Update Python dependencies

client/src/api/schema/schema.ts

@@ -3555,7 +3555,10 @@ export interface components {
              */
             name: string;
         };
-        /** CustomBuildsCollection */
+        /**
+         * CustomBuildsCollection
+         * @description The custom builds associated with the user.
+         */
         CustomBuildsCollection: components["schemas"]["CustomBuildModel"][];
         /** CustomBuildsMetadataResponse */
         CustomBuildsMetadataResponse: {
@@ -9381,11 +9384,13 @@ export interface components {
         /**
          * ListJstreeResponse
          * @deprecated
+         * @description List of files in Jstree format.
          * @default []
          */
         ListJstreeResponse: Record<string, never>[];
         /**
          * ListUriResponse
+         * @description List of directories and files.
          * @default []
          */
         ListUriResponse: (components["schemas"]["RemoteFile"] | components["schemas"]["RemoteDirectory"])[];

lib/galaxy/dependencies/__init__.py

@@ -298,7 +298,7 @@ def check_pkce(self):
         return self.pkce_support
 
     def check_rucio_clients(self):
-        return sys.version_info >= (3, 9)
+        return "rucio" in self.object_stores and sys.version_info >= (3, 9)
 
 
 def optional(config_file=None):

lib/galaxy/dependencies/conditional-requirements.txt

@@ -61,5 +61,5 @@ weasyprint
 # AWS Batch runner
 boto3
 
-#For Rucio storage plugin
-rucio-clients==33.6.0
+# For Rucio storage plugin
+rucio-clients>=33.6.0

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,4 +1,4 @@
-aiohttp==3.9.4 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
 anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -7,7 +7,7 @@ async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
 axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
 babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
-backports-tarfile==1.1.0 ; python_version >= "3.8" and python_version < "3.12"
+backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 black==24.4.0 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -24,11 +24,13 @@ cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
-darkgraylib==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
+darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
+decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
-exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
+dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
+exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -48,9 +50,11 @@ isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-functools==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
+jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
+jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
 keyring==25.1.0 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
@@ -68,19 +72,20 @@ more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+myst-parser==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
+pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
 playwright==1.43.0 ; python_version >= "3.8" and python_version < "3.13"
-pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
+pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
@@ -114,13 +119,16 @@ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
+referencing==0.34.0 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
+rpds-py==0.18.0 ; python_version >= "3.9" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
+rucio-clients==34.2.0 ; python_version >= "3.9" and python_version < "3.13"
 schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
@@ -142,6 +150,8 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13
 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
+stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13"
+tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
 testfixtures==8.1.0 ; python_version >= "3.8" and python_version < "3.13"
 text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -1,7 +1,7 @@
 attrs==23.2.0
 flake8==7.0.0
-flake8-bugbear==24.2.6
+flake8-bugbear==24.4.21
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.3.7
+ruff==0.4.1

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,15 +5,15 @@ adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
 aiobotocore==2.12.3 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.9.4 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
 aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13"
 amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
 aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13"
 annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
-apispec==6.6.0 ; python_version >= "3.8" and python_version < "3.13"
+apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13"
 appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13"
 arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13"
 argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -36,7 +36,7 @@ boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
 botocore==1.34.69 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
+celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -65,8 +65,8 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13"
 edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13"
 email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
-exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
-fastapi==0.110.1 ; python_version >= "3.8" and python_version < "3.13"
+exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
+fastapi==0.110.2 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
@@ -80,10 +80,10 @@ graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
 graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32")
-gunicorn==21.2.0 ; python_version >= "3.8" and python_version < "3.13"
+gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13"
 gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-h5grove==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
+h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -96,7 +96,7 @@ jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
 jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13"
-jsonschema==4.21.1 ; python_version >= "3.8" and python_version < "3.13"
+jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13"
 lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -126,18 +126,17 @@ paste==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
-pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
 prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
 psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13"
 pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
+pydantic[email]==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
 pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -156,11 +155,11 @@ python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13"
 python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
-pyzmq==26.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pyzmq==26.0.2 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.34.0 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
-regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13"
+regex==2024.4.16 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
 requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -5,17 +5,17 @@ lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.9.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13"
+pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
 types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
-types-docutils==0.20.0.20240406 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.21.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
 types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
 types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
-types-paramiko==3.4.0.20240311 ; python_version >= "3.8" and python_version < "3.13"
+types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13"
 types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"

lib/tool_shed/webapp/frontend/src/schema/schema.ts

@@ -337,7 +337,10 @@ export interface components {
          * @enum {string}
          */
         DescriptorType: "CWL" | "WDL" | "NFL" | "GALAXY" | "SMK"
-        /** DescriptorTypeVersion */
+        /**
+         * DescriptorTypeVersion
+         * @description The language version for a given descriptor type. The version should correspond to the actual declared version of the descriptor. For example, tools defined in CWL could have a version of `v1.0.2` whereas WDL tools may have a version of `1.0` or `draft-2`
+         */
         DescriptorTypeVersion: string
         /** DetailedRepository */
         DetailedRepository: {

pyproject.toml

@@ -153,6 +153,7 @@ pytest-playwright = "*"
 pytest-postgresql = "!=3.0.0"  # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426
 pytest-shard = "*"
 responses = "*"
+rucio-clients = {version = ">=33.6.0", python = ">=3.9"}  # https://github.com/galaxyproject/galaxy/pull/17156
 selenium = "*"
 urllib3 = "<2"  # Necessary for poetry for resolve deps for Python 3.8+
 seletools = "*"

test/integration/test_celery_user_rate_limit.py

@@ -83,7 +83,7 @@ def _test_mock_pass_user_id_task(self, num_users: int, num_calls: int, tasks_per
             expected_duration = secs_between_tasks_per_user * (num_calls - 1)
             expected_duration_lbound = expected_duration - 4
         expected_duration_hbound = expected_duration + 4
-        start_time = datetime.datetime.utcnow()
+        start_time = datetime.datetime.now(datetime.timezone.utc)
         timer = ExecutionTimer()
         #  Invoke test task num_calls times for each user
         results: Dict[int, List[AsyncResult]] = {}