Format Python code with black 23.1.0

with manual fixes to 3 files to make them compatible with black 22.12.0 .

We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.

config/plugins/webhooks/demo/tool_list/__init__.py

@@ -9,15 +9,13 @@ def main(trans, webhook, params):
     tools = trans.app.toolbox.tools()
 
     for tool in tools:
-
         try:
             ts_data = tool[1].tool_shed_repository.to_dict()
             panel = tool[1].get_panel_section()
         except AttributeError:
             continue
 
         if ts_data["name"] + ts_data["installed_changeset_revision"] not in unique_tools:
-
             unique_tools.append(ts_data["name"] + ts_data["installed_changeset_revision"])
 
             data["tools"].append(

contrib/galaxy_config_merger.py

@@ -47,7 +47,7 @@ def main():
         if not config_sample.has_section(section):
             logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored.", section)
         else:
-            for (name, value) in config.items(section):
+            for name, value in config.items(section):
                 if not config_sample.has_option(section, name):
                     if f"#{name}" not in config_sample_content:
                         logging.warning(

lib/galaxy/actions/library.py

@@ -213,7 +213,7 @@ def _get_path_paste_uploaded_datasets(self, trans, params, library_bunch, respon
         (files_and_folders, _response_code, _message) = self._get_path_files_and_folders(params, preserve_dirs)
         if _response_code:
             return (uploaded_datasets, _response_code, _message)
-        for (path, name, folder) in files_and_folders:
+        for path, name, folder in files_and_folders:
             uploaded_datasets.append(
                 self._make_library_uploaded_dataset(trans, params, name, path, "path_paste", library_bunch, folder)
             )
@@ -224,7 +224,7 @@ def _get_path_files_and_folders(self, params, preserve_dirs):
         if problem_response:
             return problem_response
         files_and_folders = []
-        for (line, path) in self._paths_list(params):
+        for line, path in self._paths_list(params):
             line_files_and_folders = self._get_single_path_files_and_folders(line, path, preserve_dirs)
             files_and_folders.extend(line_files_and_folders)
         return files_and_folders, None, None
@@ -257,7 +257,7 @@ def _check_path_paste_params(self, params):
             response_code = 400
             return None, response_code, message
         bad_paths = []
-        for (_, path) in self._paths_list(params):
+        for _, path in self._paths_list(params):
             if not os.path.exists(path):
                 bad_paths.append(path)
         if bad_paths:

lib/galaxy/auth/providers/pam_auth.py

@@ -55,7 +55,6 @@
 
 
 class PAM(AuthProvider):
-
     plugin_type = "PAM"
 
     def authenticate(self, email, username, password, options, request):

lib/galaxy/authnz/custos_authnz.py

@@ -264,7 +264,6 @@ def _create_oauth2_session(self, state=None, scope=None):
         return session
 
     def _fetch_token(self, oauth2_session, trans):
-
         if self.config.get("iam_client_secret"):
             # Custos uses the Keycloak client secret to get the token
             client_secret = self.config["iam_client_secret"]

lib/galaxy/celery/__init__.py

@@ -147,7 +147,6 @@ def decorate(func: Callable):
         @shared_task(**celery_task_kwd)
         @wraps(func)
         def wrapper(*args, **kwds):
-
             app = get_galaxy_app()
             assert app
 

lib/galaxy/config/__init__.py

@@ -412,7 +412,6 @@ def _set_alt_paths(self, option, *alt_paths):
                     return path
 
     def _update_raw_config_from_kwargs(self, kwargs):
-
         type_converters: Dict[str, Callable[[Any], Union[bool, int, float, str]]] = {
             "bool": string_as_bool,
             "int": int,

lib/galaxy/datatypes/binary.py

@@ -327,7 +327,6 @@ def display_peek(self, dataset: "DatasetInstance") -> str:
 
 
 class DynamicCompressedArchive(CompressedArchive):
-
     compressed_format: str
     uncompressed_datatype_instance: Data
 

lib/galaxy/datatypes/converters/fasta_to_len.py

@@ -10,7 +10,6 @@
 
 
 def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):
-
     infile = fasta_file
     keep_first_char = int(keep_first_char)
 

lib/galaxy/datatypes/converters/interval_to_bed_converter.py

@@ -65,7 +65,6 @@ def __main__():
             except Exception:
                 name = "region_%i" % count
             try:
-
                 out.write("%s\t%i\t%i\t%s\t%i\t%s\n" % (region.chrom, region.start, region.end, name, 0, region.strand))
             except Exception:
                 skipped_lines += 1

lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py

@@ -15,7 +15,6 @@
 
 
 def main():
-
     # Read options, args.
     parser = optparse.OptionParser()
     parser.add_option("-c", "--chr-col", type="int", dest="chrom_col", default=1)

lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py

@@ -12,7 +12,6 @@
 
 
 def main():
-
     # Read options, args.
     parser = optparse.OptionParser()
     (options, args) = parser.parse_args()

lib/galaxy/datatypes/dataproviders/decorators.py

@@ -94,6 +94,7 @@ def dataprovider_factory(name, settings=None):
         to __init__ arguments
     :type settings: dictionary
     """
+
     # TODO:?? use *args for settings allowing mulitple dictionaries
     # make a function available through the name->provider dispatch to parse query strings
     #   callable like:
@@ -123,6 +124,7 @@ def _parse_query_string_settings(query_kwargs, settings=None):
     Parse the values in `query_kwargs` from strings to the proper types
     listed in the same key in `settings`.
     """
+
     # TODO: this was a relatively late addition: review and re-think
     def list_from_query_string(s):
         # assume csv

lib/galaxy/datatypes/goldenpath.py

@@ -125,7 +125,6 @@ class AGPFile:
     """
 
     def __init__(self, in_file):
-
         self._agp_version = "2.1"
         self._fname = os.path.abspath(in_file)
 
@@ -193,7 +192,6 @@ def _read_file(self):
     def _add_line(self, agp_line):
         # Perform validity checks if this is a new object
         if agp_line.obj != self._current_obj:
-
             # Check if we have already seen this object before
             if agp_line.obj in self._seen_objs:
                 raise AGPError(self.fname, agp_line.line_number, "object identifier out of order")

lib/galaxy/datatypes/isa.py

@@ -108,7 +108,6 @@ def _get_main_file(self, dataset: "DatasetInstance") -> Optional[str]:
         isa_folder = self._get_isa_folder_path(dataset)
 
         if os.path.exists(isa_folder):
-
             # Get ISA archive older
             isa_files = os.listdir(isa_folder)
 
@@ -350,7 +349,6 @@ def __init__(self, **kwd):
     ################################################################
 
     def _make_investigation_instance(self, filename: str) -> "Investigation":
-
         # Parse ISA-Tab investigation file
         parser = isatab_meta.InvestigationParser()
         isa_dir = os.path.dirname(filename)
@@ -384,7 +382,6 @@ def __init__(self, **kwd):
     ################################################################
 
     def _make_investigation_instance(self, filename: str) -> "Investigation":
-
         # Parse JSON file
         with open(filename, newline="", encoding="utf8") as fp:
             isa = isajson.load(fp)

lib/galaxy/datatypes/media.py

@@ -35,7 +35,6 @@ def ffprobe(path):
 
 
 class Audio(Binary):
-
     MetadataElement(
         name="duration",
         default=0,
@@ -90,7 +89,6 @@ def set_meta(self, dataset: "DatasetInstance", overwrite: bool = True, **kwd) ->
 
 
 class Video(Binary):
-
     MetadataElement(
         name="resolution_w",
         default=0,

lib/galaxy/datatypes/msa.py

@@ -246,7 +246,6 @@ def _write_part_stockholm_file(accumulated_lines):
                 part_file.writelines(accumulated_lines)
 
         try:
-
             stockholm_records = _read_stockholm_records(input_files[0])
             stockholm_lines_accumulated = []
             for counter, stockholm_record in enumerate(stockholm_records, start=1):

lib/galaxy/datatypes/speech.py

@@ -41,7 +41,6 @@ class TextGrid(Text):
     )
 
     def sniff(self, filename: str) -> bool:
-
         with open(filename) as fd:
             text = fd.read(len(self.header))
             return text == self.header

lib/galaxy/datatypes/tabular.py

@@ -1813,9 +1813,7 @@ def set_meta(
                 for i, line in enumerate(dataset_fh):
                     line = line.strip("\n")
                     if line.startswith("#"):
-
                         if line.startswith("#h"):
-
                             column_headers = line.split("\t")[1:]
                         elif line.startswith("#f"):
                             cleaned_column_types = []

lib/galaxy/datatypes/text.py

@@ -443,7 +443,7 @@ def _transform_dict_list_ids(dict_list):
                     return []
 
                 b_transform = {"rows": _transform_dict_list_ids, "columns": _transform_dict_list_ids}
-                for (m_name, b_name) in [
+                for m_name, b_name in [
                     ("table_rows", "rows"),
                     ("table_matrix_element_type", "matrix_element_type"),
                     ("table_format", "format"),

lib/galaxy/datatypes/util/maf_utilities.py

@@ -134,7 +134,6 @@ def __del__(self):
 
 # an object corresponding to a reference layered alignment
 class RegionAlignment:
-
     DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca")
     MAX_SEQUENCE_SIZE = sys.maxsize  # Maximum length of sequence allowed
 
@@ -226,7 +225,6 @@ def __init__(self, start, end, species=None, temp_file_handler=None):
 
 
 class SplicedAlignment:
-
     DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca")
 
     def __init__(self, exon_starts, exon_ends, species=None, temp_file_handler=None):

lib/galaxy/files/sources/posix.py

@@ -44,7 +44,7 @@ def _list(self, path="/", recursive=True, user_context=None):
         if recursive:
             res: List[Dict[str, Any]] = []
             effective_root = self._effective_root(user_context)
-            for (p, dirs, files) in safe_walk(dir_path, allowlist=self._allowlist):
+            for p, dirs, files in safe_walk(dir_path, allowlist=self._allowlist):
                 rel_dir = os.path.relpath(p, effective_root)
                 to_dict = functools.partial(self._resource_info_to_dict, rel_dir, user_context=user_context)
                 res.extend(map(to_dict, dirs))

lib/galaxy/job_execution/actions/post.py

@@ -402,7 +402,7 @@ def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state
                         )
                     else:
                         creating_jobs.append((input_dataset, input_dataset.dataset.creating_job))
-                for (input_dataset, creating_job) in creating_jobs:
+                for input_dataset, creating_job in creating_jobs:
                     sa_session.refresh(creating_job)
                     sa_session.refresh(input_dataset)
                 for input_dataset in [
@@ -497,7 +497,6 @@ def _execute(cls, tag_handler, user, output, tags):
 
 
 class ActionBox:
-
     actions = {
         "RenameDatasetAction": RenameDatasetAction,
         "HideDatasetAction": HideDatasetAction,

lib/galaxy/job_execution/output_collect.py

@@ -189,7 +189,6 @@ def collect_dynamic_outputs(
 
 
 class BaseJobContext(ModelPersistenceContext):
-
     max_discovered_files: Union[int, float]
     tool_provided_metadata: BaseToolProvidedMetadata
     job_working_directory: str
@@ -575,7 +574,7 @@ def discover_files(output_name, tool_provided_metadata, extra_file_collectors, j
                 JsonCollectedDatasetMatch(dataset, extra_file_collector, filename, path=path),
             )
     else:
-        for (match, collector) in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable):
+        for match, collector in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable):
             yield DiscoveredFile(match.path, collector, match)
 
 

lib/galaxy/job_execution/setup.py

@@ -222,7 +222,7 @@ def get_output_path(self, dataset):
         if getattr(dataset, "fake_dataset_association", False):
             return dataset.file_name
         assert dataset.id is not None, f"{dataset} needs to be flushed to find output path"
-        for (hda, dataset_path) in self.output_hdas_and_paths.values():
+        for hda, dataset_path in self.output_hdas_and_paths.values():
             if hda.id == dataset.id:
                 return dataset_path
         raise KeyError(f"Couldn't find job output for [{dataset}] in [{self.output_hdas_and_paths.values()}]")

lib/galaxy/jobs/dynamic_tool_destination.py

@@ -416,7 +416,6 @@ def __validate_destination(cls, valid_rule: bool, app, return_bool: bool, rule:
                         valid_rule = False
             elif isinstance(rule["destination"], dict):
                 if "priority" in rule["destination"] and isinstance(rule["destination"]["priority"], dict):
-
                     for priority in rule["destination"]["priority"]:
                         if priority not in priority_list:
                             error = "Invalid priority '"
@@ -530,7 +529,6 @@ def __validate_bounds(cls, valid_rule, return_bool, rule, tool, counter):
                 upper_bound = -1
 
             if upper_bound != -1 and lower_bound > upper_bound:
-
                 error = f"lower_bound exceeds upper_bound for rule {str(counter)}"
                 error += f" in '{str(tool)}'."
                 if not return_bool:
@@ -850,11 +848,9 @@ def infinite_defaultdict():
                     valid_config = False
 
             elif isinstance(obj["default_destination"], dict):
-
                 if "priority" in obj["default_destination"] and isinstance(
                     obj["default_destination"]["priority"], dict
                 ):
-
                     for priority in obj["default_destination"]["priority"]:
                         if isinstance(obj["default_destination"]["priority"][priority], str):
                             priority_list.add(priority)
@@ -936,7 +932,6 @@ def infinite_defaultdict():
 
                     if isinstance(curr, dict):
                         if "priority" in curr and isinstance(curr["priority"], str):
-
                             if curr["priority"] in priority_list:
                                 new_config["users"][user]["priority"] = curr["priority"]
                             else:
@@ -980,7 +975,6 @@ def infinite_defaultdict():
                     curr_tool_rules = []
 
                     if curr is not None:
-
                         # in each tool, there should always be only 2 sub-categories:
                         # default_destination (not mandatory) and rules (mandatory)
                         if "default_destination" in curr:
@@ -998,16 +992,13 @@ def infinite_defaultdict():
                                 else:
                                     valid_config = False
                             elif isinstance(curr["default_destination"], dict):
-
                                 if "priority" in curr["default_destination"] and isinstance(
                                     curr["default_destination"]["priority"], dict
                                 ):
-
                                     for priority in curr["default_destination"]["priority"]:
                                         destination = curr["default_destination"]["priority"][priority]
                                         if priority in priority_list:
                                             if isinstance(destination, str):
-
                                                 is_valid = validate_destination(
                                                     app,
                                                     destination,
@@ -1401,7 +1392,6 @@ def map_tool_to_destination(job, app, tool, user_email, test=False, path=None, j
     if fail_message is not None:
         destination = "fail"
     elif config is not None:
-
         # Get the default priority from the config if necessary.
         # If there isn't one, choose an arbitrary one as a fallback
         if "default_destination" in config:
@@ -1477,7 +1467,6 @@ def map_tool_to_destination(job, app, tool, user_email, test=False, path=None, j
                         if user_authorized:
                             matched = False
                             if rule["rule_type"] == "file_size":
-
                                 # bounds comparisons
                                 upper_bound = str_to_bytes(rule["upper_bound"])
                                 lower_bound = str_to_bytes(rule["lower_bound"])
@@ -1491,7 +1480,6 @@ def map_tool_to_destination(job, app, tool, user_email, test=False, path=None, j
                                         matched = True
 
                             elif rule["rule_type"] == "num_input_datasets":
-
                                 # bounds comparisons
                                 upper_bound = rule["upper_bound"]
                                 lower_bound = rule["lower_bound"]
@@ -1504,7 +1492,6 @@ def map_tool_to_destination(job, app, tool, user_email, test=False, path=None, j
                                         matched = True
 
                             elif rule["rule_type"] == "records":
-
                                 # bounds comparisons
                                 upper_bound = str_to_bytes(rule["upper_bound"])
                                 lower_bound = str_to_bytes(rule["lower_bound"])