Update to black 2024 stable style

.flake8

@@ -4,7 +4,8 @@
 # E203 is whitespace before ':'; we follow black's formatting here. See https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length (delegated to black)
+# E701,E704 are multiple statements on one line; we follow black's formatting here. See https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#configuration
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E203,E402,E501,E701,E704,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/tool_shed/test/test_data/repos

.github/workflows/lint.yaml

@@ -55,6 +55,4 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
-        with:
-          version: "23.3.0"
       - uses: isort/isort-action@master

lib/galaxy/actions/library.py

@@ -1,6 +1,7 @@
 """
 Contains library functions
 """
+
 import json
 import logging
 import os.path

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -1,6 +1,7 @@
 """
 Mock infrastructure for testing ModelManagers.
 """
+
 import os
 import shutil
 import tempfile

lib/galaxy/auth/__init__.py

@@ -1,6 +1,7 @@
 """
 Contains implementations of the authentication logic.
 """
+
 import logging
 
 from galaxy.auth.util import (

lib/galaxy/auth/providers/__init__.py

@@ -3,6 +3,7 @@
 
 @author: Andrew Robinson
 """
+
 import abc
 
 

lib/galaxy/auth/providers/alwaysreject.py

@@ -3,6 +3,7 @@
 
 @author: Andrew Robinson
 """
+
 import logging
 
 from . import AuthProvider

lib/galaxy/auth/providers/ldap_ad.py

@@ -89,7 +89,6 @@ def _parse_ldap_options(options_unparsed):
 
 
 class LDAP(AuthProvider):
-
     """
     Attempts to authenticate users against an LDAP server.
 

lib/galaxy/auth/providers/localdb.py

@@ -3,6 +3,7 @@
 
 @author: Andrew Robinson
 """
+
 import logging
 
 from . import AuthProvider

lib/galaxy/auth/providers/pam_auth.py

@@ -3,6 +3,7 @@
 
 Author Peter van Heusden ([email protected])
 """
+
 import logging
 import shlex
 

lib/galaxy/config/__init__.py

@@ -1,6 +1,7 @@
 """
 Universe configuration builder.
 """
+
 # absolute_import needed for tool_shed package.
 
 import configparser
@@ -231,9 +232,9 @@ class BaseAppConfiguration(HasDynamicProperties):
     # If VALUE == first directory in a user-supplied path that resolves to KEY, it will be stripped from that path
     renamed_options: Optional[Dict[str, str]] = None
     deprecated_dirs: Dict[str, str] = {}
-    paths_to_check_against_root: Set[
-        str
-    ] = set()  # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root
+    paths_to_check_against_root: Set[str] = (
+        set()
+    )  # backward compatibility: if resolved path doesn't exist, try resolving w.r.t root
     add_sample_file_to_defaults: Set[str] = set()  # for these options, add sample config files to their defaults
     listify_options: Set[str] = set()  # values for these options are processed as lists of values
     object_store_store_by: str

lib/galaxy/datatypes/anvio.py

@@ -2,6 +2,7 @@
 Datatypes for Anvi'o
 https://github.com/merenlab/anvio
 """
+
 import glob
 import logging
 import os

lib/galaxy/datatypes/checkers.py

@@ -2,6 +2,7 @@
 
 External datatypes may make use of these functions.
 """
+
 from galaxy.util.checkers import (
     check_binary,
     check_bz2,

lib/galaxy/datatypes/constructive_solid_geometry.py

@@ -193,6 +193,7 @@ class Vtk:
     TODO: only legacy formats are currently supported and support for XML formats
     should be added.
     """
+
     subtype = ""
     # Add metadata elements.
     MetadataElement(name="vtk_version", default=None, desc="Vtk version", readonly=True, optional=True, visible=True)

lib/galaxy/datatypes/converters/interval_to_fli.py

@@ -13,6 +13,7 @@
 
 and symbols are sorted in lexigraphical order.
 """
+
 import optparse
 
 from bx.tabular.io import (

lib/galaxy/datatypes/data.py

@@ -425,9 +425,9 @@ def _serve_raw(
         self, dataset: DatasetHasHidProtocol, to_ext: Optional[str], headers: Headers, **kwd
     ) -> Tuple[IO, Headers]:
         headers["Content-Length"] = str(os.stat(dataset.get_file_name()).st_size)
-        headers[
-            "content-type"
-        ] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+        headers["content-type"] = (
+            "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+        )
         filename = self._download_filename(
             dataset,
             to_ext,
@@ -476,9 +476,9 @@ def _serve_file_download(self, headers, data, trans, to_ext, file_size, **kwd):
                 element_identifier=kwd.get("element_identifier"),
                 filename_pattern=kwd.get("filename_pattern"),
             )
-            headers[
-                "content-type"
-            ] = "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+            headers["content-type"] = (
+                "application/octet-stream"  # force octet-stream so Safari doesn't append mime extensions to filename
+            )
             headers["Content-Disposition"] = f'attachment; filename="{filename}"'
             return open(data.get_file_name(), "rb"), headers
 

lib/galaxy/datatypes/dataproviders/base.py

@@ -1,6 +1,7 @@
 """
 Base class(es) for all DataProviders.
 """
+
 # there's a blurry line between functionality here and functionality in datatypes module
 # attempting to keep parsing to a minimum here and focus on chopping/pagination/reformat(/filtering-maybe?)
 #   and using as much pre-computed info/metadata from the datatypes module as possible

lib/galaxy/datatypes/dataproviders/chunk.py

@@ -4,6 +4,7 @@
 Primarily for file sources but usable by any iterator that has both
 seek and read( N ).
 """
+
 import base64
 import logging
 import os

lib/galaxy/datatypes/dataproviders/column.py

@@ -2,6 +2,7 @@
 Providers that provide lists of lists generally where each line of a source
 is further subdivided into multiple data (e.g. columns from a line).
 """
+
 import logging
 import re
 from urllib.parse import unquote_plus

lib/galaxy/datatypes/dataproviders/dataset.py

@@ -5,6 +5,7 @@
     - or provide data in some way relevant to bioinformatic data
         (e.g. parsing genomic regions from their source)
 """
+
 import logging
 import sys
 

lib/galaxy/datatypes/dataproviders/external.py

@@ -2,6 +2,7 @@
 Data providers that iterate over a source that is not in memory
 or not in a file.
 """
+
 import gzip
 import logging
 import subprocess

lib/galaxy/datatypes/dataproviders/hierarchy.py

@@ -1,6 +1,7 @@
 """
 Dataproviders that iterate over lines from their sources.
 """
+
 import logging
 
 from galaxy.util import (

lib/galaxy/datatypes/dataproviders/line.py

@@ -1,6 +1,7 @@
 """
 Dataproviders that iterate over lines from their sources.
 """
+
 import collections
 import logging
 import re

lib/galaxy/datatypes/genetics.py

@@ -11,6 +11,7 @@
 ross lazarus for rgenetics
 august 20 2007
 """
+
 import logging
 import os
 import re

lib/galaxy/datatypes/gis.py

@@ -1,6 +1,7 @@
 """
 GIS classes
 """
+
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.protocols import (
     DatasetProtocol,

lib/galaxy/datatypes/goldenpath.py

@@ -365,7 +365,6 @@ def _validate_line(self):
 
 
 class AGPSeqLine(AGPLine):
-
     """
     A subclass of AGPLine specifically for AGP lines that represent sequences.
     """
@@ -462,7 +461,6 @@ def _validate_line(self):
 
 
 class AGPGapLine(AGPLine):
-
     """
     A subclass of AGPLine specifically for AGP lines that represent sequence gaps.
     """

lib/galaxy/datatypes/graph.py

@@ -1,6 +1,7 @@
 """
 Graph content classes.
 """
+
 import logging
 from typing import List
 

lib/galaxy/datatypes/hdf5.py

@@ -2,6 +2,7 @@
 
 This datatype was created for use with the iSEE interactive tool.
 """
+
 from typing import Optional
 
 from galaxy.datatypes.data import Data

lib/galaxy/datatypes/images.py

@@ -1,6 +1,7 @@
 """
 Image classes
 """
+
 import base64
 import json
 import logging

lib/galaxy/datatypes/interval.py

@@ -1,6 +1,7 @@
 """
 Interval datatypes
 """
+
 import logging
 import sys
 import tempfile

lib/galaxy/datatypes/media.py

@@ -1,4 +1,5 @@
 """Video classes"""
+
 import json
 import subprocess
 import wave

lib/galaxy/datatypes/mothur.py

@@ -1,6 +1,7 @@
 """
 Mothur Metagenomics Datatypes
 """
+
 import logging
 import re
 from typing import (

lib/galaxy/datatypes/neo4j.py

@@ -1,6 +1,7 @@
 """
 Neo4j Composite Dataset
 """
+
 import logging
 
 from galaxy.datatypes.data import Data

lib/galaxy/datatypes/ngsindex.py

@@ -1,6 +1,7 @@
 """
 NGS indexes
 """
+
 import logging
 import os
 

lib/galaxy/datatypes/phylip.py

@@ -7,6 +7,7 @@
 @githuborganization: C3BI
 Phylip datatype sniffer
 """
+
 from typing import TYPE_CHECKING
 
 from galaxy import util

lib/galaxy/datatypes/proteomics.py

@@ -1,6 +1,7 @@
 """
 Proteomics Datatypes
 """
+
 import logging
 import re
 from typing import (