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/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,
 )

lib/galaxy/tools/remote_tool_eval.py

@@ -3,8 +3,8 @@ import os
 import shutil
 import tempfile
 import traceback
+from collections.abc import Callable
 from typing import (
-    Callable,
     NamedTuple,
 )
 

lib/galaxy/tools/wrappers.py

@@ -15,12 +15,12 @@ from typing import (
     cast,
     Optional,
     TYPE_CHECKING,
+    TypeAlias,
     Union,
 )
 
 from typing_extensions import (
     Self,
-    TypeAlias,
 )
 
 from galaxy.model import (

lib/galaxy/visualization/data_providers/registry.py

@@ -1,10 +1,9 @@
 from typing import (
+    Literal,
     Optional,
     Union,
 )
 
-from typing_extensions import Literal
-
 from galaxy.datatypes.data import (
     Data,
     Newick,

lib/galaxy/visualization/plugins/resource_parser.py

@@ -6,8 +6,8 @@ a dictionary of string data/ids (often from a query string).
 import json
 import logging
 import weakref
+from collections.abc import Callable
 from typing import (
-    Callable,
     Optional,
     Union,
 )