From a3e129fa4ec467eff31dbfaba930fcc6aa7223f3 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 7 Mar 2026 03:44:11 +0000 Subject: [PATCH 1/3] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 35 ++++----- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 73 +++++++++---------- .../dependencies/pinned-test-requirements.txt | 27 +++---- .../pinned-typecheck-requirements.txt | 4 +- 5 files changed, 67 insertions(+), 74 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index d829b4acb9e..bc4ff42e6c4 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -4,7 +4,6 @@ aiohappyeyeballs==2.6.1 aiohttp==3.13.3 aiosignal==1.4.0 alabaster==1.0.0 -anyio==4.12.1 ase==3.27.0 async-timeout==5.0.1 ; python_full_version < '3.11' attrs==25.4.0 @@ -12,18 +11,18 @@ axe-selenium-python==2.1.6 babel==2.18.0 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==26.1.0 -boto3==1.42.55 -botocore==1.42.55 +black==26.3.0 +boto3==1.42.61 +botocore==1.42.61 build==1.4.0 cachecontrol==0.14.4 -cachetools==7.0.1 +cachetools==7.0.3 cattrs==26.1.0 certifi==2026.2.25 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy' -charset-normalizer==3.4.4 +charset-normalizer==3.4.5 click==8.3.1 -codespell==2.4.1 +codespell==2.4.2 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32' colorlog==6.10.1 contourpy==1.3.2 ; python_full_version < '3.11' @@ -41,7 +40,7 @@ docutils==0.22.4 ; python_full_version >= '3.11' dogpile-cache==1.5.0 enum-tools==0.12.0 exceptiongroup==1.3.1 ; python_full_version < '3.11' -filelock==3.24.3 +filelock==3.25.0 fluent-logger==0.11.1 fonttools==4.61.1 frozenlist==1.8.0 @@ -49,30 +48,28 @@ fsspec==2026.2.0 galaxy-release-util==0.3.2 gcsfs==2026.2.0 google-api-core==2.30.0 -google-auth==2.48.0 +google-auth==2.49.0 google-auth-oauthlib==1.3.0 google-cloud-core==2.5.0 google-cloud-storage==3.9.0 google-cloud-storage-control==1.10.0 google-crc32c==1.8.0 google-resumable-media==2.8.0 -googleapis-common-protos==1.72.0 +googleapis-common-protos==1.73.0 greenlet==3.3.2 grpc-google-iam-v1==0.14.3 grpcio==1.78.0 grpcio-status==1.78.0 h11==0.16.0 html5rdf==1.2.1 -httpcore==1.0.9 -httpx==0.28.1 id==1.6.1 idna==3.11 -imagesize==1.4.1 +imagesize==2.0.0 importlib-metadata==8.7.1 ; python_full_version < '3.12' iniconfig==2.3.0 inquirerpy==0.3.4 isodate==0.7.2 ; python_full_version < '3.11' -isort==8.0.0 +isort==8.0.1 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' @@ -116,7 +113,7 @@ pathspec==1.0.4 pfzy==0.3.4 pillow==12.1.1 pkce==1.0.3 -platformdirs==4.9.2 +platformdirs==4.9.4 playwright==1.58.0 pluggy==1.6.0 port-for==1.0.0 @@ -161,7 +158,7 @@ rdflib==7.5.0 readme-renderer==44.0 referencing==0.37.0 requests==2.32.5 -requests-cache==1.3.0 +requests-cache==1.3.1 requests-oauthlib==2.0.0 requests-toolbelt==1.0.0 responses==0.26.0 @@ -174,7 +171,7 @@ 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==39.3.1 +rucio-clients==39.4.0 s3transfer==0.16.0 schema-salad==8.9.20251102115403 scipy==1.15.3 ; python_full_version < '3.11' @@ -199,7 +196,7 @@ sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 statsd==4.0.1 stevedore==5.7.0 -tabulate==0.9.0 +tabulate==0.10.0 testfixtures==8.3.0 ; python_full_version < '3.11' testfixtures==10.0.0 ; python_full_version >= '3.11' text-unidecode==1.3 @@ -223,5 +220,5 @@ wcwidth==0.6.0 websocket-client==1.9.0 werkzeug==3.1.6 wsproto==1.3.2 -yarl==1.22.0 +yarl==1.23.0 zipp==3.23.0 ; python_full_version < '3.12' diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index fb7160b7755..b6563819312 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==25.11.29 mccabe==0.7.0 pycodestyle==2.14.0 pyflakes==3.4.0 -ruff==0.15.4 +ruff==0.15.5 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 654edee7347..7692be671d1 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -3,7 +3,7 @@ a2wsgi==1.10.10 adal==1.2.7 ag-ui-protocol==0.1.13 -aiobotocore==3.2.0 +aiobotocore==3.2.1 aiofile==3.9.0 aiofiles==25.1.0 aiohappyeyeballs==2.6.1 @@ -16,14 +16,13 @@ annotated-doc==0.0.4 annotated-types==0.7.0 anthropic==0.84.0 anyio==4.12.1 -apispec==6.9.0 +apispec==6.10.0 appdirs==1.4.4 arcp==0.2.1 argcomplete==3.6.3 async-timeout==5.0.1 ; python_full_version < '3.11' -attmap==0.13.2 attrs==25.4.0 -authlib==1.6.8 +authlib==1.6.9 babel==2.18.0 backports-tarfile==1.2.0 ; python_full_version < '3.12' bagit==1.9.0 @@ -37,16 +36,16 @@ bioblend==1.8.0 bleach==6.3.0 boltons==25.0.0 boto==2.49.0 -boto3==1.42.55 -botocore==1.42.55 +boto3==1.42.61 +botocore==1.42.61 bx-python==0.14.0 cachecontrol==0.14.4 -cachetools==7.0.1 +cachetools==7.0.3 caio==0.9.25 celery==5.6.2 certifi==2026.2.25 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy' -charset-normalizer==3.4.4 +charset-normalizer==3.4.5 circus==0.19.0 click==8.3.1 click-didyoumean==0.3.1 @@ -63,7 +62,7 @@ ct3==3.4.0.post5 cwl-upgrader==1.2.14 cwl-utils==0.40 cwltool==3.1.20260108082145 -cyclopts==4.6.0 +cyclopts==4.7.0 defusedxml==0.7.1 deprecated==1.3.1 deprecation==2.1.0 @@ -81,10 +80,10 @@ et-xmlfile==2.0.0 eval-type-backport==0.3.1 exceptiongroup==1.3.1 executing==2.2.1 -fastapi==0.134.0 +fastapi==0.135.1 fastavro==1.12.1 ; sys_platform != 'emscripten' -fastmcp==3.0.2 -filelock==3.24.3 +fastmcp==3.1.0 +filelock==3.25.0 fissix==24.4.24 frozenlist==1.8.0 fs==2.4.16 @@ -92,10 +91,10 @@ fsspec==2026.2.0 future==1.0.0 genai-prices==0.0.55 google-api-core==2.30.0 -google-auth==2.48.0 +google-auth==2.49.0 google-cloud-batch==0.20.0 -google-genai==1.65.0 -googleapis-common-protos==1.72.0 +google-genai==1.66.0 +googleapis-common-protos==1.73.0 gravity==1.2.0 greenlet==3.3.2 ; 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' griffelib==2.0.0 @@ -106,12 +105,12 @@ gunicorn==25.0.3 gxformat2==0.22.0 h11==0.16.0 h5grove==3.0.0 -h5py==3.15.1 +h5py==3.16.0 hf-xet==1.3.2 ; platform_machine == 'AMD64' or 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 -huggingface-hub==1.5.0 +huggingface-hub==1.6.0 humanfriendly==10.0 idna==3.11 ijson==3.5.0 @@ -130,15 +129,15 @@ jiter==0.13.0 jmespath==1.1.0 jsonref==1.1.0 jsonschema==4.26.0 -jsonschema-path==0.4.3 +jsonschema-path==0.4.5 jsonschema-specifications==2025.9.1 keyring==25.7.0 kombu==5.6.2 lagom==2.7.7 legacy-cgi==2.6.4 ; python_full_version >= '3.13' limits==5.8.0 -logfire==4.25.0 -logfire-api==4.25.0 +logfire==4.27.0 +logfire-api==4.27.0 lxml==6.0.2 mako==1.3.10 markdown==3.10.2 @@ -152,7 +151,7 @@ mistralai==1.12.4 mistune==3.1.4 more-itertools==10.8.0 mrcfile==1.5.4 -msal==1.35.0 +msal==1.35.1 msgpack==1.1.2 multidict==6.7.1 mypy-extensions==1.1.0 @@ -164,7 +163,7 @@ nodejs-wheel-binaries==22.20.0 numpy==2.2.6 ; python_full_version < '3.11' numpy==2.4.2 ; python_full_version >= '3.11' oauthlib==3.3.1 -openai==2.24.0 +openai==2.26.0 openapi-pydantic==0.5.1 openpyxl==3.1.5 opentelemetry-api==1.39.1 @@ -177,7 +176,6 @@ opentelemetry-sdk==1.39.1 opentelemetry-semantic-conventions==0.60b1 opentelemetry-util-http==0.60b1 orjson==3.11.7 -oyaml==1.0 packaging==25.0 paramiko==4.0.0 parsley==1.3 @@ -186,7 +184,7 @@ pastedeploy==3.1.0 pathable==0.5.0 pebble==5.2.0 pillow==12.1.1 -platformdirs==4.9.2 +platformdirs==4.9.4 prompt-toolkit==3.0.52 propcache==0.4.1 proto-plus==1.27.1 @@ -200,11 +198,11 @@ pyasn1-modules==0.4.2 pycparser==3.0 ; (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==1.63.0 -pydantic-ai-slim==1.63.0 +pydantic-ai==1.67.0 +pydantic-ai-slim==1.67.0 pydantic-core==2.41.5 -pydantic-evals==1.63.0 -pydantic-graph==1.63.0 +pydantic-evals==1.67.0 +pydantic-graph==1.67.0 pydantic-settings==2.13.1 pydantic-tes==0.3.0 pydicom==3.0.1 @@ -222,12 +220,12 @@ pypng==0.20220715.0 pyreadline3==3.5.4 ; sys_platform == 'win32' pysam==0.23.3 python-dateutil==2.9.0.post0 -python-dotenv==1.2.1 +python-dotenv==1.2.2 python-magic==0.4.27 python-multipart==0.0.22 python-slugify==8.0.4 python3-openid==3.2.0 -pytz==2025.2 +pytz==2026.1.post1 pywin32==311 ; sys_platform == 'win32' pywin32-ctypes==0.2.3 ; sys_platform == 'win32' pyyaml==6.0.3 @@ -262,18 +260,18 @@ sniffio==1.3.1 social-auth-core==4.8.5 sortedcontainers==2.4.0 spython==0.3.14 -sqlalchemy==2.0.47 +sqlalchemy==2.0.48 sqlparse==0.5.5 -sse-starlette==3.2.0 +sse-starlette==3.3.2 starlette==0.52.1 -starlette-context==0.4.0 +starlette-context==0.5.1 supervisor==4.3.0 svgwrite==1.4.3 temporalio==1.20.0 tenacity==9.1.4 text-unidecode==1.3 tifffile==2025.5.10 ; python_full_version < '3.11' -tifffile==2026.2.24 ; python_full_version >= '3.11' +tifffile==2026.3.3 ; python_full_version >= '3.11' tiktoken==0.12.0 tinydb==4.8.2 tokenizers==0.22.2 ; sys_platform != 'emscripten' @@ -290,6 +288,7 @@ typing-inspection==0.4.2 tzdata==2025.3 tzlocal==5.3.1 ubiquerg==0.9.1 +uncalled-for==0.2.0 urllib3==2.6.3 uvicorn==0.41.0 uvloop==0.22.1 @@ -301,9 +300,9 @@ webob==1.8.9 websockets==16.0 whoosh==2.7.4 wrapt==1.17.3 -xai-sdk==1.7.0 -yacman==0.9.5 -yarl==1.22.0 +xai-sdk==1.8.0 +yacman==1.0.0 +yarl==1.23.0 zipp==3.23.0 zipstream-new==1.1.8 zstandard==0.25.0 diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt index 5d49db3e35d..c9ad14e396b 100644 --- a/lib/galaxy/dependencies/pinned-test-requirements.txt +++ b/lib/galaxy/dependencies/pinned-test-requirements.txt @@ -3,20 +3,19 @@ aiohappyeyeballs==2.6.1 aiohttp==3.13.3 aiosignal==1.4.0 -anyio==4.12.1 ase==3.27.0 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==1.42.55 -botocore==1.42.55 +boto3==1.42.61 +botocore==1.42.61 cachecontrol==0.14.4 -cachetools==7.0.1 +cachetools==7.0.3 cattrs==26.1.0 certifi==2026.2.25 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy' -charset-normalizer==3.4.4 +charset-normalizer==3.4.5 click==8.3.1 colorama==0.4.6 ; sys_platform == 'win32' colorlog==6.10.1 @@ -31,29 +30,27 @@ defusedxml==0.7.1 dogpile-cache==1.5.0 enum-tools==0.12.0 exceptiongroup==1.3.1 ; python_full_version < '3.11' -filelock==3.24.3 +filelock==3.25.0 fluent-logger==0.11.1 fonttools==4.61.1 frozenlist==1.8.0 fsspec==2026.2.0 gcsfs==2026.2.0 google-api-core==2.30.0 -google-auth==2.48.0 +google-auth==2.49.0 google-auth-oauthlib==1.3.0 google-cloud-core==2.5.0 google-cloud-storage==3.9.0 google-cloud-storage-control==1.10.0 google-crc32c==1.8.0 google-resumable-media==2.8.0 -googleapis-common-protos==1.72.0 +googleapis-common-protos==1.73.0 greenlet==3.3.2 grpc-google-iam-v1==0.14.3 grpcio==1.78.0 grpcio-status==1.78.0 h11==0.16.0 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' iniconfig==2.3.0 @@ -91,7 +88,7 @@ pathspec==1.0.4 pfzy==0.3.4 pillow==12.1.1 pkce==1.0.3 -platformdirs==4.9.2 +platformdirs==4.9.4 playwright==1.58.0 pluggy==1.6.0 port-for==1.0.0 @@ -129,7 +126,7 @@ pyyaml==6.0.3 rdflib==7.5.0 referencing==0.37.0 requests==2.32.5 -requests-cache==1.3.0 +requests-cache==1.3.1 requests-oauthlib==2.0.0 responses==0.26.0 rich==13.9.4 @@ -139,7 +136,7 @@ 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==39.3.1 +rucio-clients==39.4.0 s3transfer==0.16.0 schema-salad==8.9.20251102115403 scipy==1.15.3 ; python_full_version < '3.11' @@ -151,7 +148,7 @@ sniffio==1.3.1 sortedcontainers==2.4.0 statsd==4.0.1 stevedore==5.7.0 -tabulate==0.9.0 +tabulate==0.10.0 testfixtures==8.3.0 ; python_full_version < '3.11' testfixtures==10.0.0 ; python_full_version >= '3.11' text-unidecode==1.3 @@ -174,5 +171,5 @@ wcwidth==0.6.0 websocket-client==1.9.0 werkzeug==3.1.6 wsproto==1.3.2 -yarl==1.22.0 +yarl==1.23.0 zipp==3.23.0 ; python_full_version < '3.12' diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 311075606a9..2a96fb7afea 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,7 +1,7 @@ # This file was autogenerated by uv via the following command: # uv export --frozen --no-annotate --no-hashes --only-group=typecheck annotated-types==0.7.0 -boto3-stubs==1.42.59 +boto3-stubs==1.42.63 botocore-stubs==1.42.41 cffi==2.0.0 ; platform_python_implementation != 'PyPy' cryptography==46.0.5 @@ -24,7 +24,7 @@ types-docutils==0.22.3.20260223 types-html5lib==1.1.11.20251117 types-markdown==3.10.2.20260211 types-paramiko==4.0.0.20250822 -types-python-dateutil==2.9.0.20260124 +types-python-dateutil==2.9.0.20260305 types-python-slugify==8.0.2.20240310 types-pyyaml==6.0.12.20250915 types-requests==2.32.4.20260107 From 22bb9caa9afa88506e58a768e5ce62cc238be0f7 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sat, 7 Mar 2026 17:59:58 +0000 Subject: [PATCH 2/3] Remove ``direction`` argument from ``list_models()`` call Dropped upstream in: https://github.com/huggingface/huggingface_hub/pull/3882 --- lib/galaxy/files/sources/huggingface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/files/sources/huggingface.py b/lib/galaxy/files/sources/huggingface.py index 1e04b8330f4..3995697dd2b 100644 --- a/lib/galaxy/files/sources/huggingface.py +++ b/lib/galaxy/files/sources/huggingface.py @@ -155,7 +155,7 @@ class HuggingFaceFilesSource( endpoint=config.endpoint, ) try: - repos_iter = api.list_models(search=query, sort=DEFAULT_SORT_BY, direction=-1, limit=MAX_REPO_LIMIT) + repos_iter = api.list_models(search=query, sort=DEFAULT_SORT_BY, limit=MAX_REPO_LIMIT) # Convert repositories to directory entries entries_list: list[AnyRemoteEntry] = [] From 677212c4d4ee48bdee4d6db90310429ca3e71c01 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sat, 7 Mar 2026 18:30:19 +0000 Subject: [PATCH 3/3] Use URLs that doesn't error with status code 429 --- lib/galaxy_test/api/test_tools.py | 7 ++----- test/unit/tool_shed/test_shed_index.py | 2 +- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py index e2f16809ee6..800e663c5a9 100644 --- a/lib/galaxy_test/api/test_tools.py +++ b/lib/galaxy_test/api/test_tools.py @@ -3186,11 +3186,8 @@ class TestToolsApi(ApiTestCase, TestsTools): def test_metadata_validator_can_fail_on_deferred_input(self, history_id): # This test fails because we just skip the validator # Fixing this is a TODO - deferred_bam_details = self.dataset_populator.create_deferred_hda( - history_id, - "https://github.com/galaxyproject/galaxy/blob/dev/test-data/3unsorted.bam?raw=true", - ext="unsorted.bam", - ) + url_1 = self.dataset_populator.base64_url_for_test_file("3unsorted.bam") + deferred_bam_details = self.dataset_populator.create_deferred_hda(history_id, url_1, ext="unsorted.bam") fasta1_contents = open(self.get_filename("1.fasta")).read() fasta = self.dataset_populator.new_dataset(history_id, content=fasta1_contents) inputs = {"input1": dataset_to_param(deferred_bam_details), "reference": dataset_to_param(fasta)} diff --git a/test/unit/tool_shed/test_shed_index.py b/test/unit/tool_shed/test_shed_index.py index 1bfce9adf3d..3041c6f3448 100644 --- a/test/unit/tool_shed/test_shed_index.py +++ b/test/unit/tool_shed/test_shed_index.py @@ -11,7 +11,7 @@ from whoosh import index from galaxy.util.compression_utils import CompressedFile from tool_shed.util.shed_index import build_index -URL = "https://github.com/mvdbeek/toolshed-test-data/blob/master/toolshed_community_files.tgz?raw=true" +URL = "https://github.com/mvdbeek/toolshed-test-data/raw/refs/heads/master/toolshed_community_files.tgz" @pytest.fixture