Merge branch 'main' into sklearn

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.1
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.0.0
+    rev: v1.1.1
     hooks:
       - id: zizmor
 

azure-pipelines.yml

@@ -112,7 +112,7 @@ stages:
           - bash: |
               set -e
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1" pandas neo pymatreader antio defusedxml
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1" pandas neo pymatreader antio defusedxml
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'

doc/changes/devel/13063.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in the colorbars created by :func:`mne.viz.plot_evoked_topomap` by `Santeri Ruuskanen`_.

doc/changes/devel/13069.bugfix.rst

@@ -0,0 +1 @@
+Fix bug cause by unnecessary assertion when loading mixed frequency EDFs without preloading :func:`mne.io.read_raw_edf` by `Simon Kern`_.

doc/conf.py

@@ -1289,7 +1289,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     rst_prolog += f"""
 .. |{icon}| raw:: html
 
-    <i class="{' '.join(classes + (f'fa-{icon}',))}"></i>
+    <i class="{" ".join(classes + (f"fa-{icon}",))}"></i>
 """
 
 rst_prolog += """

doc/sphinxext/credit_tools.py

@@ -169,7 +169,7 @@ def generate_credit_rst(app=None, *, verbose=False):
                 if author["e"] is not None:
                     if author["e"] not in name_map:
                         unknown_emails.add(
-                            f'{author["e"].ljust(29)} '
+                            f"{author['e'].ljust(29)} "
                             "https://github.com/mne-tools/mne-python/pull/"
                             f"{commit}/files"
                         )
@@ -178,9 +178,9 @@ def generate_credit_rst(app=None, *, verbose=False):
                 else:
                     name = author["n"]
                     if name in manual_renames:
-                        assert _good_name(
-                            manual_renames[name]
-                        ), f"Bad manual rename: {name}"
+                        assert _good_name(manual_renames[name]), (
+                            f"Bad manual rename: {name}"
+                        )
                         name = manual_renames[name]
                     if " " in name:
                         first, last = name.rsplit(" ", maxsplit=1)

doc/sphinxext/related_software.py

@@ -163,9 +163,9 @@ def _get_packages() -> dict[str, str]:
     assert not dups, f"Duplicates in MANUAL_PACKAGES and PYPI_PACKAGES: {sorted(dups)}"
     # And the installer and PyPI-only should be disjoint:
     dups = set(PYPI_PACKAGES) & set(packages)
-    assert (
-        not dups
-    ), f"Duplicates in PYPI_PACKAGES and installer packages: {sorted(dups)}"
+    assert not dups, (
+        f"Duplicates in PYPI_PACKAGES and installer packages: {sorted(dups)}"
+    )
     for name in PYPI_PACKAGES | set(MANUAL_PACKAGES):
         if name not in packages:
             packages.append(name)

doc/sphinxext/unit_role.py

@@ -10,8 +10,7 @@ def unit_role(name, rawtext, text, lineno, inliner, options={}, content=[]):  #
 
     def pass_error_to_sphinx(rawtext, text, lineno, inliner):
         msg = inliner.reporter.error(
-            "The :unit: role requires a space-separated number and unit; "
-            f"got {text}",
+            f"The :unit: role requires a space-separated number and unit; got {text}",
             line=lineno,
         )
         prb = inliner.problematic(rawtext, rawtext, msg)

examples/inverse/vector_mne_solution.py

@@ -79,7 +79,7 @@
 # inverse was computed with loose=0.2
 print(
     "Absolute cosine similarity between source normals and directions: "
-    f'{np.abs(np.sum(directions * inv["source_nn"][2::3], axis=-1)).mean()}'
+    f"{np.abs(np.sum(directions * inv['source_nn'][2::3], axis=-1)).mean()}"
 )
 brain_max = stc_max.plot(
     initial_time=peak_time,

examples/visualization/evoked_topomap.py

@@ -5,8 +5,8 @@
 Plotting topographic maps of evoked data
 ========================================
 
-Load evoked data and plot topomaps for selected time points using multiple
-additional options.
+Load evoked data and plot topomaps for selected time points using
+multiple additional options.
 """
 # Authors: Christian Brodbeck <[email protected]>
 #          Tal Linzen <[email protected]>

examples/visualization/evoked_whitening.py

@@ -85,7 +85,7 @@
 
 print("Covariance estimates sorted from best to worst")
 for c in noise_covs:
-    print(f'{c["method"]} : {c["loglik"]}')
+    print(f"{c['method']} : {c['loglik']}")
 
 # %%
 # Show the evoked data:

mne/_fiff/_digitization.py

@@ -328,8 +328,7 @@ def _get_data_as_dict_from_dig(dig, exclude_ref_channel=True):
         dig_coord_frames = set([FIFF.FIFFV_COORD_HEAD])
     if len(dig_coord_frames) != 1:
         raise RuntimeError(
-            "Only single coordinate frame in dig is supported, "
-            f"got {dig_coord_frames}"
+            f"Only single coordinate frame in dig is supported, got {dig_coord_frames}"
         )
     dig_ch_pos_location = np.array(dig_ch_pos_location)
     dig_ch_pos_location.shape = (-1, 3)  # empty will be (0, 3)

mne/_fiff/meas_info.py

@@ -455,7 +455,7 @@ def _check_set(ch, projs, ch_type):
         for proj in projs:
             if ch["ch_name"] in proj["data"]["col_names"]:
                 raise RuntimeError(
-                    f'Cannot change channel type for channel {ch["ch_name"]} in '
+                    f"Cannot change channel type for channel {ch['ch_name']} in "
                     f'projector "{proj["desc"]}"'
                 )
     ch["kind"] = new_kind
@@ -1867,7 +1867,7 @@ def _check_consistency(self, prepend_error=""):
             ):
                 raise RuntimeError(
                     f'{prepend_error}info["meas_date"] must be a datetime object in UTC'
-                    f' or None, got {repr(self["meas_date"])!r}'
+                    f" or None, got {repr(self['meas_date'])!r}"
                 )
 
         chs = [ch["ch_name"] for ch in self["chs"]]
@@ -3680,8 +3680,7 @@ def _write_ch_infos(fid, chs, reset_range, ch_names_mapping):
     # only write new-style channel information if necessary
     if len(ch_names_mapping):
         logger.info(
-            "    Writing channel names to FIF truncated to 15 characters "
-            "with remapping"
+            "    Writing channel names to FIF truncated to 15 characters with remapping"
         )
         for ch in chs:
             start_block(fid, FIFF.FIFFB_CH_INFO)

mne/_fiff/proj.py

@@ -76,7 +76,7 @@ def __repr__(self):  # noqa: D105
         s += f", active : {self['active']}"
         s += f", n_channels : {len(self['data']['col_names'])}"
         if self["explained_var"] is not None:
-            s += f', exp. var : {self["explained_var"] * 100:0.2f}%'
+            s += f", exp. var : {self['explained_var'] * 100:0.2f}%"
         return f"<Projection | {s}>"
 
     # speed up info copy by taking advantage of mutability
@@ -324,8 +324,7 @@ def apply_proj(self, verbose=None):
 
         if all(p["active"] for p in self.info["projs"]):
             logger.info(
-                "Projections have already been applied. "
-                "Setting proj attribute to True."
+                "Projections have already been applied. Setting proj attribute to True."
             )
             return self
 
@@ -663,9 +662,9 @@ def _read_proj(fid, node, *, ch_names_mapping=None, verbose=None):
         for proj in projs:
             misc = "active" if proj["active"] else " idle"
             logger.info(
-                f'        {proj["desc"]} '
-                f'({proj["data"]["nrow"]} x '
-                f'{len(proj["data"]["col_names"])}) {misc}'
+                f"        {proj['desc']} "
+                f"({proj['data']['nrow']} x "
+                f"{len(proj['data']['col_names'])}) {misc}"
             )
 
     return projs
@@ -795,8 +794,7 @@ def _make_projector(projs, ch_names, bads=(), include_active=True, inplace=False
         if not p["active"] or include_active:
             if len(p["data"]["col_names"]) != len(np.unique(p["data"]["col_names"])):
                 raise ValueError(
-                    f"Channel name list in projection item {k}"
-                    " contains duplicate items"
+                    f"Channel name list in projection item {k} contains duplicate items"
                 )
 
             # Get the two selection vectors to pick correct elements from
@@ -832,7 +830,7 @@ def _make_projector(projs, ch_names, bads=(), include_active=True, inplace=False
                         )
                     ):
                         warn(
-                            f'Projection vector {repr(p["desc"])} has been '
+                            f"Projection vector {repr(p['desc'])} has been "
                             f"reduced to {100 * psize:0.2f}% of its "
                             "original magnitude by subselecting "
                             f"{len(vecsel)}/{orig_n} of the original "

mne/_fiff/reference.py

@@ -102,7 +102,7 @@ def _check_before_dict_reference(inst, ref_dict):
             raise TypeError(
                 f"{elem_name.capitalize()}s in the ref_channels dict must be strings. "
                 f"Your dict has {elem_name}s of type "
-                f'{", ".join(map(lambda x: x.__name__, bad_elem))}.'
+                f"{', '.join(map(lambda x: x.__name__, bad_elem))}."
             )
 
     # Check that keys are valid channels and values are lists-of-valid-channels
@@ -113,8 +113,8 @@ def _check_before_dict_reference(inst, ref_dict):
     for elem_name, elem in dict(key=keys, value=values).items():
         if bad_elem := elem - ch_set:
             raise ValueError(
-                f'ref_channels dict contains invalid {elem_name}(s) '
-                f'({", ".join(bad_elem)}) '
+                f"ref_channels dict contains invalid {elem_name}(s) "
+                f"({', '.join(bad_elem)}) "
                 "that are not names of channels in the instance."
             )
         # Check that values are not bad channels

mne/_fiff/tag.py

@@ -70,8 +70,7 @@ def _frombuffer_rows(fid, tag_size, dtype=None, shape=None, rlims=None):
         have_shape = tag_size // item_size
         if want_shape != have_shape:
             raise ValueError(
-                f"Wrong shape specified, requested {want_shape} but got "
-                f"{have_shape}"
+                f"Wrong shape specified, requested {want_shape} but got {have_shape}"
             )
         if not len(rlims) == 2:
             raise ValueError("rlims must have two elements")

mne/_fiff/tests/test_meas_info.py

@@ -1118,7 +1118,7 @@ def test_channel_name_limit(tmp_path, monkeypatch, fname):
         meas_info, "_read_extended_ch_info", _read_extended_ch_info
     )
     short_proj_names = [
-        f"{name[:13 - bool(len(ref_names))]}-{ni}"
+        f"{name[: 13 - bool(len(ref_names))]}-{ni}"
         for ni, name in enumerate(long_proj_names)
     ]
     assert raw_read.info["projs"][0]["data"]["col_names"] == short_proj_names

mne/_fiff/tests/test_pick.py

@@ -136,7 +136,7 @@ def _channel_type_old(info, idx):
         else:
             return t
 
-    raise ValueError(f'Unknown channel type for {ch["ch_name"]}')
+    raise ValueError(f"Unknown channel type for {ch['ch_name']}")
 
 
 def _assert_channel_types(info):

mne/beamformer/_compute_beamformer.py

@@ -507,13 +507,13 @@ def __repr__(self):  # noqa: D105
             n_channels,
         )
         if self["pick_ori"] is not None:
-            out += f', {self["pick_ori"]} ori'
+            out += f", {self['pick_ori']} ori"
         if self["weight_norm"] is not None:
-            out += f', {self["weight_norm"]} norm'
+            out += f", {self['weight_norm']} norm"
         if self.get("inversion") is not None:
-            out += f', {self["inversion"]} inversion'
+            out += f", {self['inversion']} inversion"
         if "rank" in self:
-            out += f', rank {self["rank"]}'
+            out += f", rank {self['rank']}"
         out += ">"
         return out
 
@@ -531,7 +531,7 @@ def save(self, fname, overwrite=False, verbose=None):
         """
         _, write_hdf5 = _import_h5io_funcs()
 
-        ending = f'-{self["kind"].lower()}.h5'
+        ending = f"-{self['kind'].lower()}.h5"
         check_fname(fname, self["kind"], (ending,))
         csd_orig = None
         try:

mne/beamformer/tests/test_lcmv.py

@@ -380,7 +380,7 @@ def test_make_lcmv_bem(tmp_path, reg, proj, kind):
     rank = 17 if proj else 20
     assert "LCMV" in repr(filters)
     assert "unknown subject" not in repr(filters)
-    assert f'{fwd["nsource"]} vert' in repr(filters)
+    assert f"{fwd['nsource']} vert" in repr(filters)
     assert "20 ch" in repr(filters)
     assert f"rank {rank}" in repr(filters)
 

mne/bem.py

@@ -91,7 +91,7 @@ class ConductorModel(dict):
 
     def __repr__(self):  # noqa: D105
         if self["is_sphere"]:
-            center = ", ".join(f"{x * 1000.:.1f}" for x in self["r0"])
+            center = ", ".join(f"{x * 1000.0:.1f}" for x in self["r0"])
             rad = self.radius
             if rad is None:  # no radius / MEG only
                 extra = f"Sphere (no layers): r0=[{center}] mm"
@@ -538,7 +538,7 @@ def _assert_complete_surface(surf, incomplete="raise"):
     prop = tot_angle / (2 * np.pi)
     if np.abs(prop - 1.0) > 1e-5:
         msg = (
-            f'Surface {_bem_surf_name[surf["id"]]} is not complete (sum of '
+            f"Surface {_bem_surf_name[surf['id']]} is not complete (sum of "
             f"solid angles yielded {prop}, should be 1.)"
         )
         _on_missing(incomplete, msg, name="incomplete", error_klass=RuntimeError)
@@ -571,7 +571,7 @@ def _check_surface_size(surf):
     sizes = surf["rr"].max(axis=0) - surf["rr"].min(axis=0)
     if (sizes < 0.05).any():
         raise RuntimeError(
-            f'Dimensions of the surface {_bem_surf_name[surf["id"]]} seem too '
+            f"Dimensions of the surface {_bem_surf_name[surf['id']]} seem too "
             f"small ({1000 * sizes.min():9.5f}). Maybe the unit of measure"
             " is meters instead of mm"
         )
@@ -599,8 +599,7 @@ def _surfaces_to_bem(
     # surfs can be strings (filenames) or surface dicts
     if len(surfs) not in (1, 3) or not (len(surfs) == len(ids) == len(sigmas)):
         raise ValueError(
-            "surfs, ids, and sigmas must all have the same "
-            "number of elements (1 or 3)"
+            "surfs, ids, and sigmas must all have the same number of elements (1 or 3)"
         )
     for si, surf in enumerate(surfs):
         if isinstance(surf, str | Path | os.PathLike):
@@ -1260,8 +1259,7 @@ def make_watershed_bem(
     if op.isdir(ws_dir):
         if not overwrite:
             raise RuntimeError(
-                f"{ws_dir} already exists. Use the --overwrite option"
-                " to recreate it."
+                f"{ws_dir} already exists. Use the --overwrite option to recreate it."
             )
         else:
             shutil.rmtree(ws_dir)
@@ -2460,7 +2458,7 @@ def check_seghead(surf_path=subj_path / "surf"):
         logger.info(f"{ii}. Creating {level} tessellation...")
         logger.info(
             f"{ii}.1 Decimating the dense tessellation "
-            f'({len(surf["tris"])} -> {n_tri} triangles)...'
+            f"({len(surf['tris'])} -> {n_tri} triangles)..."
         )
         points, tris = decimate_surface(
             points=surf["rr"], triangles=surf["tris"], n_triangles=n_tri

mne/channels/channels.py

@@ -1382,7 +1382,7 @@ def read_ch_adjacency(fname, picks=None):
             raise ValueError(
                 f"No built-in channel adjacency matrix found with name: "
                 f"{ch_adj_name}. Valid names are: "
-                f'{", ".join(get_builtin_ch_adjacencies())}'
+                f"{', '.join(get_builtin_ch_adjacencies())}"
             )
 
         ch_adj = [a for a in _BUILTIN_CHANNEL_ADJACENCIES if a.name == ch_adj_name][0]

mne/channels/montage.py

@@ -1287,7 +1287,7 @@ def _backcompat_value(pos, ref_pos):
             f"Not setting position{_pl(extra)} of {len(extra)} {types} "
             f"channel{_pl(extra)} found in montage:\n{names}\n"
             "Consider setting the channel types to be of "
-            f'{docdict["montage_types"]} '
+            f"{docdict['montage_types']} "
             "using inst.set_channel_types before calling inst.set_montage, "
             "or omit these channels when creating your montage."
         )

mne/channels/tests/test_channels.py

@@ -404,8 +404,7 @@ def test_adjacency_matches_ft(tmp_path):
 
         if hash_mne.hexdigest() != hash_ft.hexdigest():
             raise ValueError(
-                f"Hash mismatch between built-in and FieldTrip neighbors "
-                f"for {fname}"
+                f"Hash mismatch between built-in and FieldTrip neighbors for {fname}"
             )
 
 

mne/channels/tests/test_montage.py

@@ -420,12 +420,7 @@ def test_documented():
         ),
         pytest.param(
             partial(read_dig_hpts, unit="m"),
-            (
-                "eeg Fp1 -95.0 -3. -3.\n"
-                "eeg AF7 -1 -1 -3\n"
-                "eeg A3 -2 -2 2\n"
-                "eeg A 0 0 0"
-            ),
+            ("eeg Fp1 -95.0 -3. -3.\neeg AF7 -1 -1 -3\neeg A3 -2 -2 2\neeg A 0 0 0"),
             make_dig_montage(
                 ch_pos={
                     "A": [0.0, 0.0, 0.0],

mne/commands/mne_make_scalp_surfaces.py

@@ -49,8 +49,7 @@ def run():
         "--force",
         dest="force",
         action="store_true",
-        help="Force creation of the surface even if it has "
-        "some topological defects.",
+        help="Force creation of the surface even if it has some topological defects.",
     )
     parser.add_option(
         "-t",