fix linter errors

Author: tien-tong

cubids/__about__.py

@@ -34,6 +34,4 @@
 )
 __url__ = "https://github.com/PennLINC/CuBIDS"
 
-DOWNLOAD_URL = (
-    f"https://github.com/PennLINC/{__packagename__}/archive/{__version__}.tar.gz"
-)
+DOWNLOAD_URL = f"https://github.com/PennLINC/{__packagename__}/archive/{__version__}.tar.gz"

cubids/cli.py

@@ -289,9 +289,7 @@ def _parse_bids_sidecar_merge():
     The `IsFile` partial function is used to validate that the provided file paths exist.
     """
     parser = argparse.ArgumentParser(
-        description=(
-            "bids-sidecar-merge: merge critical keys from one sidecar to another"
-        ),
+        description=("bids-sidecar-merge: merge critical keys from one sidecar to another"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         allow_abbrev=False,
     )
@@ -382,9 +380,7 @@ def _parse_group():
         default="subject",
         choices=["subject", "session"],
         action="store",
-        help=(
-            "Level at which acquisition groups are created options: 'subject' or 'session'"
-        ),
+        help=("Level at which acquisition groups are created options: 'subject' or 'session'"),
     )
     parser.add_argument(
         "--config",
@@ -446,9 +442,7 @@ def _parse_apply():
         The argument parser with the defined arguments.
     """
     parser = argparse.ArgumentParser(
-        description=(
-            "cubids apply: apply the changes specified in a tsv to a BIDS directory"
-        ),
+        description=("cubids apply: apply the changes specified in a tsv to a BIDS directory"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         allow_abbrev=False,
     )
@@ -512,9 +506,7 @@ def _parse_apply():
         default="subject",
         choices=["subject", "session"],
         action="store",
-        help=(
-            "Level at which acquisition groups are created options: 'subject' or 'session'"
-        ),
+        help=("Level at which acquisition groups are created options: 'subject' or 'session'"),
     )
     parser.add_argument(
         "--config",
@@ -1072,9 +1064,7 @@ def _get_parser():
     from cubids import __version__
 
     parser = argparse.ArgumentParser(prog="cubids", allow_abbrev=False)
-    parser.add_argument(
-        "-v", "--version", action="version", version=f"cubids v{__version__}"
-    )
+    parser.add_argument("-v", "--version", action="version", version=f"cubids v{__version__}")
     subparsers = parser.add_subparsers(help="CuBIDS commands")
 
     for command, parser_func, run_func in COMMANDS:

cubids/cubids.py

@@ -123,9 +123,7 @@ def __init__(
         self.data_dict = {}  # data dictionary for TSV outputs
         self.use_datalad = use_datalad  # True if flag set, False if flag unset
         self.schema = load_schema(schema_json)
-        self.is_longitudinal = (
-            self._infer_longitudinal()
-        )  # inferred from dataset structure
+        self.is_longitudinal = self._infer_longitudinal()  # inferred from dataset structure
 
         if self.use_datalad:
             self.init_datalad()
@@ -188,9 +186,7 @@ def reset_bids_layout(self, validate=False):
             re.compile(r"/\."),
         ]
 
-        indexer = bids.BIDSLayoutIndexer(
-            validate=validate, ignore=ignores, index_metadata=False
-        )
+        indexer = bids.BIDSLayoutIndexer(validate=validate, ignore=ignores, index_metadata=False)
 
         self._layout = bids.BIDSLayout(self.path, validate=validate, indexer=indexer)
 
@@ -297,9 +293,7 @@ def datalad_undo_last_commit(self):
             If there are untracked changes in the datalad dataset.
         """
         if not self.is_datalad_clean():
-            raise Exception(
-                "Untracked changes present. Run clear_untracked_changes first"
-            )
+            raise Exception("Untracked changes present. Run clear_untracked_changes first")
         reset_proc = subprocess.run(["git", "reset", "--hard", "HEAD~1"], cwd=self.path)
         reset_proc.check_returncode()
 
@@ -423,9 +417,7 @@ def add_file_collections(self):
                 continue
 
             # Add file collection metadata to the sidecar
-            files, collection_metadata = utils.collect_file_collections(
-                self.layout, path
-            )
+            files, collection_metadata = utils.collect_file_collections(self.layout, path)
             filepaths = [f.path for f in files]
             checked_files.extend(filepaths)
 
@@ -447,9 +439,7 @@ def add_file_collections(self):
 
         self.reset_bids_layout()
 
-    def apply_tsv_changes(
-        self, summary_tsv, files_tsv, new_prefix, raise_on_error=True
-    ):
+    def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=True):
         """Apply changes documented in the edited summary tsv and generate the new tsv files.
 
         This function looks at the RenameEntitySet and MergeInto
@@ -485,15 +475,11 @@ def apply_tsv_changes(
         files_df = pd.read_table(files_tsv)
 
         # Check that the MergeInto column only contains valid merges
-        ok_merges, deletions = check_merging_operations(
-            summary_tsv, raise_on_error=raise_on_error
-        )
+        ok_merges, deletions = check_merging_operations(summary_tsv, raise_on_error=raise_on_error)
 
         merge_commands = []
         for source_id, dest_id in ok_merges:
-            dest_files = files_df.loc[
-                (files_df[["ParamGroup", "EntitySet"]] == dest_id).all(1)
-            ]
+            dest_files = files_df.loc[(files_df[["ParamGroup", "EntitySet"]] == dest_id).all(1)]
             source_files = files_df.loc[
                 (files_df[["ParamGroup", "EntitySet"]] == source_id).all(1)
             ]
@@ -504,16 +490,12 @@ def apply_tsv_changes(
             for dest_nii in dest_files.FilePath:
                 dest_json = utils.img_to_new_ext(self.path + dest_nii, ".json")
                 if Path(dest_json).exists() and Path(source_json).exists():
-                    merge_commands.append(
-                        f"cubids bids-sidecar-merge {source_json} {dest_json}"
-                    )
+                    merge_commands.append(f"cubids bids-sidecar-merge {source_json} {dest_json}")
 
         # Get the delete commands
         to_remove = []
         for rm_id in deletions:
-            files_to_rm = files_df.loc[
-                (files_df[["ParamGroup", "EntitySet"]] == rm_id).all(1)
-            ]
+            files_to_rm = files_df.loc[(files_df[["ParamGroup", "EntitySet"]] == rm_id).all(1)]
 
             for rm_me in files_to_rm.FilePath:
                 if Path(self.path + rm_me).exists():
@@ -748,17 +730,13 @@ def change_filename(self, filepath, entities):
                         # remove old filename
                         data["IntendedFor"].remove(item)
                         # add new filename
-                        data["IntendedFor"].append(
-                            utils._get_participant_relative_path(new_path)
-                        )
+                        data["IntendedFor"].append(utils._get_participant_relative_path(new_path))
 
                     if item == utils._get_bidsuri(filepath, self.path):
                         # remove old filename
                         data["IntendedFor"].remove(item)
                         # add new filename
-                        data["IntendedFor"].append(
-                            utils._get_bidsuri(new_path, self.path)
-                        )
+                        data["IntendedFor"].append(utils._get_bidsuri(new_path, self.path))
 
                 # update the json with the new data dictionary
                 utils._update_json(filename_with_if, data)
@@ -935,9 +913,7 @@ def _purge_associations(self, scans):
 
                 if "/func/" in str(path):
                     # add tsvs
-                    tsv = utils.img_to_new_ext(str(path), ".tsv").replace(
-                        "_bold", "_events"
-                    )
+                    tsv = utils.img_to_new_ext(str(path), ".tsv").replace("_bold", "_events")
                     if Path(tsv).exists():
                         to_remove.append(tsv)
                     # add tsv json (if exists)
@@ -1292,23 +1268,17 @@ def get_param_groups_dataframes(self):
             long_name = big_df.loc[row, "FilePath"]
             big_df.loc[row, "FilePath"] = long_name.replace(self.path, "")
 
-        summary = utils._order_columns(
-            pd.concat(param_group_summaries, ignore_index=True)
-        )
+        summary = utils._order_columns(pd.concat(param_group_summaries, ignore_index=True))
 
         # create new col that strings key and param group together
-        summary["KeyParamGroup"] = (
-            summary["EntitySet"] + "__" + summary["ParamGroup"].map(str)
-        )
+        summary["KeyParamGroup"] = summary["EntitySet"] + "__" + summary["ParamGroup"].map(str)
 
         # move this column to the front of the dataframe
         key_param_col = summary.pop("KeyParamGroup")
         summary.insert(0, "KeyParamGroup", key_param_col)
 
         # do the same for the files df
-        big_df["KeyParamGroup"] = (
-            big_df["EntitySet"] + "__" + big_df["ParamGroup"].map(str)
-        )
+        big_df["KeyParamGroup"] = big_df["EntitySet"] + "__" + big_df["ParamGroup"].map(str)
 
         # move this column to the front of the dataframe
         key_param_col = big_df.pop("KeyParamGroup")
@@ -1383,12 +1353,8 @@ def get_tsvs(self, path_prefix):
 
         big_df, summary = self.get_param_groups_dataframes()
 
-        summary = summary.sort_values(
-            by=["Modality", "EntitySetCount"], ascending=[True, False]
-        )
-        big_df = big_df.sort_values(
-            by=["Modality", "EntitySetCount"], ascending=[True, False]
-        )
+        summary = summary.sort_values(by=["Modality", "EntitySetCount"], ascending=[True, False])
+        big_df = big_df.sort_values(by=["Modality", "EntitySetCount"], ascending=[True, False])
 
         # Create json dictionaries for summary and files tsvs
         self.create_data_dictionary()

cubids/metadata_merge.py

@@ -54,18 +54,14 @@ def check_merging_operations(action_tsv, raise_on_error=False):
     )
 
     def _check_sdc_cols(meta1, meta2):
-        return {key: meta1[key] for key in sdc_cols} == {
-            key: meta2[key] for key in sdc_cols
-        }
+        return {key: meta1[key] for key in sdc_cols} == {key: meta2[key] for key in sdc_cols}
 
     needs_merge = actions[np.isfinite(actions["MergeInto"])]
     for _, row_needs_merge in needs_merge.iterrows():
         source_param_key = tuple(row_needs_merge[["MergeInto", "EntitySet"]])
         dest_param_key = tuple(row_needs_merge[["ParamGroup", "EntitySet"]])
         dest_metadata = row_needs_merge.to_dict()
-        source_row = actions.loc[
-            (actions[["ParamGroup", "EntitySet"]] == source_param_key).all(1)
-        ]
+        source_row = actions.loc[(actions[["ParamGroup", "EntitySet"]] == source_param_key).all(1)]
 
         if source_param_key[0] == 0:
             print("going to delete ", dest_param_key)
@@ -304,9 +300,7 @@ def get_acq_dictionary(is_longitudinal=False):
     return acq_dict
 
 
-def group_by_acquisition_sets(
-    files_tsv, output_prefix, acq_group_level, is_longitudinal=False
-):
+def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level, is_longitudinal=False):
     """Find unique sets of Key/Param groups across subjects.
 
     This writes out the following files:
@@ -371,9 +365,7 @@ def group_by_acquisition_sets(
     acq_group_info = []
     for groupnum, content_id_row in enumerate(descending_order, start=1):
         content_id = content_ids[content_id_row]
-        acq_group_info.append(
-            (groupnum, content_id_counts[content_id_row]) + content_id
-        )
+        acq_group_info.append((groupnum, content_id_counts[content_id_row]) + content_id)
         if is_longitudinal:
             for subject, session in contents_to_subjects[content_id]:
                 grouped_sub_sess.append(
@@ -385,9 +377,7 @@ def group_by_acquisition_sets(
                 )
         elif not is_longitudinal:
             for subject in contents_to_subjects[content_id]:
-                grouped_sub_sess.append(
-                    {"subject": "sub-" + subject, "AcqGroup": groupnum}
-                )
+                grouped_sub_sess.append({"subject": "sub-" + subject, "AcqGroup": groupnum})
 
     # Write the mapping of subject/session to
     acq_group_df = pd.DataFrame(grouped_sub_sess)

cubids/tests/test_apply.py

@@ -14,18 +14,14 @@
                     "dir": "AP",
                     "suffix": "epi",
                     "metadata": {
-                        "IntendedFor": [
-                            "ses-01/dwi/sub-01_ses-01_dir-AP_run-01_dwi.nii.gz"
-                        ],
+                        "IntendedFor": ["ses-01/dwi/sub-01_ses-01_dir-AP_run-01_dwi.nii.gz"],
                     },
                 },
                 {
                     "dir": "PA",
                     "suffix": "epi",
                     "metadata": {
-                        "IntendedFor": [
-                            "ses-01/dwi/sub-01_ses-01_dir-AP_run-01_dwi.nii.gz"
-                        ],
+                        "IntendedFor": ["ses-01/dwi/sub-01_ses-01_dir-AP_run-01_dwi.nii.gz"],
                     },
                 },
             ],
@@ -122,18 +118,14 @@
                     "dir": "AP",
                     "suffix": "epi",
                     "metadata": {
-                        "IntendedFor": [
-                            "bids::sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz"
-                        ],
+                        "IntendedFor": ["bids::sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz"],
                     },
                 },
                 {
                     "dir": "PA",
                     "suffix": "epi",
                     "metadata": {
-                        "IntendedFor": [
-                            "bids::sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz"
-                        ],
+                        "IntendedFor": ["bids::sub-01/dwi/sub-01_dir-AP_run-01_dwi.nii.gz"],
                     },
                 },
             ],