[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

datashuttle/command_line_interface.py

@@ -412,7 +412,6 @@ def show_next_ses_number(project: DataShuttle, args: Any) -> None:
 
 
 def check_name_formatting(project: DataShuttle, args: Any) -> None:
-
     kwargs = make_kwargs(args)
 
     run_command(
@@ -427,7 +426,6 @@ def check_name_formatting(project: DataShuttle, args: Any) -> None:
 
 
 def supply_config_file(project: DataShuttle, args: Any) -> None:
-
     kwargs = make_kwargs(args)
 
     run_command(

datashuttle/configs/canonical_configs.py

@@ -205,7 +205,6 @@ def check_config_types(config_dict: Configs) -> None:
     fail = False
 
     for key in config_dict.keys():
-
         expected_type = required_types[key]
 
         if get_origin(expected_type) is Literal:

datashuttle/configs/load_configs.py

@@ -50,7 +50,6 @@ def make_config_file_attempt_load(
         new_cfg.load_from_file()
 
     except BaseException:
-
         new_cfg = None
 
         utils.log_and_raise_error(
@@ -144,7 +143,6 @@ def handle_bool(key: str, value: ConfigValueTypes) -> ConfigValueTypes:
     here. This assumes bool are always passed as flags.
     """
     if key in canonical_configs.get_flags():
-
         if value in ["None", "none", None]:
             value = False
 

datashuttle/datashuttle.py

@@ -75,7 +75,6 @@ class DataShuttle:
     """
 
     def __init__(self, project_name: str, print_startup_message: bool = True):
-
         if " " in project_name:
             utils.log_and_raise_error(
                 "'project_name' must not include spaces."

datashuttle/utils/data_transfer.py

@@ -17,7 +17,6 @@ def __init__(
         dry_run: bool,
         log: bool,
     ):
-
         self.cfg = cfg
         self.upload_or_download = upload_or_download
         self.local_or_central = (
@@ -34,7 +33,6 @@ def __init__(
         include_list = self.build_a_list_of_all_files_and_folders_to_transfer()
 
         if any(include_list):
-
             output = rclone.transfer_data(
                 cfg,
                 upload_or_download,
@@ -62,7 +60,6 @@ def build_a_list_of_all_files_and_folders_to_transfer(self) -> List[str]:
         extra_filenames: List[str] = []
 
         for sub in processed_sub_names:
-
             # subjects at top level folder ---------------------------------------
 
             if sub == "all_non_sub":
@@ -82,7 +79,6 @@ def build_a_list_of_all_files_and_folders_to_transfer(self) -> List[str]:
             processed_ses_names = self.get_processed_names(self.ses_names, sub)
 
             for ses in processed_ses_names:
-
                 if ses == "all_non_ses":
                     self.update_list_with_non_ses_sub_level_folders(
                         extra_folder_names, extra_filenames, sub
@@ -177,7 +173,6 @@ def update_list_with_non_ses_sub_level_folders(
     def update_list_with_non_dtype_ses_level_folders(
         self, extra_folder_names, extra_filenames, sub, ses
     ):
-
         (
             ses_level_folders,
             ses_level_filenames,
@@ -228,7 +223,6 @@ def update_list_with_dtype_paths(
         level = "ses" if ses else "sub"
 
         for data_type_key, data_type_folder in data_type_items:  # type: ignore
-
             if data_type_folder.level == level:
                 if ses:
                     filepath = Path(sub) / ses / data_type_folder.name

datashuttle/utils/decorators.py

@@ -35,7 +35,6 @@ def check_configs_set(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-
         if args[0].cfg is None:
             log_and_raise_error(
                 "Must set configs with make_config_file() "

datashuttle/utils/folders.py

@@ -52,7 +52,6 @@ def make_folder_trees(
         formatting.check_data_type_is_valid(cfg, data_type, error_on_fail=True)
 
     for sub in sub_names:
-
         sub_path = cfg.make_path(
             "local",
             sub,
@@ -64,7 +63,6 @@ def make_folder_trees(
             make_data_type_folders(cfg, data_type, sub_path, "sub")
 
         for ses in ses_names:
-
             ses_path = cfg.make_path(
                 "local",
                 [sub, ses],
@@ -108,7 +106,6 @@ def make_data_type_folders(
     data_type_items = cfg.get_data_type_items(data_type)
 
     for data_type_key, data_type_folder in data_type_items:  # type: ignore
-
         if data_type_folder.used and data_type_folder.level == level:
             data_type_path = sub_or_ses_level_path / data_type_folder.name
 
@@ -137,7 +134,6 @@ def make_folders(paths: Union[Path, List[Path]], log: bool = True) -> None:
         paths = [paths]
 
     for path_ in paths:
-
         if not path_.is_dir():
             path_.mkdir(parents=True)
             if log:
@@ -223,7 +219,6 @@ def check_no_duplicate_sub_ses_key_values(
                 "ses",
                 return_as_int=True,
             ):
-
                 if new_ses in existing_ses_values:
                     utils.log_and_raise_error(
                         f"Cannot make folders. "
@@ -446,14 +441,12 @@ def search_for_folders(  # TODO: change name
     search_prefix : file / folder name to search (e.g. "sub-*")
     """
     if local_or_central == "central" and cfg["connection_method"] == "ssh":
-
         all_folder_names, all_filenames = ssh.search_ssh_central_for_folders(
             search_path,
             search_prefix,
             cfg,
         )
     else:
-
         if not search_path.exists():
             utils.log_and_message(f"No file found at {search_path.as_posix()}")
             return [], []

datashuttle/utils/formatting.py

@@ -112,9 +112,7 @@ def update_names_with_range_to_flag(
     new_names = []
 
     for i, name in enumerate(names):
-
         if tags("to") in name:
-
             check_name_is_formatted_correctly(name, prefix)
 
             prefix_tag = re.search(f"{prefix}-[0-9]+{tags('to')}[0-9]+", name)[0]  # type: ignore
@@ -224,7 +222,6 @@ def update_names_with_datetime(names: List[str]) -> None:
     format_time = f"time-{time_}"
 
     for i, name in enumerate(names):
-
         if tags("datetime") in name:  # must come first
             name = add_underscore_before_after_if_not_there(
                 name, tags("datetime")
@@ -320,7 +317,6 @@ def check_data_type_is_valid(
 def check_dashes_and_underscore_alternate_correctly(all_names):
     """ """
     for name in all_names:
-
         if name in RESERVED_KEYWORDS:
             continue
 

datashuttle/utils/rclone.py

@@ -64,7 +64,6 @@ def setup_central_as_rclone_target(
         call_rclone(f"config create {rclone_config_name} local", pipe_std=True)
 
     elif connection_method == "ssh":
-
         call_rclone(
             f"config create "
             f"{rclone_config_name} "
@@ -124,15 +123,13 @@ def transfer_data(
     )  # TODO: fix this is not a list
 
     if upload_or_download == "upload":
-
         output = call_rclone(
             f"{rclone_args('copy')} "
             f'"{local_filepath}" "{cfg.get_rclone_config_name()}:{central_filepath}" {extra_arguments}',
             pipe_std=True,
         )
 
     elif upload_or_download == "download":
-
         output = call_rclone(
             f"{rclone_args('copy')} "
             f'"{cfg.get_rclone_config_name()}:{central_filepath}" "{local_filepath}"  {extra_arguments}',

datashuttle/utils/ssh.py

@@ -113,7 +113,6 @@ def add_public_key_to_central_authorized_keys(
     """
     client: paramiko.SSHClient
     with paramiko.SSHClient() as client:
-
         connect_client(client, cfg, password=password)
 
         client.exec_command("mkdir -p ~/.ssh/")
@@ -227,7 +226,6 @@ def get_list_of_folder_names_over_sftp(
     all_filenames = []
     try:
         for file_or_folder in sftp.listdir_attr(search_path.as_posix()):
-
             if fnmatch.fnmatch(file_or_folder.filename, search_prefix):
                 if stat.S_ISDIR(file_or_folder.st_mode):
                     all_folder_names.append(file_or_folder.filename)

datashuttle/utils/utils.py

@@ -158,7 +158,6 @@ def get_values_from_bids_formatted_name(
     """
     all_values = []
     for name in all_names:
-
         if key not in name:
             raise_error(f"The key {key} is not found in {name}")
 
@@ -209,7 +208,6 @@ def unpack_nested_list(main_list):
 
 
 def integers_are_consecutive(list_of_ints: List[int]) -> bool:
-
     diff_between_ints = diff(list_of_ints)
     return all([diff == 1 for diff in diff_between_ints])
 

tests/test_utils.py

@@ -284,17 +284,14 @@ def check_folder_tree_is_correct(
     as this doesn't explicitly test this.
     """
     for sub in subs:
-
         path_to_sub_folder = join(base_folder, sub)
         check_and_cd_folder(path_to_sub_folder)
 
         for ses in sessions:
-
             path_to_ses_folder = join(base_folder, sub, ses)
             check_and_cd_folder(path_to_ses_folder)
 
             for key, folder in project.cfg.data_type_folders.items():
-
                 assert key in folder_used.keys(), (
                     "Key not found in folder_used. "
                     "Update folder used and hard-coded tests: "
@@ -304,7 +301,6 @@ def check_folder_tree_is_correct(
                 if check_folder_is_used(
                     base_folder, folder, folder_used, key, sub, ses
                 ):
-
                     if folder.level == "sub":
                         data_type_path = join(path_to_sub_folder, folder.name)
                     elif folder.level == "ses":
@@ -369,7 +365,6 @@ def check_data_type_sub_ses_uploaded_correctly(
 
         # Check ses are all uploaded + histology if transferred
         if ses_to_upload:
-
             for sub in subs_to_upload:
                 ses_names = glob_basenames(
                     join(
@@ -477,7 +472,6 @@ def check_project_configs(
     Paths are stored as pathlib in the cfg but str in the .yaml
     """
     for arg_name, value in kwargs[0].items():
-
         if arg_name in project.cfg.keys_str_on_file_but_path_in_class:
             assert type(project.cfg[arg_name]) in [
                 pathlib.PosixPath,
@@ -502,6 +496,7 @@ def check_config_file(config_path, *kwargs):
 # Test Helpers
 # -----------------------------------------------------------------------------
 
+
 # TODO: rename this 'top level folder path'
 def get_top_level_folder_path(
     project, local_or_central="local", folder_name="rawdata"
@@ -534,7 +529,6 @@ def handle_upload_or_download(
     local machine to central, but using the download function).
     """
     if upload_or_download == "download":
-
         central_path = swap_local_and_central_paths(
             project, swap_last_folder_only
         )

tests/tests_integration/test_command_line_interface.py

@@ -172,7 +172,6 @@ def test_make_config_file_non_default_variables(self, tmp_path):
 
     @pytest.mark.parametrize("sep", ["-", "_"])
     def test_make_sub_folders_variable(self, sep):
-
         stdout, _ = test_utils.run_cli(
             f" make{sep}sub{sep}folders "
             f"--data_type all "
@@ -335,7 +334,6 @@ def test_update_config(self, clean_project_name, sep, tmp_path):
         test_utils.move_some_keys_to_end_of_dict(not_set_configs)
 
         for key, value in not_set_configs.items():
-
             format_value = (
                 test_utils.add_quotes(value) if "path" in key else value
             )
@@ -624,9 +622,7 @@ def convert_kwargs_to_cli(self, kwargs, sep="-"):
 
         kwargs_list = []
         for key, value in kwargs.items():
-
             if key not in positionals:
-
                 if "path" in key:
                     value = test_utils.add_quotes(value)
                 else:
@@ -646,13 +642,11 @@ def convert_kwargs_to_cli(self, kwargs, sep="-"):
         return prepend_positionals + kwargs_list
 
     def check_kwargs(self, required_options, kwargs_):
-
         for key in required_options.keys():
             assert kwargs_.pop(key) == required_options[key]
         assert kwargs_ == {}
 
     def check_upload_download_args(self, args_, kwargs_, dry_run_is):
-
         assert kwargs_["data_type"] == ["all"]
         assert kwargs_["sub_names"] == ["one"]
         assert kwargs_["ses_names"] == ["two"]

tests/tests_integration/test_configs.py

@@ -213,7 +213,6 @@ def test_update_config(self, project, tmp_path):
     # -------------------------------------------------------------
 
     def test_supplied_config_file_bad_path(self, setup_project):
-
         # Test path supplied that doesn't exist
 
         non_existant_path = setup_project._datashuttle_path / "fake.file"
@@ -248,7 +247,6 @@ def test_supplied_config_file_missing_key(self, setup_project, tmp_path):
         test_utils.dump_config(missing_key_configs, bad_configs_path)
 
         with pytest.raises(BaseException) as e:
-
             setup_project.supply_config_file(bad_configs_path, warn=False)
 
         assert (
@@ -281,7 +279,6 @@ def test_supplied_config_file_bad_types(self, setup_project, tmp_path):
         bad_configs_path = setup_project._datashuttle_path / "bad_config.yaml"
 
         for key in setup_project.cfg.keys():
-
             if key in setup_project.cfg.keys_str_on_file_but_path_in_class:
                 continue
 
@@ -320,7 +317,6 @@ def test_supplied_config_file_bad_types(self, setup_project, tmp_path):
     def test_supplied_config_file_changes_wrong_order(
         self, setup_project, tmp_path
     ):
-
         bad_order_configs_path = (
             setup_project._datashuttle_path / "new_configs.yaml"
         )

tests/tests_integration/test_filesystem_transfer.py

@@ -313,9 +313,7 @@ def test_transfer_with_keyword_parameters(
             project.cfg["local_path"],
             project.cfg["central_path"],
         ]:
-
             for sub in ["sub-001", "sub-02", "sub-03"]:
-
                 sessions_in_path = test_utils.glob_basenames(
                     (base_local / "rawdata" / sub / "ses*").as_posix()
                 )

tests/tests_integration/test_formatting.py

@@ -97,7 +97,6 @@ def test_format_names_prefix(self):
         ]
 
     def test_warning_non_consecutive_numbers(self, project):
-
         project.make_sub_folders(
             ["sub-01", "sub-2", "sub-04"], ["ses-05", "ses-10"]
         )