Merge pull request #21583 from nsoranzo/drop_py3.9

Drop support for Python 3.9

.circleci/config.yml

@@ -15,7 +15,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: cimg/python:3.9
+      - image: cimg/python:3.10
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -73,7 +73,7 @@ jobs:
             - ~/repo
   validate_test_tools:
     docker:
-      - image: cimg/python:3.9
+      - image: cimg/python:3.10
     <<: *set_workdir
     steps:
       - *restore_repo_cache

.github/workflows/api.yaml

@@ -31,7 +31,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         chunk: [0, 1]
     services:
       postgres:

.github/workflows/bioblend.yaml

@@ -32,7 +32,7 @@ jobs:
       fail-fast: false
       matrix:
         tox_env: [py314]
-        galaxy_python_version: ['3.9']
+        galaxy_python_version: ['3.10']
     steps:
       - name: Checkout Galaxy
         uses: actions/checkout@v6

.github/workflows/check_test_class_names.yaml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     steps:
       - uses: actions/checkout@v6
         with:

.github/workflows/converter_tests.yaml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     steps:
       - if: github.event_name == 'schedule'
         run: |

.github/workflows/cwl_conformance.yaml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         marker: ['green', 'red and required', 'red and not required']
         conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
     services:

.github/workflows/db_indexes.yaml

@@ -26,11 +26,11 @@ jobs:
       matrix:
         db: ['postgresql', 'sqlite']
         postgresql-version: ['17']
-        python-version: ['3.9']
+        python-version: ['3.10']
         include:
           - db: postgresql
             postgresql-version: '9.6'
-            python-version: '3.9'
+            python-version: '3.10'
     services:
       postgres:
         image: postgres:${{ matrix.postgresql-version }}

.github/workflows/dependencies.yaml

@@ -14,7 +14,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - name: Install uv
         uses: astral-sh/setup-uv@v7
       - name: Update dependencies

.github/workflows/deployment.yaml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     steps:
       - uses: actions/checkout@v6
         with:

.github/workflows/docs.yaml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     steps:
       - name: Get target branch name (push)
         if: github.event_name == 'push'

.github/workflows/first_startup.yaml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/framework_tools.yaml

@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         use-legacy-api: ['if_needed', 'always']
     services:
       postgres:

.github/workflows/framework_workflows.yaml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     services:
       postgres:
         image: postgres:17

.github/workflows/integration.yaml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         chunk: ['0', '1', '2', '3']
     steps:
       - if: github.event_name == 'schedule'

.github/workflows/integration_selenium.yaml

@@ -33,7 +33,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     services:
       postgres:
         image: postgres:17

.github/workflows/lint.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'

.github/workflows/lint_openapi_schema.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     steps:
       - uses: actions/checkout@v6
         with:

.github/workflows/main_tools.yaml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     services:
       postgres:
         image: postgres:17

.github/workflows/mulled.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     steps:
       - uses: actions/checkout@v6
         with:

.github/workflows/osx_startup.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/performance.yaml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     services:
       postgres:
         image: postgres:17

.github/workflows/playwright.yaml

@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         chunk: [0, 1, 2]
     services:
       postgres:

.github/workflows/publish_artifacts.yaml

@@ -41,7 +41,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
         matrix:
-            python-version: ['3.9']
+            python-version: ['3.10']
     steps:
       - uses: actions/checkout@v6
         with:

.github/workflows/selenium.yaml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
         chunk: [0, 1, 2]
     services:
       postgres:

.github/workflows/test_galaxy_packages.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     steps:
       - uses: actions/checkout@v6
         with:

.github/workflows/toolshed.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

.github/workflows/unit-postgres.yaml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     services:
       postgres:
         image: postgres:17

.github/workflows/unit.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     steps:
       - uses: actions/checkout@v6
         with:

Makefile

@@ -62,8 +62,8 @@ format:  ## Format Python code base
 remove-unused-imports:  ## Remove unused imports in Python code base
 	$(IN_VENV) autoflake --in-place --remove-all-unused-imports --recursive --verbose lib/ test/
 
-pyupgrade:  ## Convert older code patterns to Python 3.8/3.9 idiomatic ones
-	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs pyupgrade --py39-plus
+pyupgrade:  ## Convert older code patterns to Python 3.8/3.10 idiomatic ones
+	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs pyupgrade --py310-plus
 	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs auto-walrus
 	ack --type=python -f $(PY38_PYUPGRADE_PATHS) | xargs pyupgrade --py38-plus
 

README.rst

@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.9 or higher. To check your Python version, run:
+Galaxy requires Python 3.10 or higher. To check your Python version, run:
 
 .. code:: console
 
     $ python -V
-    Python 3.9.21
+    Python 3.10.12
 
 Start Galaxy:
 

doc/source/admin/python.md

@@ -1,6 +1,6 @@
 # Supported Python versions
 
-Galaxy's core functionality is currently supported on Python **>=3.9** .
+Galaxy's core functionality is currently supported on Python **>=3.10** .
 
 If Galaxy complains about the version of Python you are using:
 

lib/galaxy/agents/base.py

@@ -8,10 +8,10 @@ from abc import (
     ABC,
     abstractmethod,
 )
+from collections.abc import Callable
 from dataclasses import dataclass
 from typing import (
     Any,
-    Callable,
     Optional,
     TYPE_CHECKING,
     Union,

lib/galaxy/app.py

@@ -6,9 +6,9 @@ import signal
 import sys
 import threading
 import time
+from collections.abc import Callable
 from typing import (
     Any,
-    Callable,
     Optional,
 )
 

lib/galaxy/authnz/psa_authnz.py

@@ -1,6 +1,5 @@
 import json
 import logging
-import sys
 import time
 from typing import TYPE_CHECKING
 from urllib.parse import quote
@@ -47,14 +46,7 @@ from ..config import GalaxyAppConfiguration
 
 if TYPE_CHECKING:
     from social_core.backends.oauth import BaseOAuth2
-
-    if sys.version_info >= (3, 10):
-        from social_core.strategy import HttpResponseProtocol
-    else:
-        from typing import Protocol
-
-        class HttpResponseProtocol(Protocol):
-            url: str
+    from social_core.strategy import HttpResponseProtocol
 
 
 log = logging.getLogger(__name__)

lib/galaxy/celery/__init__.py

@@ -1,5 +1,6 @@
 import os
 import uuid
+from collections.abc import Callable
 from functools import (
     lru_cache,
     wraps,
@@ -8,7 +9,6 @@ from multiprocessing import get_context
 from threading import local
 from typing import (
     Any,
-    Callable,
 )
 
 import pebble

lib/galaxy/celery/tasks.py

@@ -1,12 +1,12 @@
 import datetime
 import json
 import shutil
+from collections.abc import Callable
 from concurrent.futures import TimeoutError
 from functools import lru_cache
 from pathlib import Path
 from typing import (
     Any,
-    Callable,
     Optional,
 )
 

lib/galaxy/config/__init__.py

@@ -16,10 +16,10 @@ import string
 import sys
 import tempfile
 import threading
+from collections.abc import Callable
 from datetime import timedelta
 from typing import (
     Any,
-    Callable,
     cast,
     Optional,
     SupportsInt,

lib/galaxy/config/config_manage.py

@@ -6,11 +6,11 @@ from argparse import (
     ArgumentParser,
     Namespace,
 )
+from collections.abc import Callable
 from io import StringIO
 from textwrap import TextWrapper
 from typing import (
     Any,
-    Callable,
     NamedTuple,
     Optional,
 )

lib/galaxy/datatypes/blast.py

@@ -32,9 +32,9 @@ Covers the ``blastxml`` format and the BLAST databases.
 """
 import logging
 import os
+from collections.abc import Callable
 from time import sleep
 from typing import (
-    Callable,
     Optional,
 )
 

lib/galaxy/datatypes/data.py

@@ -6,21 +6,21 @@ import shutil
 import string
 import tempfile
 from collections.abc import (
+    Callable,
     Generator,
     Iterable,
 )
 from inspect import isclass
 from typing import (
     Any,
-    Callable,
     IO,
+    Literal,
     Optional,
     TYPE_CHECKING,
     Union,
 )
 
 from markupsafe import escape
-from typing_extensions import Literal
 
 from galaxy import util
 from galaxy.datatypes.metadata import (

lib/galaxy/datatypes/display_applications/parameters.py

@@ -1,8 +1,8 @@
 # Contains parameters that are used in Display Applications
 import mimetypes
+from collections.abc import Callable
 from dataclasses import dataclass
 from typing import (
-    Callable,
     Optional,
     TYPE_CHECKING,
     Union,

lib/galaxy/datatypes/images.py

@@ -10,6 +10,7 @@ import struct
 from collections.abc import Iterator
 from typing import (
     Any,
+    Literal,
     Optional,
     Union,
 )
@@ -18,7 +19,6 @@ import mrcfile
 import numpy as np
 import png
 import tifffile
-from typing_extensions import Literal
 
 try:
     import PIL

lib/galaxy/datatypes/molecules.py

@@ -1,8 +1,8 @@
 import logging
 import os
 import re
+from collections.abc import Callable
 from typing import (
-    Callable,
     Optional,
 )
 

lib/galaxy/datatypes/msa.py

@@ -2,8 +2,8 @@ import abc
 import logging
 import os
 import re
+from collections.abc import Callable
 from typing import (
-    Callable,
     Optional,
 )
 

lib/galaxy/datatypes/sequence.py

@@ -9,11 +9,13 @@ import os
 import re
 import string
 import subprocess
-from collections.abc import Iterable
+from collections.abc import (
+    Callable,
+    Iterable,
+)
 from itertools import islice
 from typing import (
     Any,
-    Callable,
     Optional,
 )
 

lib/galaxy/datatypes/sniff.py

@@ -12,10 +12,12 @@ import shutil
 import struct
 import tempfile
 import zipfile
-from collections.abc import Iterable
+from collections.abc import (
+    Callable,
+    Iterable,
+)
 from functools import partial
 from typing import (
-    Callable,
     IO,
     NamedTuple,
     Optional,

lib/galaxy/datatypes/spaln.py

@@ -4,8 +4,8 @@ spaln Composite Dataset
 
 import logging
 import os.path
+from collections.abc import Callable
 from typing import (
-    Callable,
     Optional,
 )
 

lib/galaxy/dependencies/dev-requirements.txt

@@ -3,44 +3,35 @@
 aiohappyeyeballs==2.6.1
 aiohttp==3.13.3
 aiosignal==1.4.0
-alabaster==0.7.16 ; python_full_version < '3.10'
-alabaster==1.0.0 ; python_full_version >= '3.10'
+alabaster==1.0.0
 anyio==4.12.1
-ase==3.26.0 ; python_full_version < '3.10'
-ase==3.27.0 ; python_full_version >= '3.10'
+ase==3.27.0
+async-generator==1.10
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.4.0
 axe-selenium-python==2.1.6
 babel==2.17.0
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
-black==25.11.0 ; python_full_version < '3.10'
-black==25.12.0 ; python_full_version >= '3.10'
-boto3==1.41.5 ; python_full_version < '3.10'
-boto3==1.42.19 ; python_full_version >= '3.10'
-botocore==1.41.5 ; python_full_version < '3.10'
-botocore==1.42.19 ; python_full_version >= '3.10'
+black==25.12.0
+boto3==1.42.19
+botocore==1.42.19
 build==1.4.0
-cachecontrol==0.14.3 ; python_full_version < '3.10'
-cachecontrol==0.14.4 ; python_full_version >= '3.10'
+cachecontrol==0.14.4
 cachetools==6.2.4
 cattrs==25.3.0
 certifi==2026.1.4
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.4
-click==8.1.8 ; python_full_version < '3.10'
-click==8.3.1 ; python_full_version >= '3.10'
+click==8.3.1
 codespell==2.4.1
 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
 colorlog==6.10.1
-contourpy==1.3.0 ; python_full_version < '3.10'
-contourpy==1.3.2 ; python_full_version == '3.10.*'
+contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.7 ; python_full_version < '3.10'
-coverage==7.13.1 ; python_full_version >= '3.10'
+coverage==7.13.1
 cryptography==46.0.3
-cwltest==2.6.20250818005349 ; python_full_version < '3.10'
-cwltest==2.6.20251216093331 ; python_full_version >= '3.10'
+cwltest==2.6.20251216093331
 cycler==0.12.1
 darker==3.0.0
 darkgraylib==2.4.1
@@ -48,35 +39,41 @@ decorator==5.2.1
 defusedxml==0.7.1
 docutils==0.21.2 ; python_full_version < '3.11'
 docutils==0.22.4 ; python_full_version >= '3.11'
-dogpile-cache==1.4.1 ; python_full_version < '3.10'
-dogpile-cache==1.5.0 ; python_full_version >= '3.10'
-enum-tools==0.12.0 ; python_full_version >= '3.10'
+dogpile-cache==1.5.0
+enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.19.1 ; python_full_version < '3.10'
-filelock==3.20.3 ; python_full_version >= '3.10'
+filelock==3.20.3
 fluent-logger==0.11.1
-fonttools==4.60.2 ; python_full_version < '3.10'
-fonttools==4.61.1 ; python_full_version >= '3.10'
+fonttools==4.61.1
 frozenlist==1.8.0
+fsspec==2026.1.0
 galaxy-release-util==0.3.1
-greenlet==3.2.4 ; python_full_version < '3.10'
-greenlet==3.3.0 ; python_full_version >= '3.10'
+gcsfs==2026.1.0
+google-api-core==2.29.0
+google-auth==2.47.0
+google-auth-oauthlib==1.2.4
+google-cloud-core==2.5.0
+google-cloud-storage==3.8.0
+google-cloud-storage-control==1.9.0
+google-crc32c==1.8.0
+google-resumable-media==2.8.0
+googleapis-common-protos==1.72.0
+greenlet==3.3.0
+grpc-google-iam-v1==0.14.3
+grpcio==1.76.0
+grpcio-status==1.76.0
 h11==0.16.0
-html5lib==1.1 ; python_full_version < '3.10'
-html5rdf==1.2.1 ; python_full_version >= '3.10'
+html5rdf==1.2.1
 httpcore==1.0.9
 httpx==0.28.1
 id==1.5.0
 idna==3.11
 imagesize==1.4.1
-importlib-metadata==8.7.1 ; python_full_version < '3.12'
-importlib-resources==6.5.2 ; python_full_version < '3.10'
-iniconfig==2.1.0 ; python_full_version < '3.10'
-iniconfig==2.3.0 ; python_full_version >= '3.10'
+importlib-metadata==8.7.1
+iniconfig==2.3.0
 inquirerpy==0.3.4
 isodate==0.7.2 ; python_full_version < '3.11'
-isort==6.1.0 ; python_full_version < '3.10'
-isort==7.0.0 ; python_full_version >= '3.10'
+isort==7.0.0
 jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-context==6.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-functools==4.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
@@ -85,63 +82,54 @@ jinja2==3.1.6
 jmespath==1.0.1
 jsonpatch==1.33
 jsonpointer==3.0.0
-jsonschema==4.25.1 ; python_full_version < '3.10'
-jsonschema==4.26.0 ; python_full_version >= '3.10'
+jsonschema==4.26.0
 jsonschema-specifications==2025.9.1
 junit-xml==1.9
 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
-kiwisolver==1.4.7 ; python_full_version < '3.10'
-kiwisolver==1.4.9 ; python_full_version >= '3.10'
+kiwisolver==1.4.9
 librt==0.7.8 ; platform_python_implementation != 'PyPy'
 lxml==6.0.2
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.0.0 ; python_full_version >= '3.11'
 markdown-it-reporter==0.0.2
 markupsafe==3.0.3
-matplotlib==3.9.4 ; python_full_version < '3.10'
-matplotlib==3.10.8 ; python_full_version >= '3.10'
-mdit-py-plugins==0.4.2 ; python_full_version < '3.10'
-mdit-py-plugins==0.5.0 ; python_full_version >= '3.10'
+matplotlib==3.10.8
+mdit-py-plugins==0.5.0
 mdurl==0.1.2
-mirakuru==2.6.1 ; python_full_version < '3.10'
-mirakuru==3.0.1 ; python_full_version >= '3.10'
+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
 mypy==1.19.1
 mypy-extensions==1.1.0
-myst-parser==3.0.1 ; python_full_version < '3.10'
-myst-parser==4.0.1 ; python_full_version == '3.10.*'
+myst-parser==4.0.1 ; python_full_version < '3.11'
 myst-parser==5.0.0 ; python_full_version >= '3.11'
 nh3==0.3.2
-numpy==2.0.2 ; python_full_version < '3.10'
-numpy==2.2.6 ; python_full_version == '3.10.*'
+numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.1 ; python_full_version >= '3.11'
+oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
-owlrl==6.0.2 ; python_full_version < '3.10'
-owlrl==7.1.4 ; python_full_version >= '3.10'
-packaging==24.2 ; python_full_version < '3.10'
-packaging==25.0 ; python_full_version >= '3.10'
+owlrl==7.1.4
+packaging==25.0
 pathspec==1.0.3
 pfzy==0.3.4
-pillow==11.3.0 ; python_full_version < '3.10'
-pillow==12.1.0 ; python_full_version >= '3.10'
+pillow==12.1.0
 pkce==1.0.3
-platformdirs==4.4.0 ; python_full_version < '3.10'
-platformdirs==4.5.1 ; python_full_version >= '3.10'
+platformdirs==4.5.1
 playwright==1.57.0
 pluggy==1.6.0
-port-for==0.7.4 ; python_full_version < '3.10'
-port-for==1.0.0 ; python_full_version >= '3.10'
-prettytable==3.16.0 ; python_full_version < '3.10'
-prettytable==3.17.0 ; python_full_version >= '3.10'
+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'
-psycopg==3.2.13 ; python_full_version < '3.10'
-psycopg==3.3.2 ; python_full_version >= '3.10'
+psycopg==3.3.2
+pyasn1==0.6.2
+pyasn1-modules==0.4.2
 pycparser==2.23 ; (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
@@ -150,67 +138,56 @@ pyjwt==2.10.1
 pynacl==1.6.2
 pyparsing==3.3.1
 pyproject-hooks==1.2.0
-pyshacl==0.26.0 ; python_full_version < '3.10'
-pyshacl==0.30.1 ; python_full_version >= '3.10'
+pyshacl==0.30.1
 pysocks==1.7.1
-pytest==8.4.2 ; python_full_version < '3.10'
-pytest==9.0.2 ; python_full_version >= '3.10'
-pytest-asyncio==1.2.0 ; python_full_version < '3.10'
-pytest-asyncio==1.3.0 ; python_full_version >= '3.10'
+pytest==9.0.2
+pytest-asyncio==1.3.0
 pytest-base-url==2.1.0
 pytest-cov==7.0.0
-pytest-html==4.1.1
+pytest-html==4.2.0
 pytest-httpserver==1.1.3
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.15.1
-pytest-playwright==0.7.1 ; python_full_version < '3.10'
-pytest-playwright==0.7.2 ; python_full_version >= '3.10'
+pytest-playwright==0.7.2
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.2.0
 python-slugify==8.0.4
-pytokens==0.3.0
+pytokens==0.4.0
 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.3
-rdflib==7.4.0 ; python_full_version < '3.10'
-rdflib==7.5.0 ; python_full_version >= '3.10'
+rdflib==7.5.0
 readme-renderer==44.0
 referencing==0.36.2
 requests==2.32.5
 requests-cache==1.2.1
+requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 responses==0.25.8
 rfc3986==2.0.0
 rich==13.9.4
 rich-click==1.9.5
-roc-validator==0.4.2 ; python_full_version < '3.9.20'
-roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
-roc-validator==0.8.0 ; python_full_version >= '3.10'
+roc-validator==0.8.0
 roman-numerals==4.1.0 ; python_full_version >= '3.11'
-rpds-py==0.27.1 ; python_full_version < '3.10'
-rpds-py==0.30.0 ; python_full_version >= '3.10'
+rpds-py==0.30.0
+rsa==4.9.1
 ruamel-yaml==0.18.17
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
 rucio-clients==39.0.0
-s3transfer==0.15.0 ; python_full_version < '3.10'
-s3transfer==0.16.0 ; python_full_version >= '3.10'
+s3transfer==0.16.0
 schema-salad==8.9.20251102115403
-scipy==1.13.1 ; python_full_version < '3.10'
-scipy==1.15.3 ; python_full_version == '3.10.*'
+scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.0 ; python_full_version >= '3.11'
-secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
-secretstorage==3.5.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
-selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.39.0 ; python_full_version >= '3.10'
+secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
+selenium==4.40.0
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
 snowballstemmer==3.0.1
 sortedcontainers==2.4.0
-sphinx==7.4.7 ; python_full_version < '3.10'
-sphinx==8.1.3 ; python_full_version == '3.10.*'
+sphinx==8.1.3 ; python_full_version < '3.11'
 sphinx==9.0.4 ; python_full_version == '3.11.*'
 sphinx==9.1.0 ; python_full_version >= '3.12'
 sphinx-rtd-theme==3.1.0
@@ -222,8 +199,7 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 statsd==4.0.1
-stevedore==5.5.0 ; python_full_version < '3.10'
-stevedore==5.6.0 ; python_full_version >= '3.10'
+stevedore==5.6.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
 testfixtures==10.0.0 ; python_full_version >= '3.11'
@@ -232,28 +208,25 @@ tinydb==4.8.2
 toml==0.10.2
 tomli==2.4.0 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.3
-trio==0.31.0 ; python_full_version < '3.10'
-trio==0.32.0 ; python_full_version >= '3.10'
+trio==0.32.0
+trio-typing==0.10.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
 twine==6.2.0
 types-cachetools==6.2.0.20251022
-types-requests==2.31.0.6 ; python_full_version < '3.10'
-types-requests==2.32.4.20260107 ; python_full_version >= '3.10'
-types-urllib3==1.26.25.14 ; python_full_version < '3.10'
+types-certifi==2021.10.8.3
+types-requests==2.32.4.20260107
+types-urllib3==1.26.25.14
 typing-extensions==4.15.0
-typos==1.42.0 ; python_full_version >= '3.10'
+typos==1.42.1
 tzdata==2025.3 ; sys_platform == 'win32'
 url-normalize==2.2.1
-urllib3==1.26.20 ; python_full_version < '3.10'
-urllib3==2.6.3 ; python_full_version >= '3.10'
+urllib3==2.6.3
 watchdog==6.0.0
 wcwidth==0.2.14
-webencodings==0.5.1 ; python_full_version < '3.10'
 websocket-client==1.9.0
 werkzeug==3.1.5
-wsproto==1.2.0 ; python_full_version < '3.10'
-wsproto==1.3.2 ; python_full_version >= '3.10'
+wsproto==1.3.2
 yarl==1.22.0
-zipp==3.23.0 ; python_full_version < '3.12'
+zipp==3.23.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -3,84 +3,73 @@
 a2wsgi==1.10.10
 adal==1.2.7
 ag-ui-protocol==0.1.10
-aiobotocore==2.26.0 ; python_full_version < '3.10'
-aiobotocore==3.1.0 ; python_full_version >= '3.10'
+aiobotocore==3.1.0
 aiofiles==25.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.13.3
 aioitertools==0.13.0
 aiosignal==1.4.0
-alembic==1.16.5 ; python_full_version < '3.10'
-alembic==1.18.1 ; python_full_version >= '3.10'
+alembic==1.18.1
 amqp==5.3.1
 annotated-doc==0.0.4
 annotated-types==0.7.0
 anthropic==0.76.0
 anyio==4.12.1
-apispec==6.8.4 ; python_full_version < '3.10'
-apispec==6.9.0 ; python_full_version >= '3.10'
+apispec==6.9.0
 appdirs==1.4.4
 arcp==0.2.1
 argcomplete==3.6.3
 async-timeout==5.0.1 ; python_full_version < '3.11.3'
 attmap==0.13.2
 attrs==25.4.0
-authlib==1.6.6 ; python_full_version >= '3.10'
+authlib==1.6.6
 babel==2.17.0
-backports-tarfile==1.2.0 ; python_full_version >= '3.10' and python_full_version < '3.12'
+backports-tarfile==1.2.0 ; python_full_version < '3.12'
 bagit==1.9.0
 bagit-profile==1.3.1
 bcrypt==5.0.0
 bdbag==1.8.0
 beaker==1.13.0
-beartype==0.22.9 ; python_full_version >= '3.10'
+beartype==0.22.9
 billiard==4.2.4
 bioblend==1.7.0
-bleach==6.2.0 ; python_full_version < '3.10'
-bleach==6.3.0 ; python_full_version >= '3.10'
+bleach==6.3.0
 boltons==25.0.0
 boto==2.49.0
-boto3==1.41.5 ; python_full_version < '3.10'
-boto3==1.42.19 ; python_full_version >= '3.10'
-botocore==1.41.5 ; python_full_version < '3.10'
-botocore==1.42.19 ; python_full_version >= '3.10'
+boto3==1.42.19
+botocore==1.42.19
 bx-python==0.14.0
-cachecontrol==0.14.3 ; python_full_version < '3.10'
-cachecontrol==0.14.4 ; python_full_version >= '3.10'
-cachetools==6.2.4 ; python_full_version >= '3.10'
+cachecontrol==0.14.4
+cachetools==6.2.4
 celery==5.6.2
 certifi==2026.1.4
 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.4
 circus==0.19.0
-click==8.1.8 ; python_full_version < '3.10'
-click==8.3.1 ; python_full_version >= '3.10'
+click==8.3.1
 click-didyoumean==0.3.1
 click-plugins==1.1.1.2
 click-repl==0.3.0
 cloudauthz==0.6.0
 cloudbridge==3.2.0
-cloudpickle==3.1.2 ; python_full_version >= '3.10'
+cloudpickle==3.1.2
 cohere==5.20.1 ; sys_platform != 'emscripten'
 colorama==0.4.6
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
 cryptography==46.0.3
 ct3==3.4.0.post5
-cwl-upgrader==1.2.12 ; python_full_version < '3.10'
-cwl-upgrader==1.2.14 ; python_full_version >= '3.10'
+cwl-upgrader==1.2.14
 cwl-utils==0.40
-cwltool==3.1.20251031082601 ; python_full_version < '3.10'
-cwltool==3.1.20260108082145 ; python_full_version >= '3.10'
-cyclopts==4.5.0 ; python_full_version >= '3.10'
+cwltool==3.1.20260108082145
+cyclopts==4.5.0
 defusedxml==0.7.1
 deprecated==1.3.1
 deprecation==2.1.0
 dictobj==0.4
-diskcache==5.6.3 ; python_full_version >= '3.10'
+diskcache==5.6.3
 distro==1.9.0
-dnspython==2.7.0 ; python_full_version < '3.10'
-dnspython==2.8.0 ; python_full_version >= '3.10'
+dnspython==2.8.0
 docopt==0.6.2
 docstring-parser==0.17.0
 docutils==0.21.2 ; python_full_version < '3.11'
@@ -91,45 +80,38 @@ email-validator==2.3.0
 et-xmlfile==2.0.0
 eval-type-backport==0.3.1
 exceptiongroup==1.3.1
-executing==2.2.1 ; python_full_version >= '3.10'
-fakeredis==2.33.0 ; python_full_version >= '3.10'
+executing==2.2.1
+fakeredis==2.33.0
 fastapi==0.128.0
 fastavro==1.12.1 ; sys_platform != 'emscripten'
-fastmcp==2.14.3 ; python_full_version >= '3.10'
-filelock==3.19.1 ; python_full_version < '3.10'
-filelock==3.20.3 ; python_full_version >= '3.10'
+fastmcp==2.14.3
+filelock==3.20.3
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
-fsspec==2025.10.0 ; python_full_version < '3.10'
-fsspec==2026.1.0 ; python_full_version >= '3.10'
+fsspec==2026.1.0
 future==1.0.0
 genai-prices==0.0.51
 google-api-core==2.29.0
 google-auth==2.47.0
 google-cloud-batch==0.20.0
-google-genai==1.47.0 ; python_full_version < '3.10'
-google-genai==1.59.0 ; python_full_version >= '3.10'
+google-genai==1.59.0
 googleapis-common-protos==1.72.0
 gravity==1.2.0
-greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64')
-greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64')
-griffe==1.14.0 ; python_full_version < '3.10'
-griffe==1.15.0 ; python_full_version >= '3.10'
+greenlet==3.3.0 ; 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'
+griffe==1.15.0
 groq==1.0.0
 grpcio==1.76.0
-grpcio-status==1.71.2 ; python_full_version < '3.10'
-grpcio-status==1.76.0 ; python_full_version >= '3.10'
+grpcio-status==1.76.0
 gunicorn==23.0.0
 gxformat2==0.21.0
 h11==0.16.0
 h5grove==2.3.0
-h5py==3.14.0 ; python_full_version < '3.10'
-h5py==3.15.1 ; python_full_version >= '3.10'
+h5py==3.15.1
 hf-xet==1.2.0 ; platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'
 httpcore==1.0.9
 httpx==0.28.1
-httpx-sse==0.4.3 ; python_full_version >= '3.10'
+httpx-sse==0.4.3
 huggingface-hub==0.36.0
 humanfriendly==10.0
 idna==3.11
@@ -140,35 +122,32 @@ invoke==2.2.1
 isa-rwval==0.10.11
 isal==1.8.0
 isodate==0.7.2 ; python_full_version < '3.11'
-jaraco-classes==3.4.0 ; python_full_version >= '3.10'
-jaraco-context==6.1.0 ; python_full_version >= '3.10'
-jaraco-functools==4.4.0 ; python_full_version >= '3.10'
-jeepney==0.9.0 ; python_full_version >= '3.10' and sys_platform == 'linux'
+jaraco-classes==3.4.0
+jaraco-context==6.1.0
+jaraco-functools==4.4.0
+jeepney==0.9.0 ; sys_platform == 'linux'
 jinja2==3.1.6
 jiter==0.12.0
 jmespath==1.0.1
 jsonref==1.1.0
-jsonschema==4.25.1 ; python_full_version < '3.10'
-jsonschema==4.26.0 ; python_full_version >= '3.10'
-jsonschema-path==0.3.4 ; python_full_version >= '3.10'
+jsonschema==4.26.0
+jsonschema-path==0.3.4
 jsonschema-specifications==2025.9.1
-keyring==25.7.0 ; python_full_version >= '3.10'
+keyring==25.7.0
 kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
-limits==4.2 ; python_full_version < '3.10'
-limits==5.6.0 ; python_full_version >= '3.10'
-logfire==4.19.0 ; python_full_version >= '3.10'
+limits==5.6.0
+logfire==4.19.0
 logfire-api==4.19.0
-lupa==2.6 ; python_full_version >= '3.10'
+lupa==2.6
 lxml==6.0.2
 mako==1.3.10
-markdown==3.9 ; python_full_version < '3.10'
-markdown==3.10 ; python_full_version >= '3.10'
+markdown==3.10
 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 ; python_full_version >= '3.10'
+mcp==1.25.0
 mdurl==0.1.2
 mercurial==7.1.2 ; python_version < '3.14'
 mercurial==7.2rc0 ; python_version >= '3.14'
@@ -180,73 +159,62 @@ msal==1.34.0
 msgpack==1.1.2
 multidict==6.7.0
 mypy-extensions==1.1.0
-networkx==3.2.1 ; python_full_version < '3.10'
-networkx==3.4.2 ; python_full_version == '3.10.*'
+networkx==3.4.2 ; python_full_version < '3.11'
 networkx==3.6.1 ; python_full_version >= '3.11'
-nexus-rpc==1.1.0 ; python_full_version < '3.10'
-nexus-rpc==1.2.0 ; python_full_version >= '3.10'
+nexus-rpc==1.2.0
 nodejs-wheel==22.20.0
 nodejs-wheel-binaries==22.20.0
-numpy==2.0.2 ; python_full_version < '3.10'
-numpy==2.2.6 ; python_full_version == '3.10.*'
+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
-openapi-pydantic==0.5.1 ; python_full_version >= '3.10'
+openapi-pydantic==0.5.1
 openpyxl==3.1.5
 opentelemetry-api==1.39.1
-opentelemetry-exporter-otlp-proto-common==1.39.1 ; python_full_version >= '3.10'
-opentelemetry-exporter-otlp-proto-http==1.39.1 ; python_full_version >= '3.10'
-opentelemetry-exporter-prometheus==0.60b1 ; python_full_version >= '3.10'
-opentelemetry-instrumentation==0.60b1 ; python_full_version >= '3.10'
-opentelemetry-instrumentation-httpx==0.60b1 ; python_full_version >= '3.10'
-opentelemetry-proto==1.39.1 ; python_full_version >= '3.10'
-opentelemetry-sdk==1.39.1 ; python_full_version >= '3.10'
-opentelemetry-semantic-conventions==0.60b1 ; python_full_version >= '3.10'
-opentelemetry-util-http==0.60b1 ; python_full_version >= '3.10'
+opentelemetry-exporter-otlp-proto-common==1.39.1
+opentelemetry-exporter-otlp-proto-http==1.39.1
+opentelemetry-exporter-prometheus==0.60b1
+opentelemetry-instrumentation==0.60b1
+opentelemetry-instrumentation-httpx==0.60b1
+opentelemetry-proto==1.39.1
+opentelemetry-sdk==1.39.1
+opentelemetry-semantic-conventions==0.60b1
+opentelemetry-util-http==0.60b1
 orjson==3.11.5
 oyaml==1.0
-packaging==24.2 ; python_full_version < '3.10'
-packaging==25.0 ; python_full_version >= '3.10'
+packaging==25.0
 paramiko==4.0.0
 parsley==1.3
 paste==3.10.1
 pastedeploy==3.1.0
-pathable==0.4.4 ; python_full_version >= '3.10'
-pathvalidate==3.3.1 ; python_full_version >= '3.10'
+pathable==0.4.4
+pathvalidate==3.3.1
 pebble==5.1.3
-pillow==11.3.0 ; python_full_version < '3.10'
-pillow==12.1.0 ; python_full_version >= '3.10'
-platformdirs==4.5.1 ; python_full_version >= '3.10'
-prometheus-client==0.24.1 ; python_full_version >= '3.10'
+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==5.29.5 ; python_full_version < '3.10'
-protobuf==6.33.4 ; python_full_version >= '3.10'
+protobuf==6.33.4
 prov==1.5.1
 psutil==7.2.1
 pulsar-galaxy-lib==0.15.13
-py-key-value-aio==0.3.0 ; python_full_version >= '3.10'
-py-key-value-shared==0.3.0 ; python_full_version >= '3.10'
+py-key-value-aio==0.3.0
+py-key-value-shared==0.3.0
 pyasn1==0.6.2
 pyasn1-modules==0.4.2
 pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
 pydantic==2.12.5
-pydantic-ai==0.8.1 ; python_full_version < '3.10'
-pydantic-ai==1.44.0 ; python_full_version >= '3.10'
-pydantic-ai-slim==0.8.1 ; python_full_version < '3.10'
-pydantic-ai-slim==1.44.0 ; python_full_version >= '3.10'
+pydantic-ai==1.44.0
+pydantic-ai-slim==1.44.0
 pydantic-core==2.41.5
-pydantic-evals==0.8.1 ; python_full_version < '3.10'
-pydantic-evals==1.44.0 ; python_full_version >= '3.10'
-pydantic-graph==0.8.1 ; python_full_version < '3.10'
-pydantic-graph==1.44.0 ; python_full_version >= '3.10'
-pydantic-settings==2.11.0 ; python_full_version < '3.10'
-pydantic-settings==2.12.0 ; python_full_version >= '3.10'
+pydantic-evals==1.44.0
+pydantic-graph==1.44.0
+pydantic-settings==2.12.0
 pydantic-tes==0.2.0
-pydocket==0.16.6 ; python_full_version >= '3.10'
+pydocket==0.16.6
 pydot==4.0.1
 pyeventsystem==0.1.0
 pyfaidx==0.9.0.3
@@ -262,20 +230,18 @@ pyreadline3==3.5.4 ; sys_platform == 'win32'
 pysam==0.23.3
 python-dateutil==2.9.0.post0
 python-dotenv==1.2.1
-python-json-logger==4.0.0 ; python_full_version >= '3.10'
+python-json-logger==4.0.0
 python-magic==0.4.27
-python-multipart==0.0.20 ; python_full_version < '3.10'
-python-multipart==0.0.21 ; python_full_version >= '3.10'
+python-multipart==0.0.21
 python-slugify==8.0.4
 python3-openid==3.2.0
 pytz==2025.2
-pywin32==311 ; python_full_version >= '3.10' and sys_platform == 'win32'
-pywin32-ctypes==0.2.3 ; python_full_version >= '3.10' and sys_platform == 'win32'
+pywin32==311 ; sys_platform == 'win32'
+pywin32-ctypes==0.2.3 ; sys_platform == 'win32'
 pyyaml==6.0.3
 pyzmq==27.1.0
-rdflib==7.4.0 ; python_full_version < '3.10'
-rdflib==7.5.0 ; python_full_version >= '3.10'
-redis==7.1.0 ; python_full_version >= '3.10'
+rdflib==7.5.0
+redis==7.1.0
 referencing==0.36.2
 refgenconf==0.12.2
 regex==2026.1.15
@@ -286,45 +252,38 @@ requests-toolbelt==1.0.0
 requests-unixsocket==0.4.1
 rich==13.9.4
 rich-argparse==1.7.2
-rich-rst==1.3.2 ; python_full_version >= '3.10'
+rich-rst==1.3.2
 rocrate==0.14.2
 routes==2.5.1
-rpds-py==0.27.1 ; python_full_version < '3.10'
-rpds-py==0.30.0 ; python_full_version >= '3.10'
+rpds-py==0.30.0
 rsa==4.9.1
 ruamel-yaml==0.18.17
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
-s3fs==2025.10.0 ; python_full_version < '3.10'
-s3fs==2026.1.0 ; python_full_version >= '3.10'
-s3transfer==0.15.0 ; python_full_version < '3.10'
-s3transfer==0.16.0 ; python_full_version >= '3.10'
+s3fs==2026.1.0
+s3transfer==0.16.0
 schema-salad==8.9.20251102115403
-secretstorage==3.5.0 ; python_full_version >= '3.10' and sys_platform == 'linux'
+secretstorage==3.5.0 ; sys_platform == 'linux'
 setuptools==80.9.0
-shellingham==1.5.4 ; python_full_version >= '3.10'
+shellingham==1.5.4
 six==1.17.0
 slowapi==0.1.9
 sniffio==1.3.1
-social-auth-core==4.7.0 ; python_full_version < '3.10'
-social-auth-core==4.8.3 ; python_full_version >= '3.10'
+social-auth-core==4.8.3
 sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.45
 sqlparse==0.5.5
-sse-starlette==3.1.2 ; python_full_version >= '3.10'
-starlette==0.49.3 ; python_full_version < '3.10'
-starlette==0.50.0 ; python_full_version >= '3.10'
+sse-starlette==3.2.0
+starlette==0.50.0
 starlette-context==0.4.0
 supervisor==4.3.0
 svgwrite==1.4.3
-temporalio==1.16.0 ; python_full_version < '3.10'
-temporalio==1.20.0 ; python_full_version >= '3.10'
+temporalio==1.20.0
 tenacity==9.1.2
 text-unidecode==1.3
-tifffile==2024.8.30 ; python_full_version < '3.10'
-tifffile==2025.5.10 ; python_full_version == '3.10.*'
+tifffile==2025.5.10 ; python_full_version < '3.11'
 tifffile==2026.1.14 ; python_full_version >= '3.11'
-tiktoken==0.12.0 ; python_full_version >= '3.10'
+tiktoken==0.12.0
 tinydb==4.8.2
 tokenizers==0.22.2 ; sys_platform != 'emscripten'
 tomli==2.4.0 ; python_full_version < '3.11'
@@ -332,20 +291,16 @@ tornado==6.5.4
 tqdm==4.67.1
 tuspy==1.1.0
 tuspyserver==4.2.3
-typer==0.21.1 ; python_full_version >= '3.10'
+typer==0.21.1
 types-protobuf==6.32.1.20251210
-types-requests==2.31.0.6 ; python_full_version < '3.10' and sys_platform != 'emscripten'
-types-requests==2.32.4.20260107 ; python_full_version >= '3.10' and sys_platform != 'emscripten'
-types-urllib3==1.26.25.14 ; python_full_version < '3.10' and sys_platform != 'emscripten'
+types-requests==2.32.4.20260107 ; sys_platform != 'emscripten'
 typing-extensions==4.15.0
 typing-inspection==0.4.2
 tzdata==2025.3
 tzlocal==5.3.1
 ubiquerg==0.8.2
-urllib3==1.26.20 ; python_full_version < '3.10'
-urllib3==2.6.3 ; python_full_version >= '3.10'
-uvicorn==0.39.0 ; python_full_version < '3.10'
-uvicorn==0.40.0 ; python_full_version >= '3.10'
+urllib3==2.6.3
+uvicorn==0.40.0
 uvloop==0.22.1
 vine==5.1.0
 wcwidth==0.2.14

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

@@ -4,170 +4,153 @@ aiohappyeyeballs==2.6.1
 aiohttp==3.13.3
 aiosignal==1.4.0
 anyio==4.12.1
-ase==3.26.0 ; python_full_version < '3.10'
-ase==3.27.0 ; python_full_version >= '3.10'
+ase==3.27.0
+async-generator==1.10
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.4.0
 axe-selenium-python==2.1.6
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
-boto3==1.41.5 ; python_full_version < '3.10'
-boto3==1.42.19 ; python_full_version >= '3.10'
-botocore==1.41.5 ; python_full_version < '3.10'
-botocore==1.42.19 ; python_full_version >= '3.10'
-cachecontrol==0.14.3 ; python_full_version < '3.10'
-cachecontrol==0.14.4 ; python_full_version >= '3.10'
+boto3==1.42.19
+botocore==1.42.19
+cachecontrol==0.14.4
 cachetools==6.2.4
 cattrs==25.3.0
 certifi==2026.1.4
 cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt'
 charset-normalizer==3.4.4
-click==8.1.8 ; python_full_version < '3.10'
-click==8.3.1 ; python_full_version >= '3.10'
+click==8.3.1
 colorama==0.4.6 ; sys_platform == 'win32'
 colorlog==6.10.1
-contourpy==1.3.0 ; python_full_version < '3.10'
-contourpy==1.3.2 ; python_full_version == '3.10.*'
+contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.10.7 ; python_full_version < '3.10'
-coverage==7.13.1 ; python_full_version >= '3.10'
-cwltest==2.6.20250818005349 ; python_full_version < '3.10'
-cwltest==2.6.20251216093331 ; python_full_version >= '3.10'
+coverage==7.13.1
+cwltest==2.6.20251216093331
 cycler==0.12.1
 decorator==5.2.1
 defusedxml==0.7.1
-dogpile-cache==1.4.1 ; python_full_version < '3.10'
-dogpile-cache==1.5.0 ; python_full_version >= '3.10'
-enum-tools==0.12.0 ; python_full_version >= '3.10'
+dogpile-cache==1.5.0
+enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.19.1 ; python_full_version < '3.10'
-filelock==3.20.3 ; python_full_version >= '3.10'
+filelock==3.20.3
 fluent-logger==0.11.1
-fonttools==4.60.2 ; python_full_version < '3.10'
-fonttools==4.61.1 ; python_full_version >= '3.10'
+fonttools==4.61.1
 frozenlist==1.8.0
-greenlet==3.2.4 ; python_full_version < '3.10'
-greenlet==3.3.0 ; python_full_version >= '3.10'
+fsspec==2026.1.0
+gcsfs==2026.1.0
+google-api-core==2.29.0
+google-auth==2.47.0
+google-auth-oauthlib==1.2.4
+google-cloud-core==2.5.0
+google-cloud-storage==3.8.0
+google-cloud-storage-control==1.9.0
+google-crc32c==1.8.0
+google-resumable-media==2.8.0
+googleapis-common-protos==1.72.0
+greenlet==3.3.0
+grpc-google-iam-v1==0.14.3
+grpcio==1.76.0
+grpcio-status==1.76.0
 h11==0.16.0
-html5lib==1.1 ; python_full_version < '3.10'
-html5rdf==1.2.1 ; python_full_version >= '3.10'
+html5rdf==1.2.1
 httpcore==1.0.9
 httpx==0.28.1
 idna==3.11
-importlib-metadata==8.7.1 ; python_full_version < '3.12'
-importlib-resources==6.5.2 ; python_full_version < '3.10'
-iniconfig==2.1.0 ; python_full_version < '3.10'
-iniconfig==2.3.0 ; python_full_version >= '3.10'
+importlib-metadata==8.7.1
+iniconfig==2.3.0
 inquirerpy==0.3.4
 isodate==0.7.2 ; python_full_version < '3.11'
 jinja2==3.1.6
 jmespath==1.0.1
 jsonpatch==1.33
 jsonpointer==3.0.0
-jsonschema==4.25.1 ; python_full_version < '3.10'
-jsonschema==4.26.0 ; python_full_version >= '3.10'
+jsonschema==4.26.0
 jsonschema-specifications==2025.9.1
 junit-xml==1.9
-kiwisolver==1.4.7 ; python_full_version < '3.10'
-kiwisolver==1.4.9 ; python_full_version >= '3.10'
+kiwisolver==1.4.9
 librt==0.7.8 ; platform_python_implementation != 'PyPy'
 lxml==6.0.2
 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
-matplotlib==3.9.4 ; python_full_version < '3.10'
-matplotlib==3.10.8 ; python_full_version >= '3.10'
+matplotlib==3.10.8
 mdurl==0.1.2
-mirakuru==2.6.1 ; python_full_version < '3.10'
-mirakuru==3.0.1 ; python_full_version >= '3.10'
+mirakuru==3.0.1
 mistune==3.1.4
 msgpack==1.1.2
 multidict==6.7.0
 mypy==1.19.1
 mypy-extensions==1.1.0
-numpy==2.0.2 ; python_full_version < '3.10'
-numpy==2.2.6 ; python_full_version == '3.10.*'
+numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.1 ; python_full_version >= '3.11'
+oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
-owlrl==6.0.2 ; python_full_version < '3.10'
-owlrl==7.1.4 ; python_full_version >= '3.10'
-packaging==24.2 ; python_full_version < '3.10'
-packaging==25.0 ; python_full_version >= '3.10'
+owlrl==7.1.4
+packaging==25.0
 pathspec==1.0.3
 pfzy==0.3.4
-pillow==11.3.0 ; python_full_version < '3.10'
-pillow==12.1.0 ; python_full_version >= '3.10'
+pillow==12.1.0
 pkce==1.0.3
-platformdirs==4.4.0 ; python_full_version < '3.10'
-platformdirs==4.5.1 ; python_full_version >= '3.10'
+platformdirs==4.5.1
 playwright==1.57.0
 pluggy==1.6.0
-port-for==0.7.4 ; python_full_version < '3.10'
-port-for==1.0.0 ; python_full_version >= '3.10'
-prettytable==3.16.0 ; python_full_version < '3.10'
-prettytable==3.17.0 ; python_full_version >= '3.10'
+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'
-psycopg==3.2.13 ; python_full_version < '3.10'
-psycopg==3.3.2 ; python_full_version >= '3.10'
+psycopg==3.3.2
+pyasn1==0.6.2
+pyasn1-modules==0.4.2
 pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt'
 pyee==13.0.0
 pygments==2.19.2
 pyparsing==3.3.1
-pyshacl==0.26.0 ; python_full_version < '3.10'
-pyshacl==0.30.1 ; python_full_version >= '3.10'
+pyshacl==0.30.1
 pysocks==1.7.1
-pytest==8.4.2 ; python_full_version < '3.10'
-pytest==9.0.2 ; python_full_version >= '3.10'
-pytest-asyncio==1.2.0 ; python_full_version < '3.10'
-pytest-asyncio==1.3.0 ; python_full_version >= '3.10'
+pytest==9.0.2
+pytest-asyncio==1.3.0
 pytest-base-url==2.1.0
 pytest-cov==7.0.0
-pytest-html==4.1.1
+pytest-html==4.2.0
 pytest-httpserver==1.1.3
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.15.1
-pytest-playwright==0.7.1 ; python_full_version < '3.10'
-pytest-playwright==0.7.2 ; python_full_version >= '3.10'
+pytest-playwright==0.7.2
 pytest-postgresql==7.0.2
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.2.0
 python-slugify==8.0.4
 pyyaml==6.0.3
-rdflib==7.4.0 ; python_full_version < '3.10'
-rdflib==7.5.0 ; python_full_version >= '3.10'
+rdflib==7.5.0
 referencing==0.36.2
 requests==2.32.5
 requests-cache==1.2.1
+requests-oauthlib==2.0.0
 responses==0.25.8
 rich==13.9.4
 rich-click==1.9.5
-roc-validator==0.4.2 ; python_full_version < '3.9.20'
-roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
-roc-validator==0.8.0 ; python_full_version >= '3.10'
-rpds-py==0.27.1 ; python_full_version < '3.10'
-rpds-py==0.30.0 ; python_full_version >= '3.10'
+roc-validator==0.8.0
+rpds-py==0.30.0
+rsa==4.9.1
 ruamel-yaml==0.18.17
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
 rucio-clients==39.0.0
-s3transfer==0.15.0 ; python_full_version < '3.10'
-s3transfer==0.16.0 ; python_full_version >= '3.10'
+s3transfer==0.16.0
 schema-salad==8.9.20251102115403
-scipy==1.13.1 ; python_full_version < '3.10'
-scipy==1.15.3 ; python_full_version == '3.10.*'
+scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.0 ; python_full_version >= '3.11'
-selenium==4.32.0 ; python_full_version < '3.10'
-selenium==4.39.0 ; python_full_version >= '3.10'
+selenium==4.40.0
 seletools==1.5.0
 six==1.17.0
 sniffio==1.3.1
 sortedcontainers==2.4.0
 statsd==4.0.1
-stevedore==5.5.0 ; python_full_version < '3.10'
-stevedore==5.6.0 ; python_full_version >= '3.10'
+stevedore==5.6.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
 testfixtures==10.0.0 ; python_full_version >= '3.11'
@@ -176,27 +159,24 @@ tinydb==4.8.2
 toml==0.10.2
 tomli==2.4.0 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.3
-trio==0.31.0 ; python_full_version < '3.10'
-trio==0.32.0 ; python_full_version >= '3.10'
+trio==0.32.0
+trio-typing==0.10.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1
 types-cachetools==6.2.0.20251022
-types-requests==2.31.0.6 ; python_full_version < '3.10'
-types-requests==2.32.4.20260107 ; python_full_version >= '3.10'
-types-urllib3==1.26.25.14 ; python_full_version < '3.10'
+types-certifi==2021.10.8.3
+types-requests==2.32.4.20260107
+types-urllib3==1.26.25.14
 typing-extensions==4.15.0
-typos==1.42.0 ; python_full_version >= '3.10'
+typos==1.42.1
 tzdata==2025.3 ; sys_platform == 'win32'
 url-normalize==2.2.1
-urllib3==1.26.20 ; python_full_version < '3.10'
-urllib3==2.6.3 ; python_full_version >= '3.10'
+urllib3==2.6.3
 watchdog==6.0.0
 wcwidth==0.2.14
-webencodings==0.5.1 ; python_full_version < '3.10'
 websocket-client==1.9.0
 werkzeug==3.1.5
-wsproto==1.2.0 ; python_full_version < '3.10'
-wsproto==1.3.2 ; python_full_version >= '3.10'
+wsproto==1.3.2
 yarl==1.22.0
-zipp==3.23.0 ; python_full_version < '3.12'
+zipp==3.23.0

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

@@ -27,13 +27,11 @@ types-paramiko==4.0.0.20250822
 types-python-dateutil==2.9.0.20251115
 types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20250915
-types-requests==2.31.0.6 ; python_full_version < '3.10'
-types-requests==2.32.4.20260107 ; python_full_version >= '3.10'
+types-requests==2.32.4.20260107
 types-s3transfer==0.16.0
 types-setuptools==80.9.0.20251223
 types-six==1.17.0.20251009
-types-urllib3==1.26.25.14 ; python_full_version < '3.10'
 types-webencodings==0.5.0.20251108
 typing-extensions==4.15.0
 typing-inspection==0.4.2
-urllib3==2.6.3 ; python_full_version >= '3.10'
+urllib3==2.6.3

lib/galaxy/files/__init__.py

@@ -1,9 +1,9 @@
 import logging
 import os
 from collections import defaultdict
+from collections.abc import Callable
 from typing import (
     Any,
-    Callable,
     NamedTuple,
     Optional,
     Protocol,

lib/galaxy/files/sources/azure.py

@@ -1,4 +1,4 @@
-from typing_extensions import Literal
+from typing import Literal
 
 try:
     from fs.azblob.blob_fs import BlobFS

lib/galaxy/files/sources/invenio.py

@@ -5,13 +5,13 @@ import urllib.request
 from typing import (
     Any,
     cast,
+    Literal,
     Optional,
 )
 from urllib.error import HTTPError
 from urllib.parse import quote
 
 from typing_extensions import (
-    Literal,
     TypedDict,
 )
 

lib/galaxy/files/templates/models.py

@@ -1,6 +1,7 @@
 from typing import (
     Annotated,
     Any,
+    Literal,
     Optional,
     Union,
 )
@@ -9,7 +10,6 @@ from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import Literal
 
 from galaxy.util.config_templates import (
     ConfiguredOAuth2Sources,

lib/galaxy/job_execution/container_monitor.py

@@ -6,8 +6,8 @@ import sys
 import tempfile
 import time
 import traceback
+from collections.abc import Callable
 from functools import partial
-from typing import Callable
 
 from galaxy.tool_util.deps import docker_util
 from galaxy.util import (

lib/galaxy/job_execution/output_collect.py

@@ -5,10 +5,10 @@ import logging
 import operator
 import os
 import re
+from collections.abc import Callable
 from tempfile import NamedTemporaryFile
 from typing import (
     Any,
-    Callable,
     Optional,
     TYPE_CHECKING,
     Union,

lib/galaxy/jobs/__init__.py

@@ -15,7 +15,10 @@ import shutil
 import sys
 import time
 import traceback
-from collections.abc import Iterable
+from collections.abc import (
+    Callable,
+    Iterable,
+)
 from dataclasses import (
     dataclass,
     field,
@@ -23,7 +26,6 @@ from dataclasses import (
 from json import loads
 from typing import (
     Any,
-    Callable,
     cast,
     Optional,
     TYPE_CHECKING,

lib/galaxy/jobs/job_destination.py

@@ -1,4 +1,3 @@
-import sys
 from dataclasses import (
     dataclass,
     field,
@@ -14,10 +13,8 @@ if TYPE_CHECKING:
     from galaxy.jobs import ResubmitConfigDict
     from galaxy.model import Job
 
-dataclass_kwargs = {"kw_only": True} if sys.version_info >= (3, 10) else {}
 
-
-@dataclass(**dataclass_kwargs, eq=False)
+@dataclass(kw_only=True, eq=False)
 class JobDestination:
     """
     Provides details about where a job runs

lib/galaxy/jobs/mapper.py

@@ -1,9 +1,9 @@
 import importlib
 import logging
+from collections.abc import Callable
 from inspect import getfullargspec
 from types import ModuleType
 from typing import (
-    Callable,
     TYPE_CHECKING,
     Union,
 )

lib/galaxy/jobs/runners/drmaa.py

@@ -10,11 +10,10 @@ import string
 import time
 from typing import (
     TYPE_CHECKING,
+    TypeAlias,
     Union,
 )
 
-from typing_extensions import TypeAlias
-
 from galaxy import model
 from galaxy.jobs.handler import DEFAULT_JOB_RUNNER_FAILURE_MESSAGE
 from galaxy.jobs.job_destination import JobDestination

lib/galaxy/jobs/runners/util/cli/job/__init__.py

@@ -7,8 +7,7 @@ from abc import (
     abstractmethod,
 )
 from enum import Enum
-
-from typing_extensions import TypeAlias
+from typing import TypeAlias
 
 try:
     from galaxy.model import Job

lib/galaxy/managers/base.py

@@ -30,10 +30,10 @@ import builtins
 import datetime
 import logging
 import re
+from collections.abc import Callable
 from functools import partial
 from typing import (
     Any,
-    Callable,
     Generic,
     NamedTuple,
     Optional,

lib/galaxy/managers/collections.py

@@ -1,6 +1,7 @@
 import logging
 from typing import (
     Any,
+    Literal,
     Optional,
     overload,
     TYPE_CHECKING,
@@ -12,7 +13,6 @@ from sqlalchemy.orm import (
     joinedload,
     Query,
 )
-from typing_extensions import Literal
 
 from galaxy import model
 from galaxy.datatypes.registry import Registry

lib/galaxy/managers/context.py

@@ -37,10 +37,10 @@ A method that requires a user but not a history should declare its
 # more checks against this issue.
 import abc
 import string
+from collections.abc import Callable
 from json import dumps
 from typing import (
     Any,
-    Callable,
     cast,
     Literal,
     Optional,

lib/galaxy/managers/histories.py

@@ -9,6 +9,7 @@ import logging
 from typing import (
     Any,
     cast,
+    Literal,
     Optional,
     TYPE_CHECKING,
     Union,
@@ -25,7 +26,6 @@ from sqlalchemy import (
     true,
 )
 from sqlalchemy.orm import aliased
-from typing_extensions import Literal
 
 from galaxy import model
 from galaxy.exceptions import (

lib/galaxy/managers/pages.py

@@ -8,10 +8,10 @@ from within Galaxy.
 
 import logging
 import re
+from collections.abc import Callable
 from html.entities import name2codepoint
 from html.parser import HTMLParser
 from typing import (
-    Callable,
     Optional,
     TYPE_CHECKING,
     Union,

lib/galaxy/managers/workflows.py

@@ -9,6 +9,7 @@ from typing import (
     NamedTuple,
     Optional,
     TYPE_CHECKING,
+    TypeAlias,
     Union,
 )
 
@@ -41,9 +42,6 @@ from sqlalchemy.orm import (
     joinedload,
     subqueryload,
 )
-from typing_extensions import (
-    TypeAlias,
-)
 
 from galaxy import (
     exceptions,

lib/galaxy/model/__init__.py

@@ -32,10 +32,12 @@ from typing import (
     cast,
     ClassVar,
     Generic,
+    Literal,
     NamedTuple,
     Optional,
     overload,
     TYPE_CHECKING,
+    TypeAlias,
     TypeVar,
     Union,
 )
@@ -132,10 +134,8 @@ from sqlalchemy.orm.session import Session
 from sqlalchemy.sql.expression import FromClause
 from typing_extensions import (
     deprecated,
-    Literal,
     NotRequired,
     Protocol,
-    TypeAlias,
     TypedDict,
 )
 

lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py

@@ -1,6 +1,7 @@
 from dataclasses import dataclass
 from typing import (
     cast,
+    Literal,
     Optional,
     Protocol,
     TYPE_CHECKING,
@@ -15,7 +16,6 @@ from pydantic import (
     BaseModel,
     Field,
 )
-from typing_extensions import Literal
 
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.model.dataset_collections.rule_target_columns import (

lib/galaxy/model/migrations/alembic/env.py

@@ -1,7 +1,7 @@
 import logging
 import re
+from collections.abc import Callable
 from typing import (
-    Callable,
     cast,
 )
 

lib/galaxy/model/store/__init__.py

@@ -8,6 +8,7 @@ import tarfile
 import tempfile
 from collections import defaultdict
 from collections.abc import (
+    Callable,
     Iterable,
     Iterator,
 )
@@ -22,7 +23,6 @@ from tempfile import mkdtemp
 from types import TracebackType
 from typing import (
     Any,
-    Callable,
     cast,
     Literal,
     Optional,

lib/galaxy/model/store/discover.py

@@ -9,10 +9,12 @@ corresponding to files in other contexts.
 import abc
 import logging
 import os
-from collections.abc import Iterable
+from collections.abc import (
+    Callable,
+    Iterable,
+)
 from typing import (
     Any,
-    Callable,
     NamedTuple,
     Optional,
     TYPE_CHECKING,

lib/galaxy/model/tool_shed_install/__init__.py

@@ -1,10 +1,10 @@
 import logging
 import os
+from collections.abc import Callable
 from datetime import datetime
 from enum import Enum
 from typing import (
     Any,
-    Callable,
     Optional,
 )
 

lib/galaxy/model/unittest_utils/model_testing_utils.py

@@ -1,9 +1,11 @@
 import os
 import uuid
-from collections.abc import Iterator
+from collections.abc import (
+    Callable,
+    Iterator,
+)
 from contextlib import contextmanager
 from typing import (
-    Callable,
     Optional,
 )
 

lib/galaxy/queue_worker.py

@@ -135,7 +135,7 @@ class ControlTask:
                     while self.response is self._response:
                         self.connection.drain_events(timeout=timeout)
                 return self.response
-        except socket.timeout:
+        except TimeoutError:
             log.exception("Error waiting for task: '%s' sent with routing key '%s'", payload, routing_key)
         except Exception:
             log.exception("Error queueing async task: '%s'. for %s", payload, routing_key)

lib/galaxy/quota/_schema.py

@@ -1,5 +1,6 @@
 from enum import Enum
 from typing import (
+    Literal,
     Optional,
 )
 
@@ -7,7 +8,6 @@ from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import Literal
 
 from galaxy.schema.fields import (
     EncodedDatabaseIdField,

lib/galaxy/schema/fetch_data.py

@@ -3,6 +3,7 @@ from enum import Enum
 from typing import (
     Annotated,
     Any,
+    Literal,
     Optional,
     Union,
 )
@@ -17,7 +18,6 @@ from pydantic import (
     TypeAdapter,
     UUID4,
 )
-from typing_extensions import Literal
 
 from galaxy.schema.fields import DecodedDatabaseIdField
 from galaxy.schema.schema import Model

lib/galaxy/schema/fields.py

@@ -1,7 +1,8 @@
 import re
+from collections.abc import Callable
 from typing import (
     Annotated,
-    Callable,
+    get_args,
     get_origin,
     TYPE_CHECKING,
     Union,
@@ -14,9 +15,6 @@ from pydantic import (
     WithJsonSchema,
 )
 from pydantic_core import PydanticCustomError
-from typing_extensions import (
-    get_args,
-)
 
 from galaxy.exceptions import MessageException
 

lib/galaxy/schema/groups.py

@@ -1,10 +1,12 @@
-from typing import Optional
+from typing import (
+    Literal,
+    Optional,
+)
 
 from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import Literal
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,

lib/galaxy/schema/history.py

@@ -1,5 +1,6 @@
 from datetime import datetime
 from typing import (
+    Literal,
     Optional,
 )
 
@@ -8,7 +9,6 @@ from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import Literal
 
 from galaxy.schema.fields import EncodedDatabaseIdField
 from galaxy.schema.schema import (

lib/galaxy/schema/invocation.py

@@ -4,6 +4,7 @@ from typing import (
     Annotated,
     Any,
     Generic,
+    Literal,
     Optional,
     Union,
 )
@@ -17,7 +18,6 @@ from pydantic import (
     UUID4,
 )
 from typing_extensions import (
-    Literal,
     TypeAliasType,
 )
 

lib/galaxy/schema/jobs.py

@@ -1,6 +1,7 @@
 import json
 from typing import (
     Any,
+    Literal,
     Optional,
     Union,
 )
@@ -11,7 +12,6 @@ from pydantic import (
     field_validator,
     UUID4,
 )
-from typing_extensions import Literal
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,

lib/galaxy/schema/library_contents.py

@@ -3,6 +3,7 @@ from enum import Enum
 from typing import (
     Annotated,
     Any,
+    Literal,
     Optional,
     Union,
 )
@@ -13,9 +14,6 @@ from pydantic import (
     RootModel,
 )
 from pydantic.functional_validators import field_validator
-from typing_extensions import (
-    Literal,
-)
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,

lib/galaxy/schema/notifications.py

@@ -4,6 +4,7 @@ from typing import (
     Annotated,
     Any,
     Generic,
+    Literal,
     Optional,
     Union,
 )
@@ -13,9 +14,6 @@ from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import (
-    Literal,
-)
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,

lib/galaxy/schema/schema.py

@@ -9,7 +9,9 @@ from enum import Enum
 from typing import (
     Annotated,
     Any,
+    Literal,
     Optional,
+    TypeAlias,
     Union,
 )
 from uuid import UUID
@@ -29,9 +31,7 @@ from pydantic import (
 )
 from pydantic_core import core_schema
 from typing_extensions import (
-    Literal,
     NotRequired,
-    TypeAlias,
     TypedDict,
 )
 

lib/galaxy/schema/storage_cleaner.py

@@ -1,11 +1,11 @@
 from datetime import datetime
 from enum import Enum
 from typing import (
+    Literal,
     Union,
 )
 
 from pydantic import Field
-from typing_extensions import Literal
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,

lib/galaxy/schema/types.py

@@ -1,14 +1,12 @@
 from datetime import datetime
 from typing import (
     Annotated,
+    Literal,
     Union,
 )
 
 from pydantic import ValidationInfo
 from pydantic.functional_validators import AfterValidator
-from typing_extensions import (
-    Literal,
-)
 
 # Relative URLs cannot be validated with AnyUrl, they need a scheme.
 # Making them an alias of `str` for now

lib/galaxy/schema/visualization.py

@@ -1,5 +1,6 @@
 from datetime import datetime
 from typing import (
+    Literal,
     Optional,
     Union,
 )
@@ -9,7 +10,6 @@ from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import Literal
 
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,

lib/galaxy/schema/workflow/comments.py

@@ -1,4 +1,5 @@
 from typing import (
+    Literal,
     Optional,
     Union,
 )
@@ -8,7 +9,6 @@ from pydantic import (
     Field,
     RootModel,
 )
-from typing_extensions import Literal
 
 
 class BaseComment(BaseModel):

lib/galaxy/security/__init__.py

@@ -4,11 +4,10 @@ Galaxy Security
 """
 
 from typing import (
+    Literal,
     Optional,
 )
 
-from typing_extensions import Literal
-
 from galaxy.util.bunch import Bunch
 
 ActionModel = Literal["grant", "restrict"]

lib/galaxy/selenium/axe_results.py

@@ -1,10 +1,10 @@
 from typing import (
     Any,
+    Literal,
     Optional,
 )
 
 from typing_extensions import (
-    Literal,
     Protocol,
 )
 

lib/galaxy/selenium/has_driver_protocol.py

@@ -5,10 +5,10 @@ allowing NavigatesGalaxy to work with either backend via composition.
 """
 
 from abc import abstractmethod
+from collections.abc import Callable
 from contextlib import AbstractContextManager
 from typing import (
     Any,
-    Callable,
     Generic,
     Literal,
     Optional,

lib/galaxy/tools/_types.py

@@ -22,11 +22,10 @@ provide strong traditional typing semantics.
 
 from typing import (
     Any,
+    Literal,
     Union,
 )
 
-from typing_extensions import Literal
-
 # Input dictionary from the API, may include map/reduce instructions. Objects are referenced by "src"
 # dictionaries and encoded IDS.
 ToolRequestT = dict[str, Any]

lib/galaxy/tools/evaluation.py

@@ -5,10 +5,10 @@ import re
 import shlex
 import string
 import tempfile
+from collections.abc import Callable
 from datetime import datetime
 from typing import (
     Any,
-    Callable,
     Literal,
     Optional,
     TYPE_CHECKING,

lib/galaxy/tools/execute.py

@@ -8,17 +8,17 @@ import collections
 import logging
 import typing
 from abc import abstractmethod
+from collections.abc import Callable
 from typing import (
     Any,
-    Callable,
     NamedTuple,
     Optional,
+    TypeAlias,
     Union,
 )
 
 from boltons.iterutils import remap
 from packaging.version import Version
-from typing_extensions import TypeAlias
 
 from galaxy import model
 from galaxy.exceptions import ToolInputsNotOKException

lib/galaxy/tools/fetch/workbooks.py

@@ -1,5 +1,6 @@
 from dataclasses import dataclass
 from typing import (
+    Literal,
     Optional,
     Union,
 )
@@ -9,7 +10,6 @@ from pydantic import (
     BaseModel,
     Field,
 )
-from typing_extensions import Literal
 
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.model.dataset_collections.auto_identifiers import (

lib/galaxy/tools/parameters/cancelable_request.py

@@ -2,11 +2,11 @@ import asyncio
 import logging
 from typing import (
     Any,
+    Literal,
     Optional,
 )
 
 import aiohttp
-from typing_extensions import Literal
 
 log = logging.getLogger()
 

lib/galaxy/tools/parameters/dynamic_options.py

@@ -15,11 +15,10 @@ from typing import (
     Any,
     cast,
     get_args,
+    Literal,
     Optional,
 )
 
-from typing_extensions import Literal
-
 from galaxy.model import (
     DatasetCollectionElement,
     HistoryDatasetAssociation,

lib/galaxy/tools/parameters/grouping.py

@@ -6,11 +6,13 @@ import io
 import logging
 import os
 import unicodedata
-from collections.abc import Mapping
+from collections.abc import (
+    Callable,
+    Mapping,
+)
 from math import inf
 from typing import (
     Any,
-    Callable,
     Optional,
     TYPE_CHECKING,
 )