From 70c56485855a1a15fff0167c29c2e6d5082e0094 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 19 May 2024 13:14:57 +0100 Subject: [PATCH 1/3] Fix boto3-stubs typecheck dependency Introduced in commit 36b5ed15fa4a5f9860feaa77dc90832e6bef87b3 . --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 95e88cf337bb..f1c23b222991 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -170,6 +170,7 @@ 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 = "*" @@ -184,7 +185,6 @@ types-python-dateutil = "*" types-PyYAML = "*" types-requests = "*" types-six = "*" -"boto3-stubs[s3]" = "*" [tool.ruff] target-version = "py38" From 7f6adf0451a50eb20306ce36188354ac9da925e8 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 19 May 2024 14:16:11 +0100 Subject: [PATCH 2/3] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 23 +++++++++++-------- .../dependencies/pinned-requirements.txt | 18 +++++++-------- .../pinned-typecheck-requirements.txt | 5 ++++ 3 files changed, 27 insertions(+), 19 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 8bfb2b04e280..37166712382c 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/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" @@ -84,8 +86,8 @@ 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" @@ -100,7 +102,7 @@ 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" @@ -130,11 +132,12 @@ 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" @@ -159,10 +162,10 @@ 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" @@ -173,4 +176,4 @@ 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" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 7c5e0d968792..f25d7b6a27c7 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/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" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 07c2b7ea2465..a18d0745af0d 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/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" From 6fe7c5fb55dae80fd11c2e622b290305791cd267 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 19 May 2024 14:16:54 +0100 Subject: [PATCH 3/3] Fix mypy error --- lib/galaxy/jobs/runners/aws.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/lib/galaxy/jobs/runners/aws.py b/lib/galaxy/jobs/runners/aws.py index 9831cc42950e..5f301b078975 100644 --- a/lib/galaxy/jobs/runners/aws.py +++ b/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))