Merge pull request #18173 from nsoranzo/followup_on_18136

Fix boto3-stubs typecheck dependency

lib/galaxy/dependencies/dev-requirements.txt

@@ -10,7 +10,8 @@ babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
-boto3==1.34.69 ; python_version >= "3.8" and python_version < "3.13"
+boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
 build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -54,6 +55,7 @@ jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
+jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
 jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
@@ -64,7 +66,7 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
-matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.9.0 ; python_version >= "3.9" and python_version < "3.13"
 mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -85,8 +87,8 @@ pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.2.1 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.43.0 ; python_version >= "3.8" and python_version < "3.13"
+platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
+playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -101,7 +103,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
 pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-asyncio==0.23.6 ; python_version >= "3.8" and python_version < "3.13"
+pytest-asyncio==0.23.7 ; python_version >= "3.8" and python_version < "3.13"
 pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -131,11 +133,12 @@ rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 rucio-clients==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
-schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13"
+s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
+schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -160,10 +163,10 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
 trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-trio==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
+trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
-twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
+twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
@@ -174,4 +177,4 @@ werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.13"
+zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 
 a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.12.3 ; python_version >= "3.8" and python_version < "3.13"
+aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
 aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
@@ -26,14 +26,14 @@ backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version <
 bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13"
 bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13"
-bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
+bdbag==1.7.3 ; python_version >= "3.8" and python_version < "3.13"
 beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
 bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
 boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.69 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -54,7 +54,7 @@ conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3
 cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
 cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
 cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13"
-cwltool==3.1.20240404144621 ; python_version >= "3.8" and python_version < "3.13"
+cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13"
 decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -70,7 +70,7 @@ fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
-fsspec==2024.3.1 ; python_version >= "3.8" and python_version < "3.13"
+fsspec==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
 future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -159,7 +159,7 @@ pyzmq==26.0.3 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
-regex==2024.5.10 ; python_version >= "3.8" and python_version < "3.13"
+regex==2024.5.15 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
 requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -171,8 +171,8 @@ routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-s3fs==2024.3.1 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13"
+s3fs==2024.5.0 ; python_version >= "3.8" and python_version < "3.13"
+schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13"
 setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -212,6 +212,6 @@ whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13"
 yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"
-zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.13"
+zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13"
 zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13"
 zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -1,13 +1,17 @@
 annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.34.108 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.34.94 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
+mypy-boto3-s3==1.34.105 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
+types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,6 +24,7 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
 types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
+types-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
 types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13"
 types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/jobs/runners/aws.py

@@ -37,9 +37,8 @@
 
 try:
     import boto3
-
 except ImportError as e:
-    boto3 = None
+    boto3 = None  # type: ignore[assignment]
     BOTO3_IMPORT_MSG.format(msg=unicodify(e))
 
 

pyproject.toml

@@ -171,6 +171,7 @@ Werkzeug = "*"
 
 [tool.poetry.group.typecheck.dependencies]
 mypy = "*"
+boto3-stubs = {version = "*", extras = ["s3"]}
 lxml-stubs = "*"
 pydantic = ">=2, !=2.6.0, !=2.6.1"  # for pydantic.mypy plugin
 types-bleach = "*"
@@ -185,7 +186,6 @@ types-python-dateutil = "*"
 types-PyYAML = "*"
 types-requests = "*"
 types-six = "*"
-"boto3-stubs[s3]" = "*"
 
 [tool.ruff]
 target-version = "py38"