diff --git a/cubids/cli.py b/cubids/cli.py
index d2f8a920..ea78680c 100644
--- a/cubids/cli.py
+++ b/cubids/cli.py
@@ -27,7 +27,8 @@ def _is_file(path, parser):
     """Ensure a given path exists and it is a file."""
     path = _path_exists(path, parser)
     if not path.is_file():
-        raise parser.error(f"Path should point to a file (or symlink of file): <{path}>.")
+        raise parser.error(
+            f"Path should point to a file (or symlink of file): <{path}>.")
     return path
 
 
@@ -144,7 +145,8 @@ def _enter_bids_version(argv=None):
 
 def _parse_bids_sidecar_merge():
     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,
     )
     IsFile = partial(_is_file, parser=parser)
@@ -216,7 +218,8 @@ 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",
@@ -244,7 +247,8 @@ def _enter_group(argv=None):
 
 def _parse_apply():
     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,
     )
     PathExists = partial(_path_exists, parser=parser)
@@ -312,7 +316,8 @@ 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",
@@ -341,7 +346,8 @@ def _enter_apply(argv=None):
 
 def _parse_datalad_save():
     parser = argparse.ArgumentParser(
-        description=("cubids-datalad-save: perform a DataLad save on a BIDS directory"),
+        description=(
+            "cubids-datalad-save: perform a DataLad save on a BIDS directory"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     PathExists = partial(_path_exists, parser=parser)
@@ -699,8 +705,10 @@ def _enter_print_metadata_fields(argv=None):
     ("copy-exemplars", _parse_copy_exemplars, workflows.copy_exemplars),
     ("undo", _parse_undo, workflows.undo),
     ("datalad-save", _parse_datalad_save, workflows.datalad_save),
-    ("print-metadata-fields", _parse_print_metadata_fields, workflows.print_metadata_fields),
-    ("remove-metadata-fields", _parse_remove_metadata_fields, workflows.remove_metadata_fields),
+    ("print-metadata-fields", _parse_print_metadata_fields,
+     workflows.print_metadata_fields),
+    ("remove-metadata-fields", _parse_remove_metadata_fields,
+     workflows.remove_metadata_fields),
 ]
 
 
@@ -709,7 +717,8 @@ def _get_parser():
     from cubids import __version__
 
     parser = argparse.ArgumentParser(prog="cubids")
-    parser.add_argument("-v", "--version", action="version", version=__version__)
+    parser.add_argument("-v", "--version",
+                        action="version", version=__version__)
     subparsers = parser.add_subparsers(help="CuBIDS commands")
 
     for command, parser_func, run_func in COMMANDS:
diff --git a/cubids/cubids.py b/cubids/cubids.py
index 27f632e3..4de83826 100644
--- a/cubids/cubids.py
+++ b/cubids/cubids.py
@@ -149,9 +149,11 @@ 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)
+        self._layout = bids.BIDSLayout(
+            self.path, validate=validate, indexer=indexer)
 
     def create_cubids_code_dir(self):
         """Create CuBIDS code directory.
@@ -201,7 +203,8 @@ def datalad_save(self, message=None):
             Commit message to use with datalad save.
         """
         if not self.datalad_ready:
-            raise Exception("DataLad has not been initialized. use datalad_init()")
+            raise Exception(
+                "DataLad has not been initialized. use datalad_init()")
 
         statuses = self.datalad_handle.save(message=message or "CuBIDS Save")
         saved_status = set([status["status"] for status in statuses])
@@ -223,7 +226,8 @@ def is_datalad_clean(self):
         """
         if not self.datalad_ready:
             raise Exception("Datalad not initialized, can't determine status")
-        statuses = set([status["state"] for status in self.datalad_handle.status()])
+        statuses = set([status["state"]
+                       for status in self.datalad_handle.status()])
         return statuses == set(["clean"])
 
     def datalad_undo_last_commit(self):
@@ -237,8 +241,10 @@ 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")
-        reset_proc = subprocess.run(["git", "reset", "--hard", "HEAD~1"], cwd=self.path)
+            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()
 
     def add_nifti_info(self):
@@ -342,11 +348,13 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
         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)
             ]
@@ -357,13 +365,15 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
             for dest_nii in dest_files.FilePath:
                 dest_json = img_to_new_ext(self.path + dest_nii, ".json")
                 if Path(dest_json).exists() and Path(source_json).exists():
-                    merge_commands.append(f"bids-sidecar-merge {source_json} {dest_json}")
+                    merge_commands.append(
+                        f"bids-sidecar-merge {source_json} {dest_json}")
 
         # Get the delete commands
         # 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():
@@ -436,7 +446,8 @@ def apply_tsv_changes(self, summary_tsv, files_tsv, new_prefix, raise_on_error=T
 
                 rename_commit = s1 + s2
 
-                self.datalad_handle.run(cmd=["bash", renames], message=rename_commit)
+                self.datalad_handle.run(
+                    cmd=["bash", renames], message=rename_commit)
             else:
                 subprocess.run(
                     ["bash", renames],
@@ -476,7 +487,8 @@ def change_filename(self, filepath, entities):
         entity_file_keys = []
 
         # Entities that may be in the filename?
-        file_keys = ["task", "acquisition", "direction", "reconstruction", "run"]
+        file_keys = ["task", "acquisition",
+                     "direction", "reconstruction", "run"]
 
         for key in file_keys:
             if key in list(entities.keys()):
@@ -490,7 +502,8 @@ def change_filename(self, filepath, entities):
             # XXX: This adds an extra leading zero to run.
             entities["run"] = "0" + str(entities["run"])
 
-        filename = "_".join([f"{key}-{entities[key]}" for key in entity_file_keys])
+        filename = "_".join(
+            [f"{key}-{entities[key]}" for key in entity_file_keys])
         filename = (
             filename.replace("acquisition", "acq")
             .replace("direction", "dir")
@@ -499,7 +512,8 @@ def change_filename(self, filepath, entities):
         if len(filename) > 0:
             filename = sub_ses + "_" + filename + "_" + suffix + old_ext
         else:
-            raise ValueError(f"Could not construct new filename for {filepath}")
+            raise ValueError(
+                f"Could not construct new filename for {filepath}")
 
         # CHECK TO SEE IF DATATYPE CHANGED
         # datatype may be overridden/changed if the original file is located in the wrong folder.
@@ -517,7 +531,8 @@ def change_filename(self, filepath, entities):
             dtype_new = dtype_orig
 
         # Construct the new filename
-        new_path = str(self.path) + "/" + sub + "/" + ses + "/" + dtype_new + "/" + filename
+        new_path = str(self.path) + "/" + sub + "/" + \
+            ses + "/" + dtype_new + "/" + filename
 
         # Add the scan path + new path to the lists of old, new filenames
         self.old_filenames.append(filepath)
@@ -536,7 +551,8 @@ def change_filename(self, filepath, entities):
                 # ensure assoc not an IntendedFor reference
                 if ".nii" not in str(assoc_path):
                     self.old_filenames.append(assoc_path)
-                    new_ext_path = img_to_new_ext(new_path, "".join(Path(assoc_path).suffixes))
+                    new_ext_path = img_to_new_ext(
+                        new_path, "".join(Path(assoc_path).suffixes))
                     self.new_filenames.append(new_ext_path)
 
         # MAKE SURE THESE AREN'T COVERED BY get_associations!!!
@@ -609,7 +625,8 @@ def change_filename(self, filepath, entities):
             if Path(old_labeling).exists():
                 self.old_filenames.append(old_labeling)
                 new_scan_end = "_" + suffix + old_ext
-                new_labeling = new_path.replace(new_scan_end, "_asllabeling.jpg")
+                new_labeling = new_path.replace(
+                    new_scan_end, "_asllabeling.jpg")
                 self.new_filenames.append(new_labeling)
 
         # RENAME INTENDED FORS!
@@ -635,7 +652,8 @@ def change_filename(self, filepath, entities):
                         # remove old filename
                         data["IntendedFor"].remove(item)
                         # add new filename
-                        data["IntendedFor"].append(_get_intended_for_reference(new_path))
+                        data["IntendedFor"].append(
+                            _get_intended_for_reference(new_path))
 
                 # update the json with the new data dictionary
                 _update_json(filename_with_if, data)
@@ -808,7 +826,8 @@ def _purge_associations(self, scans):
 
                 if "/func/" in str(path):
                     # add tsvs
-                    tsv = img_to_new_ext(str(path), ".tsv").replace("_bold", "_events")
+                    tsv = img_to_new_ext(str(path), ".tsv").replace(
+                        "_bold", "_events")
                     if Path(tsv).exists():
                         to_remove.append(tsv)
                     # add tsv json (if exists)
@@ -922,7 +941,8 @@ def get_param_groups_from_entity_set(self, entity_set):
             2. A data frame with param group summaries
         """
         if not self.fieldmaps_cached:
-            raise Exception("Fieldmaps must be cached to find parameter groups.")
+            raise Exception(
+                "Fieldmaps must be cached to find parameter groups.")
         key_entities = _entity_set_to_entities(entity_set)
         key_entities["extension"] = ".nii[.gz]*"
 
@@ -975,7 +995,8 @@ def create_data_dictionary(self):
             mod_dict = sidecar_params[mod]
             for s_param in mod_dict.keys():
                 if s_param not in self.data_dict.keys():
-                    self.data_dict[s_param] = {"Description": "Scanning Parameter"}
+                    self.data_dict[s_param] = {
+                        "Description": "Scanning Parameter"}
 
         relational_params = self.grouping_config.get("relational_params")
         for r_param in relational_params.keys():
@@ -987,7 +1008,8 @@ def create_data_dictionary(self):
             mod_dict = derived_params[mod]
             for d_param in mod_dict.keys():
                 if d_param not in self.data_dict.keys():
-                    self.data_dict[d_param] = {"Description": "NIfTI Header Parameter"}
+                    self.data_dict[d_param] = {
+                        "Description": "NIfTI Header Parameter"}
 
         # Manually add non-sidecar columns/descriptions to data_dict
         desc1 = "Column where users mark groups to manually check"
@@ -1094,17 +1116,20 @@ def get_param_groups_dataframes(self):
             long_name = big_df.loc[row, "FilePath"]
             big_df.loc[row, "FilePath"] = long_name.replace(self.path, "")
 
-        summary = _order_columns(pd.concat(param_group_summaries, ignore_index=True))
+        summary = _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")
@@ -1253,8 +1278,10 @@ 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()
@@ -1273,7 +1300,8 @@ def get_tsvs(self, path_prefix):
         summary.to_csv(f"{path_prefix}_summary.tsv", sep="\t", index=False)
 
         # Calculate the acq groups
-        group_by_acquisition_sets(f"{path_prefix}_files.tsv", path_prefix, self.acq_group_level)
+        group_by_acquisition_sets(
+            f"{path_prefix}_files.tsv", path_prefix, self.acq_group_level)
 
         print(f"CuBIDS detected {len(summary)} Parameter Groups.")
 
@@ -1492,7 +1520,8 @@ def _get_param_groups(
             # Get the fieldmaps out and add their types
             if "FieldmapKey" in relational_params:
                 fieldmap_types = sorted(
-                    [_file_to_entity_set(fmap.path) for fmap in fieldmap_lookup[path]]
+                    [_file_to_entity_set(fmap.path)
+                     for fmap in fieldmap_lookup[path]]
                 )
 
                 # check if config says columns or bool
@@ -1514,7 +1543,8 @@ def _get_param_groups(
             # If it's a fieldmap, see what entity set it's intended to correct
             if "IntendedForKey" in relational_params:
                 intended_entity_sets = sorted(
-                    [_file_to_entity_set(intention) for intention in intentions]
+                    [_file_to_entity_set(intention)
+                     for intention in intentions]
                 )
 
                 # check if config says columns or bool
@@ -1568,11 +1598,14 @@ def _get_param_groups(
         {"Counts": value_counts.to_numpy(), "ParamGroup": value_counts.index.to_numpy()}
     )
 
-    param_groups_with_counts = pd.merge(deduped, param_group_counts, on=["ParamGroup"])
+    param_groups_with_counts = pd.merge(
+        deduped, param_group_counts, on=["ParamGroup"])
 
     # Sort by counts and relabel the param groups
-    param_groups_with_counts.sort_values(by=["Counts"], inplace=True, ascending=False)
-    param_groups_with_counts["ParamGroup"] = np.arange(param_groups_with_counts.shape[0]) + 1
+    param_groups_with_counts.sort_values(
+        by=["Counts"], inplace=True, ascending=False)
+    param_groups_with_counts["ParamGroup"] = np.arange(
+        param_groups_with_counts.shape[0]) + 1
 
     # Send the new, ordered param group ids to the files list
     ordered_labeled_files = pd.merge(
@@ -1580,13 +1613,15 @@ def _get_param_groups(
     )
 
     # sort ordered_labeled_files by param group
-    ordered_labeled_files.sort_values(by=["Counts"], inplace=True, ascending=False)
+    ordered_labeled_files.sort_values(
+        by=["Counts"], inplace=True, ascending=False)
 
     # now get rid of cluster cols from deduped and df
     for col in list(ordered_labeled_files.columns):
         if col.startswith("Cluster_"):
             ordered_labeled_files = ordered_labeled_files.drop(col, axis=1)
-            param_groups_with_counts = param_groups_with_counts.drop(col, axis=1)
+            param_groups_with_counts = param_groups_with_counts.drop(
+                col, axis=1)
         if col.endswith("_x"):
             ordered_labeled_files = ordered_labeled_files.drop(col, axis=1)
 
diff --git a/cubids/metadata_merge.py b/cubids/metadata_merge.py
index 6562f35b..ddaa585f 100644
--- a/cubids/metadata_merge.py
+++ b/cubids/metadata_merge.py
@@ -57,7 +57,8 @@ def _check_sdc_cols(meta1, meta2):
         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)
@@ -298,7 +299,8 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
         file_entities = parse_file_entities(row.FilePath)
 
         if acq_group_level == "subject":
-            acq_id = (file_entities.get("subject"), file_entities.get("session"))
+            acq_id = (file_entities.get("subject"),
+                      file_entities.get("session"))
             acq_groups[acq_id].append((row.EntitySet, row.ParamGroup))
         else:
             acq_id = (file_entities.get("subject"), None)
@@ -325,7 +327,8 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
     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)
         for subject, session in contents_to_subjects[content_id]:
             grouped_sub_sess.append(
                 {"subject": "sub-" + subject, "session": session, "AcqGroup": groupnum}
@@ -333,7 +336,8 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
 
     # Write the mapping of subject/session to
     acq_group_df = pd.DataFrame(grouped_sub_sess)
-    acq_group_df.to_csv(output_prefix + "_AcqGrouping.tsv", sep="\t", index=False)
+    acq_group_df.to_csv(output_prefix + "_AcqGrouping.tsv",
+                        sep="\t", index=False)
 
     # Create data dictionary for acq group tsv
     acq_dict = get_acq_dictionary()
@@ -342,7 +346,8 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
 
     # Write the summary of acq groups to a text file
     with open(output_prefix + "_AcqGroupInfo.txt", "w") as infotxt:
-        infotxt.write("\n".join([" ".join(map(str, line)) for line in acq_group_info]))
+        infotxt.write("\n".join([" ".join(map(str, line))
+                      for line in acq_group_info]))
 
     # Create and save AcqGroupInfo data dictionary
     header_dict = {}
diff --git a/cubids/tests/test_bond.py b/cubids/tests/test_bond.py
index 28211cc2..4c2266e1 100644
--- a/cubids/tests/test_bond.py
+++ b/cubids/tests/test_bond.py
@@ -88,7 +88,8 @@ def test_ok_json_merge_cli(tmp_path):
 
     assert os.path.isfile(source_json)
     assert os.path.isfile(dest_json)
-    merge_proc = subprocess.run(["bids-sidecar-merge", str(source_json), str(dest_json)])
+    merge_proc = subprocess.run(
+        ["bids-sidecar-merge", str(source_json), str(dest_json)])
     assert merge_proc.returncode == 0
     assert not _get_json_string(dest_json) == orig_dest_json_content
 
@@ -143,7 +144,8 @@ def test_purge_no_datalad(tmp_path):
         / "sub-03_ses-phdiff_task-rest_bold.json"
     )
     scans.append(scan_name)
-    scans.append("sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz")
+    scans.append(
+        "sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz")
 
     # create and save .txt with list of scans
     purge_path = str(tmp_path / "purge_scans.txt")
@@ -276,7 +278,8 @@ def test_bad_json_merge_cli(tmp_path):
         / "sub-01_ses-phdiff_acq-HASC55AP_dwi.json"
     )
 
-    merge_proc = subprocess.run(["bids-sidecar-merge", str(invalid_source_json), str(dest_json)])
+    merge_proc = subprocess.run(
+        ["bids-sidecar-merge", str(invalid_source_json), str(dest_json)])
     assert merge_proc.returncode > 0
     assert _get_json_string(dest_json) == orig_dest_json_content
 
@@ -356,10 +359,12 @@ def test_tsv_merge_no_datalad(tmp_path):
     original_files_tsv = tsv_prefix + "_files.tsv"
 
     # give tsv with no changes (make sure it does nothing)
-    bod.apply_tsv_changes(original_summary_tsv, original_files_tsv, str(tmp_path / "unmodified"))
+    bod.apply_tsv_changes(original_summary_tsv,
+                          original_files_tsv, str(tmp_path / "unmodified"))
 
     # these will not actually be equivalent because of the auto renames
-    assert file_hash(original_summary_tsv) != file_hash(tmp_path / "unmodified_summary.tsv")
+    assert file_hash(original_summary_tsv) != file_hash(
+        tmp_path / "unmodified_summary.tsv")
 
     # Find the dwi with no FlipAngle
     summary_df = pd.read_table(original_summary_tsv)
@@ -369,28 +374,33 @@ def test_tsv_merge_no_datalad(tmp_path):
     )
     # Find the dwi with and EchoTime ==
     (complete_dwi_row,) = np.flatnonzero(
-        summary_df.EntitySet.str.fullmatch("acquisition-HASC55AP_datatype-dwi_suffix-dwi")
+        summary_df.EntitySet.str.fullmatch(
+            "acquisition-HASC55AP_datatype-dwi_suffix-dwi")
         & (summary_df.FlipAngle == 90.0)
         & (summary_df.EchoTime > 0.05)
     )
     (cant_merge_echotime_dwi_row,) = np.flatnonzero(
-        summary_df.EntitySet.str.fullmatch("acquisition-HASC55AP_datatype-dwi_suffix-dwi")
+        summary_df.EntitySet.str.fullmatch(
+            "acquisition-HASC55AP_datatype-dwi_suffix-dwi")
         & (summary_df.FlipAngle == 90.0)
         & (summary_df.EchoTime < 0.05)
     )
 
     # Set a legal MergeInto value. This effectively fills in data
     # where there was previously as missing FlipAngle
-    summary_df.loc[fa_nan_dwi_row, "MergeInto"] = summary_df.ParamGroup[complete_dwi_row]
+    summary_df.loc[fa_nan_dwi_row,
+                   "MergeInto"] = summary_df.ParamGroup[complete_dwi_row]
 
     valid_tsv_file = tsv_prefix + "_valid_summary.tsv"
     summary_df.to_csv(valid_tsv_file, sep="\t", index=False)
 
     # about to apply merges!
 
-    bod.apply_tsv_changes(valid_tsv_file, original_files_tsv, str(tmp_path / "ok_modified"))
+    bod.apply_tsv_changes(valid_tsv_file, original_files_tsv,
+                          str(tmp_path / "ok_modified"))
 
-    assert not file_hash(original_summary_tsv) == file_hash(tmp_path / "ok_modified_summary.tsv")
+    assert not file_hash(original_summary_tsv) == file_hash(
+        tmp_path / "ok_modified_summary.tsv")
 
     # Add an illegal merge to MergeInto
     summary_df.loc[cant_merge_echotime_dwi_row, "MergeInto"] = summary_df.ParamGroup[
@@ -401,7 +411,8 @@ def test_tsv_merge_no_datalad(tmp_path):
 
     with pytest.raises(Exception):
         bod.apply_tsv_changes(
-            invalid_tsv_file, str(tmp_path / "originals_files.tsv"), str(tmp_path / "ok_modified")
+            invalid_tsv_file, str(
+                tmp_path / "originals_files.tsv"), str(tmp_path / "ok_modified")
         )
 
 
@@ -419,7 +430,8 @@ def test_tsv_merge_changes(tmp_path):
     original_files_tsv = tsv_prefix + "_files.tsv"
 
     # give tsv with no changes (make sure it does nothing except rename)
-    bod.apply_tsv_changes(original_summary_tsv, original_files_tsv, str(tmp_path / "unmodified"))
+    bod.apply_tsv_changes(original_summary_tsv,
+                          original_files_tsv, str(tmp_path / "unmodified"))
     orig = pd.read_table(original_summary_tsv)
     # TEST RenameEntitySet column got populated CORRECTLY
     for row in range(len(orig)):
@@ -446,7 +458,8 @@ def test_tsv_merge_changes(tmp_path):
                     applied_f.loc[row, "KeyParamGroup"]
                 )
             else:
-                occurrences[applied_f.loc[row, "FilePath"]] = [applied_f.loc[row, "KeyParamGroup"]]
+                occurrences[applied_f.loc[row, "FilePath"]] = [
+                    applied_f.loc[row, "KeyParamGroup"]]
 
     assert len(orig) == len(applied)
 
@@ -464,7 +477,8 @@ def test_tsv_merge_changes(tmp_path):
     assert renamed
 
     # will no longer be equal because of auto rename!
-    assert file_hash(original_summary_tsv) != file_hash(tmp_path / "unmodified_summary.tsv")
+    assert file_hash(original_summary_tsv) != file_hash(
+        tmp_path / "unmodified_summary.tsv")
 
     # Find the dwi with no FlipAngle
     summary_df = pd.read_table(original_summary_tsv)
@@ -474,27 +488,32 @@ def test_tsv_merge_changes(tmp_path):
     )
     # Find the dwi with and EchoTime ==
     (complete_dwi_row,) = np.flatnonzero(
-        summary_df.EntitySet.str.fullmatch("acquisition-HASC55AP_datatype-dwi_suffix-dwi")
+        summary_df.EntitySet.str.fullmatch(
+            "acquisition-HASC55AP_datatype-dwi_suffix-dwi")
         & (summary_df.FlipAngle == 90.0)
         & (summary_df.EchoTime > 0.05)
     )
     (cant_merge_echotime_dwi_row,) = np.flatnonzero(
-        summary_df.EntitySet.str.fullmatch("acquisition-HASC55AP_datatype-dwi_suffix-dwi")
+        summary_df.EntitySet.str.fullmatch(
+            "acquisition-HASC55AP_datatype-dwi_suffix-dwi")
         & (summary_df.FlipAngle == 90.0)
         & (summary_df.EchoTime < 0.05)
     )
 
     # Set a legal MergeInto value. This effectively fills in data
     # where there was previously as missing FlipAngle
-    summary_df.loc[fa_nan_dwi_row, "MergeInto"] = summary_df.ParamGroup[complete_dwi_row]
+    summary_df.loc[fa_nan_dwi_row,
+                   "MergeInto"] = summary_df.ParamGroup[complete_dwi_row]
 
     valid_tsv_file = tsv_prefix + "_valid_summary.tsv"
     summary_df.to_csv(valid_tsv_file, sep="\t", index=False)
 
     # about to merge
-    bod.apply_tsv_changes(valid_tsv_file, original_files_tsv, str(tmp_path / "ok_modified"))
+    bod.apply_tsv_changes(valid_tsv_file, original_files_tsv,
+                          str(tmp_path / "ok_modified"))
 
-    assert not file_hash(original_summary_tsv) == file_hash(tmp_path / "ok_modified_summary.tsv")
+    assert not file_hash(original_summary_tsv) == file_hash(
+        tmp_path / "ok_modified_summary.tsv")
 
     # Add an illegal merge to MergeInto
     summary_df.loc[cant_merge_echotime_dwi_row, "MergeInto"] = summary_df.ParamGroup[
@@ -505,7 +524,8 @@ def test_tsv_merge_changes(tmp_path):
 
     with pytest.raises(Exception):
         bod.apply_tsv_changes(
-            invalid_tsv_file, str(tmp_path / "originals_files.tsv"), str(tmp_path / "ok_modified")
+            invalid_tsv_file, str(
+                tmp_path / "originals_files.tsv"), str(tmp_path / "ok_modified")
         )
 
     # Make sure MergeInto == 0 deletes the param group and all associations
@@ -689,7 +709,8 @@ def test_tsv_creation(tmp_path):
         # if entity sets in rows i and i+1 are the same
         if isummary_df.iloc[i]["EntitySet"] == isummary_df.iloc[i + 1]["EntitySet"]:
             # param group i = param group i+1
-            assert isummary_df.iloc[i]["ParamGroup"] == isummary_df.iloc[i + 1]["ParamGroup"] - 1
+            assert isummary_df.iloc[i]["ParamGroup"] == isummary_df.iloc[i +
+                                                                         1]["ParamGroup"] - 1
             # and count i < count i + 1
             assert isummary_df.iloc[i]["Counts"] >= isummary_df.iloc[i + 1]["Counts"]
 
@@ -801,11 +822,13 @@ def test_apply_tsv_changes(tmp_path):
 
     for f in deleted_f:
         assert Path(str(data_root / "complete") + f).exists()
-        assert Path(str(data_root / "complete") + f.replace("nii.gz", "json")).exists()
+        assert Path(str(data_root / "complete") +
+                    f.replace("nii.gz", "json")).exists()
 
     # apply deletion
     complete_cubids.apply_tsv_changes(
-        mod2_path, str(tmp_path / "modified2_files.tsv"), str(tmp_path / "deleted")
+        mod2_path, str(
+            tmp_path / "modified2_files.tsv"), str(tmp_path / "deleted")
     )
 
     # make sure deleted_keyparam gone from files_tsv
@@ -838,7 +861,8 @@ def test_session_apply(tmp_path):
 
     data_root = get_data(tmp_path)
 
-    ses_cubids = CuBIDS(data_root / "inconsistent", acq_group_level="session", use_datalad=True)
+    ses_cubids = CuBIDS(data_root / "inconsistent",
+                        acq_group_level="session", use_datalad=True)
 
     ses_cubids.get_tsvs(str(tmp_path / "originals"))
 
@@ -1039,7 +1063,8 @@ def test_docker():
     """
     try:
         return_status = 1
-        ret = subprocess.run(["docker", "version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        ret = subprocess.run(["docker", "version"],
+                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     except OSError as e:
         from errno import ENOENT
 
diff --git a/cubids/tests/test_cli.py b/cubids/tests/test_cli.py
index a0e9066a..78e15501 100644
--- a/cubids/tests/test_cli.py
+++ b/cubids/tests/test_cli.py
@@ -14,9 +14,10 @@
 """
 
 import argparse
+
 import pytest
 
-from cubids.cli import _path_exists, _is_file, _get_parser, _main
+from cubids.cli import _get_parser, _is_file, _main, _path_exists
 
 
 def _test_path_exists():
@@ -27,7 +28,8 @@ def _test_path_exists():
     It asserts that the function returns the expected path when the path exists,
     and raises an `argparse.ArgumentTypeError` when the path does not exist.
     """
-    assert _path_exists("/path/to/existing/file", None) == "/path/to/existing/file"
+    assert _path_exists("/path/to/existing/file",
+                        None) == "/path/to/existing/file"
 
     with pytest.raises(argparse.ArgumentTypeError):
         _path_exists("/path/to/nonexistent/file", None)
diff --git a/cubids/tests/test_cubids.py b/cubids/tests/test_cubids.py
index 6ab847fd..ca70d21a 100644
--- a/cubids/tests/test_cubids.py
+++ b/cubids/tests/test_cubids.py
@@ -74,7 +74,8 @@ def _test_copy_exemplars(cubids_instance):
     exemplars_dir = "/path/to/exemplars"
     exemplars_tsv = "/path/to/exemplars.tsv"
     min_group_size = 2
-    cubids_instance.copy_exemplars(exemplars_dir, exemplars_tsv, min_group_size)
+    cubids_instance.copy_exemplars(
+        exemplars_dir, exemplars_tsv, min_group_size)
     # Add assertions here
 
 
@@ -204,8 +205,10 @@ def _test__get_intended_for_reference(cubids_instance):
 
 
 def _test__get_param_groups(cubids_instance):
-    files = ["sub-01_ses-01_task-rest_bold.nii.gz", "sub-02_ses-01_task-rest_bold.nii.gz"]
-    fieldmap_lookup = {"sub-01_ses-01_task-rest_bold.nii.gz": "fieldmap.nii.gz"}
+    files = ["sub-01_ses-01_task-rest_bold.nii.gz",
+             "sub-02_ses-01_task-rest_bold.nii.gz"]
+    fieldmap_lookup = {
+        "sub-01_ses-01_task-rest_bold.nii.gz": "fieldmap.nii.gz"}
     entity_set_name = "group-01"
     grouping_config = {"group-01": {"modality": "bold"}}
     modality = "bold"
@@ -220,7 +223,8 @@ def _test_round_params(cubids_instance):
     param_group_df = pd.DataFrame({"param": [0.123456789]})
     config = {"param": {"round": 3}}
     modality = "bold"
-    rounded_params = cubids_instance.round_params(param_group_df, config, modality)
+    rounded_params = cubids_instance.round_params(
+        param_group_df, config, modality)
     # Add assertions here
 
 
@@ -234,7 +238,8 @@ def _test_format_params(cubids_instance):
     param_group_df = pd.DataFrame({"param": [0.123456789]})
     config = {"param": {"format": "{:.2f}"}}
     modality = "bold"
-    formatted_params = cubids_instance.format_params(param_group_df, config, modality)
+    formatted_params = cubids_instance.format_params(
+        param_group_df, config, modality)
     # Add assertions here
 
 
diff --git a/cubids/tests/utils.py b/cubids/tests/utils.py
index c64da372..9bf6bda1 100644
--- a/cubids/tests/utils.py
+++ b/cubids/tests/utils.py
@@ -27,7 +27,8 @@ def _remove_a_json(json_file):
 
 def _edit_a_nifti(nifti_file):
     img = nb.load(nifti_file)
-    new_img = nb.Nifti1Image(np.random.rand(*img.shape), affine=img.affine, header=img.header)
+    new_img = nb.Nifti1Image(np.random.rand(
+        *img.shape), affine=img.affine, header=img.header)
     new_img.to_filename(nifti_file)
 
 
@@ -76,7 +77,8 @@ def _add_ext_files(img_path):
     if "/dwi/" in img_path:
         # add bval and bvec
         for ext in dwi_exts:
-            dwi_ext_file = img_path.replace(".nii.gz", "").replace(".nii", "") + ext
+            dwi_ext_file = img_path.replace(
+                ".nii.gz", "").replace(".nii", "") + ext
             Path(dwi_ext_file).touch()
     if "bold" in img_path:
         no_suffix = img_path.rpartition("_")[0]
diff --git a/cubids/validator.py b/cubids/validator.py
index fe0e08ef..bb721212 100644
--- a/cubids/validator.py
+++ b/cubids/validator.py
@@ -5,8 +5,8 @@
 import logging
 import os
 import pathlib
-import subprocess
 import re
+import subprocess
 
 import pandas as pd
 
@@ -17,7 +17,8 @@ def build_validator_call(path, ignore_headers=False):
     """Build a subprocess command to the bids validator."""
     # New schema BIDS validator doesn't have option to ignore subject consistency.
     # Build the deno command to run the BIDS validator.
-    command = ["deno", "run", "-A", "jsr:@bids/validator", path, "--verbose", "--json"]
+    command = ["deno", "run", "-A", "jsr:@bids/validator",
+               path, "--verbose", "--json"]
 
     if ignore_headers:
         command.append("--ignoreNiftiHeaders")
@@ -34,10 +35,12 @@ def get_bids_validator_version():
         Version of the BIDS validator.
     """
     command = ["deno", "run", "-A", "jsr:@bids/validator", "--version"]
-    result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    result = subprocess.run(
+        command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
     output = result.stdout.decode("utf-8").strip()
     version = output.split()[-1]
-    clean_ver = re.sub(r'\x1b\[[0-9;]*m', '', version)  # Remove ANSI color codes
+    # Remove ANSI color codes
+    clean_ver = re.sub(r"\x1b\[[0-9;]*m", "", version)
     return {"ValidatorVersion": clean_ver}
 
 
@@ -54,7 +57,8 @@ def build_subject_paths(bids_dir):
     subjects = glob.glob(bids_dir)
 
     if len(subjects) < 1:
-        raise ValueError("Couldn't find any subjects in the specified directory:\n" + bids_dir)
+        raise ValueError(
+            "Couldn't find any subjects in the specified directory:\n" + bids_dir)
 
     subjects_dict = {}
 
@@ -62,7 +66,8 @@ def build_subject_paths(bids_dir):
         purepath = pathlib.PurePath(sub)
         sub_label = purepath.name
 
-        files = [x for x in glob.glob(sub + "**", recursive=True) if os.path.isfile(x)]
+        files = [x for x in glob.glob(
+            sub + "**", recursive=True) if os.path.isfile(x)]
         files.extend(root_files)
         subjects_dict[sub_label] = files
 
@@ -82,7 +87,8 @@ def build_first_subject_path(bids_dir, subject):
     purepath = pathlib.PurePath(subject)
     sub_label = purepath.name
 
-    files = [x for x in glob.glob(subject + "**", recursive=True) if os.path.isfile(x)]
+    files = [x for x in glob.glob(
+        subject + "**", recursive=True) if os.path.isfile(x)]
     files.extend(root_files)
     subject_dict[sub_label] = files
 
@@ -153,8 +159,9 @@ def parse_issue(issue_dict):
     issues = data.get("issues", {}).get("issues", [])
     if not issues:
         return pd.DataFrame(
-            columns=["location", "code", "issueMessage", "subCode", "severity", "rule"]
-            )
+            columns=["location", "code", "issueMessage",
+                     "subCode", "severity", "rule"]
+        )
 
     # Parse all issues
     parsed_issues = [parse_issue(issue) for issue in issues]
@@ -229,7 +236,7 @@ def update_dataset_description(path, new_info):
 
     # Write the updated data back to the file
     with open(description_path, "w") as f:
-        json.dump(existing_data, f, indent=4) 
+        json.dump(existing_data, f, indent=4)
     print(f"Updated dataset_description.json at: {description_path}")
 
     # Check if .datalad directory exists before running the DataLad save command
@@ -237,10 +244,14 @@ def update_dataset_description(path, new_info):
     if os.path.exists(datalad_dir) and os.path.isdir(datalad_dir):
         try:
             subprocess.run(
-                ["datalad", "save", "-m",
-                 "Save BIDS validator and schema version to dataset_description",
-                 description_path],
-                check=True
+                [
+                    "datalad",
+                    "save",
+                    "-m",
+                    "Save BIDS validator and schema version to dataset_description",
+                    description_path,
+                ],
+                check=True,
             )
             print("Changes saved with DataLad.")
         except subprocess.CalledProcessError as e:
@@ -263,11 +274,11 @@ def bids_validator_version(output, path, write=False):
     validator_version = get_bids_validator_version()
     # Extract schemaVersion
     summary_info = extract_summary_info(output)
-    
+
     combined_info = {**validator_version, **summary_info}
 
     if write:
-        # Update the dataset_description.json file 
+        # Update the dataset_description.json file
         update_dataset_description(path, combined_info)
     elif not write:
-        print(combined_info)
\ No newline at end of file
+        print(combined_info)
diff --git a/cubids/workflows.py b/cubids/workflows.py
index 69bed501..a28b61a3 100644
--- a/cubids/workflows.py
+++ b/cubids/workflows.py
@@ -17,13 +17,13 @@
 from cubids.metadata_merge import merge_json_into_json
 from cubids.utils import _get_container_type
 from cubids.validator import (
+    bids_validator_version,
+    build_first_subject_path,
     build_subject_paths,
     build_validator_call,
     get_val_dictionary,
     parse_validator_output,
     run_validator,
-    build_first_subject_path,
-    bids_validator_version,
 )
 
 warnings.simplefilter(action="ignore", category=FutureWarning)
@@ -82,7 +82,8 @@ def validate(
             # parse the string output
             parsed = parse_validator_output(ret.stdout.decode("UTF-8"))
             if parsed.shape[1] < 1:
-                logger.info("No issues/warnings parsed, your dataset is BIDS valid.")
+                logger.info(
+                    "No issues/warnings parsed, your dataset is BIDS valid.")
                 sys.exit(0)
             else:
                 logger.info("BIDS issues/warnings found in the dataset")
@@ -129,7 +130,8 @@ def validate(
                 subjects_dict = {
                     k: v for k, v in subjects_dict.items() if k in sequential_subjects
                 }
-            assert len(list(subjects_dict.keys())) > 1, "No subjects found in filter"
+            assert len(list(subjects_dict.keys())
+                       ) > 1, "No subjects found in filter"
             for subject, files_list in tqdm.tqdm(subjects_dict.items()):
                 # logger.info(" ".join(["Processing subject:", subject]))
                 # create a temporary directory and symlink the data
@@ -158,7 +160,8 @@ def validate(
                     ret = run_validator(call)
                     # parse output
                     if ret.returncode != 0:
-                        logger.error("Errors returned from validator run, parsing now")
+                        logger.error(
+                            "Errors returned from validator run, parsing now")
 
                     # parse the output and add to list if it returns a df
                     decoded = ret.stdout.decode("UTF-8")
@@ -169,7 +172,8 @@ def validate(
 
             # concatenate the parsed data and exit
             if len(parsed) < 1:
-                logger.info("No issues/warnings parsed, your dataset is BIDS valid.")
+                logger.info(
+                    "No issues/warnings parsed, your dataset is BIDS valid.")
                 sys.exit(0)
 
             else:
@@ -260,10 +264,7 @@ def validate(
     sys.exit(proc.returncode)
 
 
-def bids_version(
-    bids_dir,
-    write=False
-):
+def bids_version(bids_dir, write=False):
     """Get BIDS validator and schema version.
 
     Parameters
@@ -284,13 +285,14 @@ def bids_version(
             if os.path.isdir(os.path.join(bids_dir, name)) and name.startswith("sub-")
         ]
         if not sub_folders:
-            raise ValueError("No folders starting with 'sub-' found. Please provide a valid BIDS.")     
+            raise ValueError(
+                "No folders starting with 'sub-' found. Please provide a valid BIDS.")
         subject = sub_folders[0]
     except FileNotFoundError:
         raise FileNotFoundError(f"The directory {bids_dir} does not exist.")
     except ValueError as ve:
         raise ve
-    
+
     # build a dictionary with {SubjectLabel: [List of files]}
     # run first subject only
     subject_dict = build_first_subject_path(bids_dir, subject)
@@ -329,7 +331,8 @@ def bids_version(
 
 def bids_sidecar_merge(from_json, to_json):
     """Merge critical keys from one sidecar to another."""
-    merge_status = merge_json_into_json(from_json, to_json, raise_on_error=False)
+    merge_status = merge_json_into_json(
+        from_json, to_json, raise_on_error=False)
     sys.exit(merge_status)
 
 
@@ -368,7 +371,8 @@ def group(bids_dir, container, acq_group_level, config, output_prefix):
 
     apply_config = config is not None
     if apply_config:
-        input_config_dir_link = str(config.parent.absolute()) + ":/in_config:ro"
+        input_config_dir_link = str(
+            config.parent.absolute()) + ":/in_config:ro"
         linked_input_config = "/in_config/" + config.name
 
     linked_output_prefix = "/tsv/" + output_prefix.name
@@ -475,14 +479,18 @@ def apply(
     # Run it through a container
     container_type = _get_container_type(container)
     bids_dir_link = str(bids_dir.absolute()) + ":/bids"
-    input_summary_tsv_dir_link = str(edited_summary_tsv.parent.absolute()) + ":/in_summary_tsv:ro"
-    input_files_tsv_dir_link = str(edited_summary_tsv.parent.absolute()) + ":/in_files_tsv:ro"
-    output_tsv_dir_link = str(new_tsv_prefix.parent.absolute()) + ":/out_tsv:rw"
+    input_summary_tsv_dir_link = str(
+        edited_summary_tsv.parent.absolute()) + ":/in_summary_tsv:ro"
+    input_files_tsv_dir_link = str(
+        edited_summary_tsv.parent.absolute()) + ":/in_files_tsv:ro"
+    output_tsv_dir_link = str(
+        new_tsv_prefix.parent.absolute()) + ":/out_tsv:rw"
 
     # FROM BOND-GROUP
     apply_config = config is not None
     if apply_config:
-        input_config_dir_link = str(config.parent.absolute()) + ":/in_config:ro"
+        input_config_dir_link = str(
+            config.parent.absolute()) + ":/in_config:ro"
         linked_input_config = "/in_config/" + config.name
 
     linked_output_prefix = "/tsv/" + new_tsv_prefix.name