Merge pull request #21707 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: jmchilton

lib/galaxy/authnz/managers.py

@@ -1,5 +1,6 @@
 import builtins
 import logging
+from typing import TYPE_CHECKING
 
 from galaxy import (
     exceptions,
@@ -22,6 +23,9 @@
     PSAAuthnz,
 )
 
+if TYPE_CHECKING:
+    from galaxy.managers.context import ProvidesAppContext
+
 OIDC_BACKEND_SCHEMA = resource_path(__name__, "xsd/oidc_backends_config.xsd")
 
 log = logging.getLogger(__name__)
@@ -215,7 +219,7 @@ def _unify_provider_name(self, provider):
                 return k.lower()
         return None
 
-    def _get_authnz_backend(self, provider, idphint=None):
+    def _get_authnz_backend(self, provider: str, idphint=None):
         unified_provider_name = self._unify_provider_name(provider)
         if unified_provider_name in self.oidc_backends_config:
             provider = unified_provider_name
@@ -326,7 +330,7 @@ def callback(self, provider, state_token, authz_code, trans, login_redirect_url,
             log.exception(msg)
             return False, msg, (None, None)
 
-    def create_user(self, provider, token, trans, login_redirect_url):
+    def create_user(self, provider: str, token: str, trans: "ProvidesAppContext", login_redirect_url: str):
         try:
             success, message, backend = self._get_authnz_backend(provider)
             if success is False:

lib/galaxy/authnz/psa_authnz.py

@@ -48,6 +48,8 @@
     from social_core.backends.oauth import BaseOAuth2
     from social_core.strategy import HttpResponseProtocol
 
+    from galaxy.managers.context import ProvidesAppContext
+
 
 log = logging.getLogger(__name__)
 
@@ -486,7 +488,7 @@ def decode_user_access_token(self, sa_session, access_token):
             # so the authentication fails with a proper error message
             raise
 
-    def create_user(self, token, trans, login_redirect_url):
+    def create_user(self, token: str, trans: "ProvidesAppContext", login_redirect_url: str):
         """
         Create a user from a stored token (deferred user creation).
 
@@ -511,6 +513,7 @@ def create_user(self, token, trans, login_redirect_url):
         userinfo = jwt.decode(id_token, options={"verify_signature": False})
 
         email = userinfo.get("email")
+        assert email
         username = userinfo.get("preferred_username", email)
         if "@" in username:
             username = username.split("@")[0]

lib/galaxy/dependencies/dev-requirements.txt

@@ -18,7 +18,7 @@ boto3==1.42.30
 botocore==1.42.30
 build==1.4.0
 cachecontrol==0.14.4
-cachetools==6.2.4
+cachetools==6.2.6
 cattrs==25.3.0
 certifi==2026.1.4
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
@@ -29,8 +29,8 @@ 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==7.13.1
-cryptography==46.0.3
+coverage==7.13.2
+cryptography==46.0.4
 cwltest==2.6.20251216093331
 cycler==0.12.1
 darker==3.0.0
@@ -50,7 +50,7 @@ fsspec==2026.1.0
 galaxy-release-util==0.3.2
 gcsfs==2026.1.0
 google-api-core==2.29.0
-google-auth==2.47.0
+google-auth==2.48.0
 google-auth-oauthlib==1.2.4
 google-cloud-core==2.5.0
 google-cloud-storage==3.8.0
@@ -100,7 +100,7 @@ mirakuru==3.0.1
 mistune==3.1.4
 more-itertools==10.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.2
-multidict==6.7.0
+multidict==6.7.1
 mypy==1.19.1
 mypy-extensions==1.1.0
 myst-parser==4.0.1 ; python_full_version < '3.11'
@@ -113,28 +113,28 @@ onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==7.1.4
 packaging==26.0
-pathspec==1.0.3
+pathspec==1.0.4
 pfzy==0.3.4
 pillow==12.1.0
 pkce==1.0.3
 platformdirs==4.5.1
-playwright==1.57.0
+playwright==1.58.0
 pluggy==1.6.0
 port-for==1.0.0
 prettytable==3.17.0
 prompt-toolkit==3.0.52
 propcache==0.4.1
 proto-plus==1.27.0
-protobuf==6.33.4
-psutil==7.2.1 ; sys_platform != 'cygwin'
+protobuf==6.33.5
+psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.2
 pyasn1==0.6.2
 pyasn1-modules==0.4.2
 pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
 pyee==13.0.0
 pygithub==2.8.1
 pygments==2.19.2
-pyjwt==2.10.1
+pyjwt==2.11.0
 pynacl==1.6.2
 pyparsing==3.3.2
 pyproject-hooks==1.2.0
@@ -155,7 +155,7 @@ pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.2.0
 python-slugify==8.0.4
-pytokens==0.4.0
+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==7.5.0
@@ -219,12 +219,12 @@ types-certifi==2021.10.8.3
 types-requests==2.32.4.20260107
 types-urllib3==1.26.25.14
 typing-extensions==4.15.0
-typos==1.42.1
+typos==1.42.3
 tzdata==2025.3 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==2.6.3
 watchdog==6.0.0
-wcwidth==0.3.2
+wcwidth==0.5.2
 websocket-client==1.9.0
 werkzeug==3.1.5
 wsproto==1.3.2

lib/galaxy/dependencies/pinned-requirements.txt

@@ -9,11 +9,11 @@ aiohappyeyeballs==2.6.1
 aiohttp==3.13.3
 aioitertools==0.13.0
 aiosignal==1.4.0
-alembic==1.18.1
+alembic==1.18.3
 amqp==5.3.1
 annotated-doc==0.0.4
 annotated-types==0.7.0
-anthropic==0.76.0
+anthropic==0.77.0
 anyio==4.12.1
 apispec==6.9.0
 appdirs==1.4.4
@@ -40,7 +40,7 @@ boto3==1.42.30
 botocore==1.42.30
 bx-python==0.14.0
 cachecontrol==0.14.4
-cachetools==6.2.4
+cachetools==6.2.6
 celery==5.6.2
 certifi==2026.1.4
 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
@@ -57,12 +57,12 @@ cohere==5.20.2 ; sys_platform != 'emscripten'
 colorama==0.4.6
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
-cryptography==46.0.3
+cryptography==46.0.4
 ct3==3.4.0.post5
 cwl-upgrader==1.2.14
 cwl-utils==0.40
 cwltool==3.1.20260108082145
-cyclopts==4.5.0
+cyclopts==4.5.1
 defusedxml==0.7.1
 deprecated==1.3.1
 deprecation==2.1.0
@@ -91,11 +91,11 @@ frozenlist==1.8.0
 fs==2.4.16
 fsspec==2026.1.0
 future==1.0.0
-genai-prices==0.0.51
+genai-prices==0.0.52
 google-api-core==2.29.0
-google-auth==2.47.0
+google-auth==2.48.0
 google-cloud-batch==0.20.0
-google-genai==1.60.0
+google-genai==1.61.0
 googleapis-common-protos==1.72.0
 gravity==1.2.0
 greenlet==3.3.1 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
@@ -138,26 +138,25 @@ kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
 limits==5.6.0
-logfire==4.19.0
-logfire-api==4.19.0
+logfire==4.21.0
+logfire-api==4.21.0
 lupa==2.6
 lxml==6.0.2
 mako==1.3.10
 markdown==3.10.1
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.0.0 ; python_full_version >= '3.11'
 markupsafe==3.0.3
-mcp==1.25.0
+mcp==1.26.0
 mdurl==0.1.2
-mercurial==7.1.2 ; python_full_version < '3.14'
-mercurial==7.2rc0 ; python_full_version >= '3.14'
+mercurial==7.2
 mistralai==1.9.11
 mistune==3.1.4
 more-itertools==10.8.0
 mrcfile==1.5.4
 msal==1.34.0
 msgpack==1.1.2
-multidict==6.7.0
+multidict==6.7.1
 mypy-extensions==1.1.0
 networkx==3.4.2 ; python_full_version < '3.11'
 networkx==3.6.1 ; python_full_version >= '3.11'
@@ -167,7 +166,7 @@ nodejs-wheel-binaries==22.20.0
 numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.1 ; python_full_version >= '3.11'
 oauthlib==3.3.1
-openai==2.15.0
+openai==2.16.0
 openapi-pydantic==0.5.1
 openpyxl==3.1.5
 opentelemetry-api==1.39.1
@@ -180,7 +179,7 @@ opentelemetry-proto==1.39.1
 opentelemetry-sdk==1.39.1
 opentelemetry-semantic-conventions==0.60b1
 opentelemetry-util-http==0.60b1
-orjson==3.11.5
+orjson==3.11.6
 oyaml==1.0
 packaging==26.0
 paramiko==4.0.0
@@ -189,16 +188,16 @@ paste==3.10.1
 pastedeploy==3.1.0
 pathable==0.4.4
 pathvalidate==3.3.1
-pebble==5.1.3
+pebble==5.2.0
 pillow==12.1.0
 platformdirs==4.5.1
 prometheus-client==0.24.1
 prompt-toolkit==3.0.52
 propcache==0.4.1
 proto-plus==1.27.0
-protobuf==6.33.4
+protobuf==6.33.5
 prov==1.5.1
-psutil==7.2.1
+psutil==7.2.2
 pulsar-galaxy-lib==0.15.14
 py-key-value-aio==0.3.0
 py-key-value-shared==0.3.0
@@ -220,7 +219,7 @@ pydot==4.0.1
 pyeventsystem==0.1.0
 pyfaidx==0.9.0.3
 pygments==2.19.2
-pyjwt==2.10.1
+pyjwt==2.11.0
 pykwalify==1.8.0
 pylibmagic==0.5.0
 pynacl==1.6.2
@@ -264,7 +263,7 @@ s3fs==2026.1.0
 s3transfer==0.16.0
 schema-salad==8.9.20251102115403
 secretstorage==3.5.0 ; sys_platform == 'linux'
-setuptools==80.10.1
+setuptools==80.10.2
 shellingham==1.5.4
 six==1.17.0
 slowapi==0.1.9
@@ -283,13 +282,13 @@ temporalio==1.20.0
 tenacity==9.1.2
 text-unidecode==1.3
 tifffile==2025.5.10 ; python_full_version < '3.11'
-tifffile==2026.1.14 ; python_full_version >= '3.11'
+tifffile==2026.1.28 ; python_full_version >= '3.11'
 tiktoken==0.12.0
 tinydb==4.8.2
 tokenizers==0.22.2 ; sys_platform != 'emscripten'
 tomli==2.4.0 ; python_full_version < '3.11'
 tornado==6.5.4
-tqdm==4.67.1
+tqdm==4.67.2
 tuspy==1.1.0
 tuspyserver==4.2.3
 typer==0.21.1
@@ -304,7 +303,7 @@ urllib3==2.6.3
 uvicorn==0.40.0
 uvloop==0.22.1
 vine==5.1.0
-wcwidth==0.3.2
+wcwidth==0.5.2
 webencodings==0.5.1
 webob==1.8.9
 websockets==15.0.1