fix lint issues

cubids/config.py

@@ -4,6 +4,7 @@
 import importlib.resources
 import yaml
 
+
 def load_config(config_file):
     """Load a YAML file containing a configuration for param groups.
 

cubids/cubids.py

@@ -113,7 +113,7 @@ def __init__(
         self.cubids_code_dir = Path(self.path + "/code/CuBIDS").is_dir()
         self.data_dict = {}  # data dictionary for TSV outputs
         self.use_datalad = use_datalad  # True if flag set, False if flag unset
-        self.is_longitudinal = is_longitudinal # True if flag set, False if flag unset
+        self.is_longitudinal = is_longitudinal  # True if flag set, False if flag unset
         if self.use_datalad:
             self.init_datalad()
 
@@ -479,7 +479,7 @@ def change_filename(self, filepath, entities, is_longitudinal=False):
             filepath=filepath,
             entities=entities,
             out_dir=str(self.path),
-            is_longitudinal=self.is_longitudinal
+            is_longitudinal=self.is_longitudinal,
         )
 
         exts = Path(filepath).suffixes
@@ -606,7 +606,7 @@ def change_filename(self, filepath, entities, is_longitudinal=False):
                 # Coerce IntendedFor to a list.
                 data["IntendedFor"] = listify(data["IntendedFor"])
                 for item in data["IntendedFor"]:
-                    if item == _get_participant_relative_path(filepath):                       
+                    if item == _get_participant_relative_path(filepath):
                         # remove old filename
                         data["IntendedFor"].remove(item)
                         # add new filename
@@ -1419,12 +1419,12 @@ def _get_participant_relative_path(scan):
     ...    "/path/to/dset/sub-01/ses-01/func/sub-01_ses-01_bold.nii.gz",
     ... )
     'ses-01/func/sub-01_ses-01_bold.nii.gz'
-    
+
     >>> _get_participant_relative_path(
     ...    "/path/to/dset/sub-01/func/sub-01_bold.nii.gz",
     ... )
     'func/sub-01_bold.nii.gz'
-    
+
     >>> _get_participant_relative_path(
     ...    "/path/to/dset/ses-01/func/ses-01_bold.nii.gz",
     ... )
@@ -1435,7 +1435,7 @@ def _get_participant_relative_path(scan):
     # Find the first part that starts with "sub-"
     for i, part in enumerate(parts):
         if part.startswith("sub-"):
-            return "/".join(parts[i+1:])
+            return "/".join(parts[i + 1 :])
     raise ValueError(f"Could not find subject in {scan}")
 
 

cubids/metadata_merge.py

@@ -304,7 +304,7 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level, is_long
             if is_longitudinal:
                 acq_id = (file_entities.get("subject"), file_entities.get("session"))
             elif not is_longitudinal:
-                acq_id = (file_entities.get("subject"))
+                acq_id = file_entities.get("subject")
             acq_groups[acq_id].append((row.EntitySet, row.ParamGroup))
         elif is_longitudinal and acq_group_level == "session":
             acq_id = (file_entities.get("subject"), None)
@@ -339,9 +339,7 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level, is_long
                 )
         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

@@ -239,28 +239,28 @@ def summary_data():
 @pytest.mark.parametrize(
     ("name", "skeleton", "intended_for", "is_longitudinal", "expected"),
     [
-        (   # doesn't have acq-VAR
+        (  # doesn't have acq-VAR
             "relpath_long",
             relpath_intendedfor_long,
             "ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
             True,
             "pass",
         ),
-        (   # doesn't have ses-01
+        (  # doesn't have ses-01
             "bidsuri_long",
             bidsuri_intendedfor_long,
             "bids::sub-01/ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
-            True,       
+            True,
             "pass",
         ),
-        (   # doesn't have acq-VAR
+        (  # doesn't have acq-VAR
             "relpath_cs",
             relpath_intendedfor_cs,
             "dwi/sub-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
             False,
             "pass",
         ),
-        (   # pass
+        (  # pass
             "bidsuri_cs",
             bidsuri_intendedfor_cs,
             "bids::sub-01/dwi/sub-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
@@ -358,4 +358,4 @@ def test_cubids_apply_intendedfor(
                 new_tsv_prefix=None,
                 container=None,
                 is_longitudinal=is_longitudinal,
-            )
+            )

cubids/tests/test_bond.py

@@ -946,8 +946,12 @@ 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, is_longitudinal=True)
+    ses_cubids = CuBIDS(
+        data_root / "inconsistent",
+        acq_group_level="session",
+        use_datalad=True,
+        is_longitudinal=True,
+    )
 
     ses_cubids.get_tsvs(str(tmp_path / "originals"))
 
@@ -1194,32 +1198,6 @@ def test_bids_version(tmp_path):
     ), f"Schema version {schema_version} is less than minimum {min_schema_version}"
 
 
-<<<<<<< HEAD
-def test_docker():
-    """Verify that docker is installed and the user has permission to run docker images.
-
-    Returns
-    -------
-    int
-        -1 if Docker can't be found.
-         0 if Docker is found, but the user can't connect to the daemon.
-         1 if the test run is OK.
-    """
-    try:
-        return_status = 1
-        ret = subprocess.run(["docker", "version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    except OSError as e:
-        from errno import ENOENT
-
-        if e.errno == ENOENT:
-            print("Cannot find Docker engine!")
-            return_status = 0
-        raise e
-    if ret.stderr.startswith(b"Cannot connect to the Docker daemon."):
-        print("Cannot connect to Docker daemon!")
-        return_status = 0
-    assert return_status
-
 # def test_image(image='pennlinc/bond:latest'):
 #     """Check whether image is present on local system."""
 #     ret = subprocess.run(['docker', 'images', '-q', image],