Merge pull request #22903 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: mvdbeek

lib/galaxy/dependencies/__init__.py

@@ -318,9 +318,6 @@ def check_pydantic_ai(self):
             self.config.get("ai_api_key", None) is not None or self.config.get("inference_services", None) is not None
         )
 
-    def check_fastmcp(self):
-        return asbool(self.config.get("enable_mcp_server", False))
-
     def check_weasyprint(self):
         # See notes in ./conditional-requirements.txt for more information.
         return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"

lib/galaxy/dependencies/conditional-requirements.txt

@@ -16,7 +16,6 @@ galaxycloudrunner
 pkce
 total-perspective-vortex>=3.2.1,<4
 openai
-fastmcp>=2.13.0
 # upper version constraint because of https://github.com/galaxyproject/galaxy/issues/20600
 redis>=5.3.0,<6
 

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,13 +1,13 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=dev
 aiocop==1.1.4
-aiohappyeyeballs==2.6.2
+aiohappyeyeballs==2.7.1
 aiohttp==3.14.1
 aiosignal==1.4.0
 alabaster==1.0.0
 annotated-types==0.7.0
-ase==3.28.0
-ast-serialize==0.5.0
+ase==3.29.0
+ast-serialize==0.6.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
 axe-selenium-python==2.1.6 ; python_full_version < '3.12'
@@ -22,17 +22,17 @@ build==1.5.0
 cachecontrol==0.14.4
 cachetools==7.1.4
 cattrs==26.1.0
-certifi==2026.5.20
-cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
-charset-normalizer==3.4.7
-click==8.4.1
+certifi==2026.6.17
+cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
+charset-normalizer==3.4.9
+click==8.4.2
 codespell==2.4.2
 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
 colorlog==6.10.1
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.14.1
-cryptography==48.0.1
+coverage==7.15.0
+cryptography==49.0.0
 cwltest==2.6.20251216093331
 cycler==0.12.1
 darker==3.0.0
@@ -44,33 +44,33 @@ docutils==0.22.4 ; python_full_version >= '3.11'
 dogpile-cache==1.5.0
 enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.29.1
+filelock==3.29.6
 fluent-logger==0.11.1
 fonttools==4.63.0
 frozenlist==1.8.0
-fsspec==2026.4.0
+fsspec==2026.6.0
 galaxy-release-util==0.3.3
-gcsfs==2026.4.0
+gcsfs==2026.7.0
 google-api-core==2.31.0
-google-auth==2.53.0
+google-auth==2.55.1
 google-auth-oauthlib==1.4.0
 google-cloud-core==2.6.0
-google-cloud-storage==3.11.0
+google-cloud-storage==3.12.0
 google-cloud-storage-control==1.12.0
 google-crc32c==1.8.0
 google-resumable-media==2.10.0
 googleapis-common-protos==1.75.0
-greenlet==3.5.1
+greenlet==3.5.3
 grpc-google-iam-v1==0.14.4
-grpcio==1.81.0
-grpcio-status==1.81.0
+grpcio==1.82.0
+grpcio-status==1.82.0
 h11==0.16.0
 html5rdf==1.2.1
 hvac==2.4.0
 id==1.6.1
 idna==3.18
 imagesize==2.0.0
-importlib-metadata==8.7.1 ; python_full_version < '3.12'
+importlib-metadata==9.0.0 ; python_full_version < '3.12'
 iniconfig==2.3.0
 inquirerpy==0.3.4
 isodate==0.7.2 ; python_full_version < '3.11'
@@ -88,13 +88,14 @@ jsonschema-specifications==2025.9.1
 junit-xml==1.9
 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.5.0
-librt==0.11.0 ; platform_python_implementation != 'PyPy'
+librt==0.12.0 ; platform_python_implementation != 'PyPy'
 lxml==6.1.1
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.2.0 ; python_full_version >= '3.11'
 markdown-it-reporter==0.0.2
 markupsafe==3.0.3
-matplotlib==3.10.9
+matplotlib==3.10.9 ; python_full_version < '3.11'
+matplotlib==3.11.0 ; python_full_version >= '3.11'
 mdit-py-plugins==0.6.1
 mdurl==0.1.2
 mirakuru==3.0.2
@@ -106,23 +107,24 @@ mypy==2.1.0
 mypy-extensions==1.1.0
 myst-parser==4.0.1 ; python_full_version < '3.11'
 myst-parser==5.1.0 ; python_full_version >= '3.11'
-nh3==0.3.5
+nh3==0.3.6
 numpy==2.2.6 ; python_full_version < '3.11'
-numpy==2.4.6 ; python_full_version >= '3.11'
+numpy==2.4.6 ; python_full_version == '3.11.*'
+numpy==2.5.1 ; python_full_version >= '3.12'
 oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
-owlrl==7.1.4
-packaging==25.0
+owlrl==7.6.1
+packaging==26.2
 pathspec==1.1.1
 pfzy==0.3.4
-pillow==12.2.0
+pillow==12.3.0
 pkce==1.0.3
 platformdirs==4.10.0
-playwright==1.60.0
+playwright==1.61.0
 pluggy==1.6.0
 port-for==1.0.0
-prettytable==3.17.0
+prettytable==3.18.0
 prompt-toolkit==3.0.52
 propcache==0.5.2
 proto-plus==1.28.0
@@ -143,7 +145,7 @@ pyparsing==3.3.2
 pyproject-hooks==1.2.0
 pyshacl==0.31.0
 pysocks==1.7.1
-pytest==9.0.3
+pytest==9.1.1
 pytest-asyncio==1.4.0
 pytest-base-url==2.1.0
 pytest-cov==7.1.0
@@ -162,29 +164,30 @@ pytokens==0.4.1
 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.3
 rdflib==7.6.0
-readme-renderer==44.0
+readme-renderer==45.0
 referencing==0.37.0
 requests==2.34.2
-requests-cache==1.3.2
+requests-cache==1.3.3
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
-responses==0.26.1
+responses==0.26.2
 rfc3986==2.0.0
 rich==13.9.4
 rich-argparse==1.8.0
 rich-click==1.9.8
-roc-validator==0.10.0
+roc-validator==0.11.2
 roman-numerals==4.1.0 ; python_full_version >= '3.11'
 rpds-py==0.30.0 ; python_full_version < '3.11'
-rpds-py==2026.5.1 ; python_full_version >= '3.11'
+rpds-py==2026.6.3 ; python_full_version >= '3.11'
 ruamel-yaml==0.19.1
-rucio-clients==40.2.0
+rucio-clients==40.4.1
 s3transfer==0.17.1
 schema-salad==8.9.20260417192335
 scipy==1.15.3 ; python_full_version < '3.11'
-scipy==1.17.1 ; python_full_version >= '3.11'
+scipy==1.17.1 ; python_full_version == '3.11.*'
+scipy==1.18.0 ; python_full_version >= '3.12'
 secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
-selenium==4.44.0
+selenium==4.45.0
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
@@ -202,10 +205,11 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 statsd==4.0.1
-stevedore==5.8.0
+stevedore==5.8.0 ; python_full_version < '3.11'
+stevedore==5.9.0 ; python_full_version >= '3.11'
 tabulate==0.10.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
-testfixtures==12.0.0 ; python_full_version >= '3.11'
+testfixtures==12.2.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
@@ -217,14 +221,13 @@ tuspy==1.1.0
 twine==6.2.0
 types-cachetools==7.0.0.20260518
 types-requests==2.33.0.20260518
-typing-extensions==4.15.0
+typing-extensions==4.16.0
 typing-inspection==0.4.2
-typos==1.47.2
 tzdata==2026.2 ; sys_platform == 'win32'
 url-normalize==3.0.0
 urllib3==2.7.0
 watchdog==6.0.0
-wcwidth==0.8.0
+wcwidth==0.8.2
 websocket-client==1.9.0
 werkzeug==3.1.8
 wsproto==1.3.2

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

@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.15.16
+ruff==0.15.20