Merge pull request #16409 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/datatypes/tabular.py

@@ -1587,12 +1587,12 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
                     if not self.header_regexp.match(line):
                         return False
                     else:
-                        length = int(re.split(r"\W+", line, 1)[0])
+                        length = int(re.split(r"\W+", line, maxsplit=1)[0])
                 else:
                     if not self.structure_regexp.match(line.upper()):
                         return False
                     else:
-                        if j != int(re.split(r"\W+", line, 1)[0]):
+                        if j != int(re.split(r"\W+", line, maxsplit=1)[0]):
                             return False
                         elif j == length:  # Last line of first sequence has been reached
                             return True

lib/galaxy/dependencies/dev-requirements.txt

@@ -22,14 +22,14 @@ charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.4 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.5 ; python_version >= "3.7" and python_version < "3.12"
 codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
 cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
 cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12"
 cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12"
-darker==1.7.1 ; python_version >= "3.7" and python_version < "3.12"
+darker==1.7.2 ; python_version >= "3.7" and python_version < "3.12"
 defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12"
 docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
@@ -83,7 +83,7 @@ pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12"
 platformdirs==3.8.1 ; python_version >= "3.7" and python_version < "3.12"
 pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
-port-for==0.7.0 ; python_version >= "3.7" and python_version < "3.12"
+port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
 prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12"
 psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin"
@@ -96,7 +96,7 @@ pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12"
 pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12"
-pytest-asyncio==0.21.0 ; python_version >= "3.7" and python_version < "3.12"
+pytest-asyncio==0.21.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-cov==4.1.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -148,7 +148,7 @@ tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
 toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12"
 tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
 trio-websocket==0.10.3 ; python_version >= "3.7" and python_version < "3.12"
-trio==0.22.1 ; python_version >= "3.7" and python_version < "3.12"
+trio==0.22.2 ; python_version >= "3.7" and python_version < "3.12"
 tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
 twill==3.1 ; python_version >= "3.7" and python_version < "3.12"
 twine==4.0.2 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
 mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
-ruff==0.0.277
+ruff==0.0.278
 typing_extensions==4.7.1
 zipp==3.15.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -42,7 +42,7 @@ circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
 click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
-click==8.1.4 ; python_version >= "3.7" and python_version < "3.12"
+click==8.1.5 ; python_version >= "3.7" and python_version < "3.12"
 cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"

lib/galaxy/model/__init__.py

@@ -578,11 +578,7 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
     default_cond = "dataset.object_store_id IS NULL" if default_quota_enabled and default_exclude_ids else ""
     exclude_cond = "dataset.object_store_id NOT IN :exclude_object_store_ids" if default_exclude_ids else ""
     use_or = " OR " if (default_cond != "" and exclude_cond != "") else ""
-    default_usage_dataset_condition = "{default_cond} {use_or} {exclude_cond}".format(
-        default_cond=default_cond,
-        exclude_cond=exclude_cond,
-        use_or=use_or,
-    )
+    default_usage_dataset_condition = f"{default_cond} {use_or} {exclude_cond}"
     if default_usage_dataset_condition.strip():
         default_usage_dataset_condition = f"AND ( {default_usage_dataset_condition} )"
     default_usage = UNIQUE_DATASET_USER_USAGE.format(and_dataset_condition=default_usage_dataset_condition)