3d(
                 glyph.Update()
                 geom = glyph.GetOutput()
                 mesh = grid.glyph(
-                    orient="vec", scale=scale_mode == "vector", factor=factor, geom=geom
+                    orient="vec",
+                    scale=scale_map[scale_mode],
+                    factor=factor,
+                    geom=geom,
                 )
             actor = _add_mesh(
                 self.plotter,
                 mesh=mesh,
                 color=color,
                 opacity=opacity,
-                scalars=None,
+                scalars=mesh_scalars,
                 colormap=colormap,
                 show_scalar_bar=False,
                 backface_culling=backface_culling,

pyproject.toml

@@ -128,7 +128,7 @@ ignore-decorators = [
 
 [tool.pytest.ini_options]
 addopts = """--durations=20 --doctest-modules -ra --cov-report= --tb=short \
-    --doctest-ignore-import-errors --junit-xml=junit-results.xml \
+    --cov-branch --doctest-ignore-import-errors --junit-xml=junit-results.xml \
     --ignore=doc --ignore=logo --ignore=examples --ignore=tutorials \
     --ignore=mne/gui/_*.py --ignore=mne/icons --ignore=tools \
     --ignore=mne/report/js_and_css \

tools/dev/Makefile

@@ -3,14 +3,25 @@
 dev-activity: check_steering_committee.py
 	python check_steering_committee.py
 
-unacknowledged-bugs: unacknowledged-bug-reports.jq bug-reports-12-to-2-months-old.json
-	@jq -f unacknowledged-bug-reports.jq bug-reports-12-to-2-months-old.json
+unacknowledged-bug-reports: unacknowledged-issues.jq bug-reports-12-to-2-months-old.json
+	@echo "MUST acknowledge bug reports (OpenSSF criterion: 50%)"
+	@jq -f unacknowledged-issues.jq bug-reports-12-to-2-months-old.json
+
+unacknowledged-feature-requests: unacknowledged-issues.jq feature-requests-12-to-2-months-old.json
+	@echo "SHOULD acknowledge feature requests (OpenSSF criterion: 50%)"
+	@jq -f unacknowledged-issues.jq feature-requests-12-to-2-months-old.json
 
 bug-reports-12-to-2-months-old.json:
 	@echo "Querying GitHub REST API..."
 	@gh issue list \
 	-l bug \
 	--json state,number,title,createdAt,comments > bug-reports-12-to-2-months-old.json
 
+feature-requests-12-to-2-months-old.json:
+	@echo "Querying GitHub REST API..."
+	@gh issue list \
+	-l enh \
+	--json state,number,title,createdAt,comments > feature-requests-12-to-2-months-old.json
+
 clean:
 	@rm bug-reports-12-to-2-months-old.json || true

tools/dev/unacknowledged-bug-reports.jq tools/dev/unacknowledged-issues.jqtools/dev/unacknowledged-bug-reports.jq renamed to tools/dev/unacknowledged-issues.jq

@@ -1,4 +1,4 @@
-# Processor for `gh issue list` output that displays unacknowledged bug reports
+# Processor for `gh issue list` output that displays unacknowledged issues
 # that are 2-12 months old. The date range is specific to OpenSSF best practices.
 
 # `now` is in seconds since the unix epoch
@@ -28,5 +28,5 @@ map(
     "range": make_pretty_date_range,
     "has_dev_comments": map(select(.devComments > 0)) | length,
     "no_dev_comments": map(select(.devComments == 0) and .state == "OPEN") | length,
-    "unaddressed_bug_reports": map(select(.devComments == 0) | make_issue_url),
+    "unaddressed": map(select(.devComments == 0) | make_issue_url),
 }

tutorials/clinical/60_sleep.py

@@ -249,7 +249,7 @@ def eeg_power_band(epochs):
 
     Returns
     -------
-    X : numpy array of shape [n_samples, 5]
+    X : numpy array of shape [n_samples, 5 * n_channels]
         Transformed data.
     """
     # specific frequency bands