[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.2
     hooks:
       - id: ruff
         name: ruff mne_bids/

examples/mark_bad_channels.py

@@ -118,7 +118,7 @@
 raw = read_raw_bids(bids_path=bids_path, verbose=False)
 print(
     f"The following channels are currently marked as bad:\n"
-    f'    {", ".join(raw.info["bads"])}\n'
+    f"    {', '.join(raw.info['bads'])}\n"
 )
 
 # %%
@@ -137,7 +137,7 @@
 raw = read_raw_bids(bids_path=bids_path, verbose=False)
 print(
     f"After marking MEG 0112 and MEG 0131 as bad, the following channels "
-    f'are now marked as bad:\n    {", ".join(raw.info["bads"])}\n'
+    f"are now marked as bad:\n    {', '.join(raw.info['bads'])}\n"
 )
 
 # %%
@@ -159,7 +159,7 @@
 print(
     f"After marking MEG 0112 and MEG 0131 as bad and passing "
     f"`overwrite=True`, the following channels "
-    f'are now marked as bad:\n    {", ".join(raw.info["bads"])}\n'
+    f"are now marked as bad:\n    {', '.join(raw.info['bads'])}\n"
 )
 
 # %%
@@ -172,5 +172,5 @@
 raw = read_raw_bids(bids_path=bids_path, verbose=False)
 print(
     f"After passing `ch_names=[]` and `overwrite=True`, the following "
-    f'channels are now marked as bad:\n    {", ".join(raw.info["bads"])}\n'
+    f"channels are now marked as bad:\n    {', '.join(raw.info['bads'])}\n"
 )

mne_bids/commands/mne_bids_calibration_to_bids.py

@@ -44,9 +44,7 @@
     opt, args = parser.parse_args()
     if args:
         parser.print_help()
-        parser.error(
-            f"Please do not specify arguments without flags. " f"Got: {args}.\n"
-        )
+        parser.error(f"Please do not specify arguments without flags. Got: {args}.\n")
 
     if opt.bids_root is None:
         parser.print_help()

mne_bids/commands/mne_bids_inspect.py

@@ -72,9 +72,7 @@
     opt, args = parser.parse_args()
     if args:
         parser.print_help()
-        parser.error(
-            f"Please do not specify arguments without flags. " f"Got: {args}.\n"
-        )
+        parser.error(f"Please do not specify arguments without flags. Got: {args}.\n")
 
     if opt.bids_root is None:
         parser.print_help()

mne_bids/commands/mne_bids_mark_channels.py

@@ -126,7 +126,7 @@ def run():
         return  # XXX should be return with an error code?
 
     logger.info(
-        f'Marking channels {", ".join(ch_names)} as bad in '
+        f"Marking channels {', '.join(ch_names)} as bad in "
         f"{len(bids_paths)} recording(s) …"
     )
     for bids_path in bids_paths:

mne_bids/config.py

@@ -530,8 +530,7 @@ def _map_options(what, key, fro, to):
         mapped_option = mapping_mne_bids.get(key, None)
     else:
         raise RuntimeError(
-            f"fro value {fro} and to value {to} are not "
-            "accepted. Use 'mne', or 'bids'."
+            f"fro value {fro} and to value {to} are not accepted. Use 'mne', or 'bids'."
         )
 
     return mapped_option

mne_bids/copyfiles.py

@@ -82,7 +82,7 @@ def _get_brainvision_paths(vhdr_path):
     """
     fname, ext = _parse_ext(vhdr_path)
     if ext != ".vhdr":
-        raise ValueError(f'Expecting file ending in ".vhdr",' f" but got {ext}")
+        raise ValueError(f'Expecting file ending in ".vhdr", but got {ext}')
 
     # Header file seems fine
     # extract encoding from brainvision header file, or default to utf-8
@@ -96,14 +96,14 @@ def _get_brainvision_paths(vhdr_path):
     eeg_file_match = re.search(r"DataFile=(.*\.(eeg|dat))", " ".join(lines))
 
     if not eeg_file_match:
-        raise ValueError("Could not find a .eeg or .dat file link in" f" {vhdr_path}")
+        raise ValueError(f"Could not find a .eeg or .dat file link in {vhdr_path}")
     else:
         eeg_file = eeg_file_match.groups()[0]
 
     # Try to find marker file .vmrk
     vmrk_file_match = re.search(r"MarkerFile=(.*\.vmrk)", " ".join(lines))
     if not vmrk_file_match:
-        raise ValueError("Could not find a .vmrk file link in" f" {vhdr_path}")
+        raise ValueError(f"Could not find a .vmrk file link in {vhdr_path}")
     else:
         vmrk_file = vmrk_file_match.groups()[0]
 
@@ -275,7 +275,7 @@ def _anonymize_brainvision(vhdr_file, date):
 
     # Go through VHDR
     pattern = re.compile(r"^Impedance \[kOhm\] at \d\d:\d\d:\d\d :$")
-    replace = f'at {date.strftime("%H:%M:%S")} :'
+    replace = f"at {date.strftime('%H:%M:%S')} :"
     _replace_file(vhdr_file, pattern, replace)
 
 
@@ -544,7 +544,7 @@ def copyfile_eeglab(src, dest):
     fname_dest, ext_dest = _parse_ext(dest)
     if ext_src != ext_dest:
         raise ValueError(
-            f"Need to move data with same extension" f" but got {ext_src}, {ext_dest}"
+            f"Need to move data with same extension but got {ext_src}, {ext_dest}"
         )
 
     # Load the EEG struct

mne_bids/dig.py

@@ -45,7 +45,7 @@ def _handle_electrodes_reading(electrodes_fname, coord_frame, coord_unit):
 
     Handle xyz coordinates and coordinate frame of each channel.
     """
-    logger.info("Reading electrode " f"coords from {electrodes_fname}.")
+    logger.info(f"Reading electrode coords from {electrodes_fname}.")
     electrodes_dict = _from_tsv(electrodes_fname)
     ch_names_tsv = electrodes_dict["name"]
 
@@ -142,7 +142,7 @@ def _write_electrodes_tsv(raw, fname, datatype, overwrite=False):
     x, y, z, names = list(), list(), list(), list()
     for ch in raw.info["chs"]:
         if ch["kind"] == FIFF.FIFFV_STIM_CH:
-            logger.debug(f"Not writing stim chan {ch['ch_name']} " f"to electrodes.tsv")
+            logger.debug(f"Not writing stim chan {ch['ch_name']} to electrodes.tsv")
             continue
         elif np.isnan(ch["loc"][:3]).any() or np.allclose(ch["loc"][:3], 0):
             x.append("n/a")

mne_bids/path.py

@@ -905,9 +905,9 @@ def fpath(self):
                     msg = (
                         "Found more than one matching data file for the "
                         "requested recording. While searching:\n"
-                        f'{indent(repr(self), "    ")}\n'
+                        f"{indent(repr(self), '    ')}\n"
                         f"Found {len(matching_paths)} paths:\n"
-                        f'{indent(matching_paths_str, "    ")}\n'
+                        f"{indent(matching_paths_str, '    ')}\n"
                         "Cannot proceed due to the "
                         "ambiguity. This is likely a problem with your "
                         "BIDS dataset. Please run the BIDS validator on "
@@ -1005,7 +1005,7 @@ def update(self, *, check=None, **kwargs):
 
             if key not in ENTITY_VALUE_TYPE:
                 raise ValueError(
-                    f"Key must be one of " f"{ALLOWED_PATH_ENTITIES}, got {key}"
+                    f"Key must be one of {ALLOWED_PATH_ENTITIES}, got {key}"
                 )
 
             if ENTITY_VALUE_TYPE[key] == "label":
@@ -1152,7 +1152,7 @@ def _check(self):
                 allowed_spaces_for_dtype = ALLOWED_SPACES.get(datatype, None)
                 if allowed_spaces_for_dtype is None:
                     raise ValueError(
-                        f"space entity is not valid for datatype " f"{self.datatype}"
+                        f"space entity is not valid for datatype {self.datatype}"
                     )
                 elif space not in allowed_spaces_for_dtype:
                     raise ValueError(
@@ -1462,7 +1462,9 @@ def _truncate_tsv_line(line, lim=10):
     """Truncate a line to the specified number of characters."""
     return "".join(
         [
-            str(val) + (lim - len(val)) * " " if len(val) < lim else f"{val[:lim - 1]} "
+            str(val) + (lim - len(val)) * " "
+            if len(val) < lim
+            else f"{val[: lim - 1]} "
             for val in line.split("\t")
         ]
     )
@@ -1762,7 +1764,7 @@ def get_entities_from_fname(fname, on_error="raise", verbose=None):
 
         if on_error in ("raise", "warn"):
             if key not in fname_vals:
-                msg = f'Unexpected entity "{key}" found in ' f'filename "{fname}"'
+                msg = f'Unexpected entity "{key}" found in filename "{fname}"'
                 if on_error == "raise":
                     raise KeyError(msg)
                 elif on_error == "warn":
@@ -1864,10 +1866,7 @@ def _find_matching_sidecar(bids_path, suffix=None, extension=None, on_error="rai
     # If this was expected, simply return None, otherwise, raise an exception.
     msg = None
     if len(best_candidates) == 0:
-        msg = (
-            f"Did not find any {search_suffix} "
-            f"associated with {bids_path.basename}."
-        )
+        msg = f"Did not find any {search_suffix} associated with {bids_path.basename}."
     elif len(best_candidates) > 1:
         # More than one candidates were tied for best match
         msg = (
@@ -2085,7 +2084,7 @@ def get_entity_vals(
 
     if entity_key not in entities:
         raise ValueError(
-            f'`key` must be one of: {", ".join(entities)}. ' f"Got: {entity_key}"
+            f"`key` must be one of: {', '.join(entities)}. Got: {entity_key}"
         )
 
     ignore_subjects = _ensure_tuple(ignore_subjects)
@@ -2530,7 +2529,7 @@ def _return_root_paths(root, datatype=None, ignore_json=True, ignore_nosub=False
 
     if datatype is not None:
         datatype = _ensure_tuple(datatype)
-        search_str = f'*/{"|".join(datatype)}/*'
+        search_str = f"*/{'|'.join(datatype)}/*"
     else:
         search_str = "*.*"
 

mne_bids/read.py

@@ -126,7 +126,7 @@ def _read_events(events, event_id, raw, bids_path=None):
     # retrieve events
     if isinstance(events, np.ndarray):
         if events.ndim != 2:
-            raise ValueError("Events must have two dimensions, " f"found {events.ndim}")
+            raise ValueError(f"Events must have two dimensions, found {events.ndim}")
         if events.shape[1] != 3:
             raise ValueError(
                 "Events must have second dimension of length 3, "
@@ -164,7 +164,7 @@ def _read_events(events, event_id, raw, bids_path=None):
                     f"The provided raw data contains annotations, but "
                     f'"event_id" does not contain entries for all annotation '
                     f"descriptions. The following entries are missing: "
-                    f'{", ".join(desc_without_id)}'
+                    f"{', '.join(desc_without_id)}"
                 )
 
     # If we have events, convert them to Annotations so they can be easily
@@ -174,7 +174,7 @@ def _read_events(events, event_id, raw, bids_path=None):
         if ids_without_desc:
             raise ValueError(
                 f"No description was specified for the following event(s): "
-                f'{", ".join([str(x) for x in sorted(ids_without_desc)])}. '
+                f"{', '.join([str(x) for x in sorted(ids_without_desc)])}. "
                 f"Please add them to the event_id dictionary, or drop them "
                 f"from the events array."
             )
@@ -409,9 +409,7 @@ def _handle_scans_reading(scans_fname, raw, bids_path):
             # Convert time offset to UTC
             acq_time = acq_time.astimezone(timezone.utc)
 
-        logger.debug(
-            f"Loaded {scans_fname} scans file to set " f"acq_time as {acq_time}."
-        )
+        logger.debug(f"Loaded {scans_fname} scans file to set acq_time as {acq_time}.")
         # First set measurement date to None and then call call anonymize() to
         # remove any traces of the measurement date we wish
         # to replace – it might lurk out in more places than just
@@ -728,7 +726,7 @@ def _handle_channels_reading(channels_fname, raw):
     if ch_diff:
         warn(
             f"Cannot set channel type for the following channels, as they "
-            f'are missing in the raw data: {", ".join(sorted(ch_diff))}'
+            f"are missing in the raw data: {', '.join(sorted(ch_diff))}"
         )
     raw.set_channel_types(
         channel_type_bids_mne_map_available_channels, on_unit_change="ignore"
@@ -744,7 +742,7 @@ def _handle_channels_reading(channels_fname, raw):
             warn(
                 f'Cannot set "bad" status for the following channels, as '
                 f"they are missing in the raw data: "
-                f'{", ".join(sorted(ch_diff))}'
+                f"{', '.join(sorted(ch_diff))}"
             )
 
         raw.info["bads"] = bads_avail
@@ -875,7 +873,7 @@ def read_raw_bids(
             and raw_path.is_symlink()
         ):
             target_path = raw_path.resolve()
-            logger.info(f"Resolving symbolic link: " f"{raw_path} -> {target_path}")
+            logger.info(f"Resolving symbolic link: {raw_path} -> {target_path}")
             raw_path = target_path
         config_path = None
 
@@ -1124,7 +1122,7 @@ def get_head_mri_trans(
 
     if t1w_json_path is None or not t1w_json_path.exists():
         raise FileNotFoundError(
-            f"Did not find T1w JSON sidecar file, tried location: " f"{t1w_json_path}"
+            f"Did not find T1w JSON sidecar file, tried location: {t1w_json_path}"
         )
     for extension in (".nii", ".nii.gz"):
         t1w_path_candidate = t1w_json_path.with_suffix(extension)
@@ -1135,7 +1133,7 @@ def get_head_mri_trans(
     if not t1w_bids_path.fpath.exists():
         raise FileNotFoundError(
             f"Did not find T1w recording file, tried location: "
-            f'{t1w_path_candidate.name.replace(".nii.gz", "")}[.nii, .nii.gz]'
+            f"{t1w_path_candidate.name.replace('.nii.gz', '')}[.nii, .nii.gz]"
         )
 
     # Get MRI landmarks from the JSON sidecar

mne_bids/report/_report.py

@@ -260,7 +260,7 @@
     if session is None:
         search_str = "*_scans.tsv"
     else:
-        search_str = f"*ses-{session}" f"*_scans.tsv"
+        search_str = f"*ses-{session}*_scans.tsv"
     scans_fpaths = list(root.rglob(search_str))
     if len(scans_fpaths) == 0:
         warn(

mne_bids/sidecar_updates.py

@@ -97,7 +97,7 @@ def update_sidecar_json(bids_path, entries, verbose=None):
     # get the file path
     fpath = bids_path.fpath
     if not fpath.exists():
-        raise RuntimeError(f"Sidecar file does not " f"exist for {fpath}.")
+        raise RuntimeError(f"Sidecar file does not exist for {fpath}.")
 
     # sidecar update either from file, or as dictionary
     if isinstance(entries, dict):
@@ -255,7 +255,7 @@ def update_anat_landmarks(
         raise ValueError(
             f"Could not find an MRI scan. Please check the provided "
             f"bids_path. Tried the following filenames: "
-            f'{", ".join([p.name for p in tried_paths])}'
+            f"{', '.join([p.name for p in tried_paths])}"
         )
 
     if not isinstance(landmarks, DigMontage):  # it's pathlike
@@ -303,7 +303,7 @@ def update_anat_landmarks(
             f"The provided DigMontage did not contain all required cardinal "
             f"points (nasion and left and right pre-auricular points). The "
             f"following points are missing: "
-            f'{", ".join(missing_points)}'
+            f"{', '.join(missing_points)}"
         )
 
     bids_path_json = bids_path.copy().update(extension=".json")

mne_bids/tests/test_path.py

@@ -177,25 +177,19 @@ def test_search_folder_for_text(capsys):
     captured = capsys.readouterr()
     assert "sub-01_ses-eeg_task-rest_eeg.json" in captured.out
     assert (
-        (
-            "    1    name      type      units     low_cutof high_cuto descripti sampling_ status    status_de\n"  # noqa: E501
-            "    2    Fp1       EEG       µV        0.0159154 1000.0    ElectroEn 5000.0    good      n/a"  # noqa: E501
-        )
-        in captured.out
-    )
+        "    1    name      type      units     low_cutof high_cuto descripti sampling_ status    status_de\n"  # noqa: E501
+        "    2    Fp1       EEG       µV        0.0159154 1000.0    ElectroEn 5000.0    good      n/a"  # noqa: E501
+    ) in captured.out
     # test if pathlib.Path object
     search_folder_for_text("n/a", Path(test_dir))
 
     # test returning a string and without line numbers
     out = search_folder_for_text("n/a", test_dir, line_numbers=False, return_str=True)
     assert "sub-01_ses-eeg_task-rest_eeg.json" in out
     assert (
-        (
-            "    name      type      units     low_cutof high_cuto descripti sampling_ status    status_de\n"  # noqa: E501
-            "    Fp1       EEG       µV        0.0159154 1000.0    ElectroEn 5000.0    good      n/a"  # noqa: E501
-        )
-        in out
-    )
+        "    name      type      units     low_cutof high_cuto descripti sampling_ status    status_de\n"  # noqa: E501
+        "    Fp1       EEG       µV        0.0159154 1000.0    ElectroEn 5000.0    good      n/a"  # noqa: E501
+    ) in out
 
 
 def test_print_dir_tree(capsys):
@@ -420,10 +414,7 @@ def test_get_entities_from_fname(fname):
     "fname",
     [
         "sub-01_ses-02_task-test_run-3_split-01_meg.fif",
-        (
-            "/bids_root/sub-01/ses-02/meg/"
-            "sub-01_ses-02_task-test_run-3_split-01_meg.fif"
-        ),
+        ("/bids_root/sub-01/ses-02/meg/sub-01_ses-02_task-test_run-3_split-01_meg.fif"),
         "sub-01_ses-02_task-test_run-3_split-01_foo-tfr_meg.fif",
     ],
 )