From 37905ec5d5f362d0c4b7b72ee1f152e71578a4ec Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 24 Jun 2024 16:17:28 +0100 Subject: [PATCH 1/5] Split contourpy requirement to support NumPy 2.0 --- lib/galaxy/dependencies/update.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh index 6bb140e8f078..c7eee2328ad7 100755 --- a/lib/galaxy/dependencies/update.sh +++ b/lib/galaxy/dependencies/update.sh @@ -89,6 +89,7 @@ split_requirement () { # supported by Galaxy, so Poetry resorts to an old version. Here we replace any # such requirement with multiple Python-version-specific requirements. # Packages which specify a maximum Python version pin: +split_requirement contourpy split_requirement matplotlib split_requirement numpy split_requirement scipy From 6948206ba707e78bf86cc70da10aa9501057832d Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sat, 29 Jun 2024 20:47:09 +0100 Subject: [PATCH 2/5] Install isa-rwval from my fork to relax pin on networkx xref. https://github.com/ISA-tools/isa-rwval/pull/17 --- packages/data/setup.cfg | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index a23240d0423a..c48c3d1825bc 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -45,7 +45,7 @@ install_requires = galaxy-sequence-utils h5grove>=1.2.1 h5py - isa-rwval>=0.10.10 + isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master isal MarkupSafe msal diff --git a/pyproject.toml b/pyproject.toml index 072f79f002e1..56147a86ef77 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,7 +70,7 @@ gxformat2 = "*" h5grove = ">=1.2.1" h5py = "*" importlib-resources = { version = "*", python = "<3.9" } # for importlib.{abc.Traversable,resources.{files, Package}} -isa-rwval = ">=0.10.10" +isa-rwval = { git = "https://github.com/nsoranzo/isa-rwval.git", branch = "master" } # https://github.com/ISA-tools/isa-rwval/pull/17 jinja2 = "*" kombu = ">=5.3" # for importlib-metadata fix isal = "*" From cb612300bb4a9289a7e05d23ea5f0490d2322315 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 22 Jun 2024 03:58:00 +0000 Subject: [PATCH 3/5] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 57 +++++++++-------- .../dependencies/pinned-lint-requirements.txt | 6 +- .../dependencies/pinned-requirements.txt | 61 +++++++++---------- .../pinned-typecheck-requirements.txt | 16 ++--- 4 files changed, 73 insertions(+), 67 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 37cfc753bfd8..1b1fcdde3007 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,3 +1,5 @@ +--extra-index-url https://wheels.galaxyproject.org/simple + aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13" @@ -10,8 +12,8 @@ babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" backports-tarfile==1.2.0 ; 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==1.34.106 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13" +boto3==1.34.131 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.131 ; 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==2024.6.2 ; python_version >= "3.8" and python_version < "3.13" @@ -20,8 +22,9 @@ charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" click==8.1.7 ; python_version >= "3.8" and python_version < "3.13" codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") -contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13" -coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13" +contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9" +contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13" +coverage[toml]==7.5.4 ; python_version >= "3.8" and python_version < "3.13" cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" @@ -33,7 +36,7 @@ deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13" docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13" exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11" -filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" +filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13" fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" @@ -45,7 +48,7 @@ httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13" httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.7 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13" -importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" +importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10" iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" @@ -61,7 +64,7 @@ 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" keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13" kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13" -lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" +lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13" 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" @@ -71,29 +74,29 @@ 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" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" -more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13" +more-itertools==10.3.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13" multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13" nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" +numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13" onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13" -packaging==24.0 ; python_version >= "3.8" and python_version < "3.13" +packaging==24.1 ; python_version >= "3.8" and python_version < "3.13" pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13" 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" +pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" -pkginfo==1.11.1 ; python_version >= "3.8" and python_version < "3.13" +pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13" platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13" -playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13" +playwright==1.45.0 ; 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" -psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" -psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13" +psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" +psycopg==3.2.1 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13" pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13" @@ -111,7 +114,7 @@ pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13" pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" -pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13" +pytest-playwright==0.5.1 ; python_version >= "3.8" and python_version < "3.13" pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13" pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13" @@ -126,21 +129,22 @@ readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13" referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" -responses==0.25.2 ; python_version >= "3.8" and python_version < "3.13" +responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13" rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" 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==34.4.2 ; python_version >= "3.9" and python_version < "3.13" -s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13" +rucio-clients==34.5.0 ; python_version >= "3.9" and python_version < "3.13" +s3transfer==0.10.2 ; 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==1.13.1 ; python_version >= "3.9" and python_version < "3.13" +scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10" +scipy==1.14.0 ; python_version >= "3.10" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" -selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13" +selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -165,14 +169,15 @@ 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==0.25.1 ; 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==5.1.0 ; python_version >= "3.8" and python_version < "3.13" +twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13" +twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.12.2 ; 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" -urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13" +urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13" +urllib3[socks]==1.26.19 ; python_version >= "3.8" and python_version < "3.13" watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" +websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13" 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" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 9cd22f68931b..3df072eefc30 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ attrs==23.2.0 -flake8==7.0.0 +flake8==7.1.0 flake8-bugbear==24.4.26 mccabe==0.7.0 -pycodestyle==2.11.1 +pycodestyle==2.12.0 pyflakes==3.2.0 -ruff==0.4.8 +ruff==0.5.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index afe0a5f04880..a0b6b7e68228 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,14 +1,14 @@ --extra-index-url https://wheels.galaxyproject.org/simple -a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13" +a2wsgi==1.10.6 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.13.1 ; 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" +aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13" aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13" aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" -alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13" +alembic==1.13.2 ; python_version >= "3.8" and python_version < "3.13" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13" annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" @@ -16,7 +16,7 @@ anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13" apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13" appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13" arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13" -argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13" +argcomplete==3.4.0 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -33,8 +33,8 @@ 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==1.34.106 ; python_version >= "3.8" and python_version < "3.13" -bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13" +bx-python==0.12.0 ; 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" certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13" @@ -55,7 +55,6 @@ cryptography==42.0.8 ; 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==3.1.20240508115724 ; 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" dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -64,13 +63,13 @@ docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13" docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13" edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13" -email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13" +email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11" 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" +filelock==3.15.4 ; 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==2024.6.0 ; python_version >= "3.8" and python_version < "3.13" +fsspec==2024.6.1 ; 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" @@ -79,7 +78,7 @@ graphene==3.3 ; python_version >= "3.8" and python_version < "3.13" graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13" graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13" gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13" -greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") +greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8" gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13" gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" @@ -87,9 +86,9 @@ h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13" h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.7 ; python_version >= "3.8" and python_version < "3.13" -importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" +importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9" -isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" +isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13" isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13" @@ -99,7 +98,7 @@ jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_versio jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13" kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" -lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" +lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13" mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown==3.6 ; python_version >= "3.8" and python_version < "3.13" @@ -108,35 +107,35 @@ mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" mercurial==6.7.4 ; python_version >= "3.8" and python_version < "3.13" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13" +msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13" multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -networkx==2.5 ; python_version >= "3.8" and python_version < "3.13" +networkx==3.1 ; python_version >= "3.8" and python_version < "3.13" nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" +numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" -orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.10.6 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" -packaging==24.0 ; python_version >= "3.8" and python_version < "3.13" +packaging==24.1 ; python_version >= "3.8" and python_version < "3.13" paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13" parsley==1.3 ; python_version >= "3.8" and python_version < "3.13" paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13" pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13" pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13" -pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13" +pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13" promise==2.3 ; python_version >= "3.8" and python_version < "3.13" -prompt-toolkit==3.0.46 ; python_version >= "3.8" and python_version < "3.13" +prompt-toolkit==3.0.47 ; python_version >= "3.8" and python_version < "3.13" prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13" -psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" +psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.7.4 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13" pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13" pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13" @@ -171,17 +170,17 @@ 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==2024.6.0 ; python_version >= "3.8" and python_version < "3.13" +s3fs==2024.6.1 ; 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==70.0.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13" shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13" -sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13" +sqlalchemy==2.0.31 ; python_version >= "3.8" and python_version < "3.13" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" @@ -189,7 +188,7 @@ starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13" starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13" supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13" svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13" -tenacity==8.3.0 ; python_version >= "3.8" and python_version < "3.13" +tenacity==8.4.2 ; python_version >= "3.8" and python_version < "3.13" tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13" tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" @@ -201,7 +200,7 @@ typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13" tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13" ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13" -urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" +urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13" uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13" uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13" vine==5.1.0 ; 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 4ea5a1375235..f37b1b56f55d 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,17 +1,19 @@ +--extra-index-url https://wheels.galaxyproject.org/simple + annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" -boto3-stubs[s3]==1.34.122 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.34.122 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.34.138 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.34.138 ; 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==42.0.8 ; 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==1.34.120 ; python_version >= "3.8" and python_version < "3.13" +mypy-boto3-s3==1.34.138 ; 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" +mypy==1.10.1 ; 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==2.18.4 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" -types-awscrt==0.20.11 ; python_version >= "3.8" and python_version < "3.13" +types-awscrt==0.20.12 ; 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" From e61f2e8999bd5507288a1d2cae633631bb9f3544 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sat, 29 Jun 2024 15:38:31 +0100 Subject: [PATCH 4/5] Fix new E721 and F811 errors from ruff 0.5.0 --- lib/galaxy/datatypes/genetics.py | 1 - lib/galaxy/datatypes/spaln.py | 1 - lib/galaxy/web_stack/message.py | 4 +++- test/unit/data/model/test_model_store.py | 1 - 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py index 83136fcb7b9e..a17ee92c9b08 100644 --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -334,7 +334,6 @@ def regenerate_primary_file(self, dataset: DatasetProtocol) -> None: ] for fname in flist: sfname = os.path.split(fname)[-1] - f, e = os.path.splitext(fname) rval.append(f'
  • {sfname}
    • ') rval.append("") with open(dataset.get_file_name(), "w") as f: diff --git a/lib/galaxy/datatypes/spaln.py b/lib/galaxy/datatypes/spaln.py index c3728ef6b4ea..8e27fde546bf 100644 --- a/lib/galaxy/datatypes/spaln.py +++ b/lib/galaxy/datatypes/spaln.py @@ -91,7 +91,6 @@ def regenerate_primary_file(self, dataset: DatasetProtocol) -> None: ] for fname in flist: sfname = os.path.split(fname)[-1] - f, e = os.path.splitext(fname) rval.append(f'
  • {sfname}
    • ') rval.append("") with open(dataset.get_file_name(), "w") as f: diff --git a/lib/galaxy/web_stack/message.py b/lib/galaxy/web_stack/message.py index f7ef7f7d2ddf..15259b4cc50e 100644 --- a/lib/galaxy/web_stack/message.py +++ b/lib/galaxy/web_stack/message.py @@ -68,7 +68,9 @@ def _merge_class_tuples(self): names = set() for cls in reversed(self.__class__.mro()): names.update( - [x for x in dir(cls) if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple] + x + for x in dir(cls) + if x.startswith("_") and not x.startswith("__") and type(getattr(cls, x)) == tuple # noqa: E721 ) for name in names: setattr(self.__class__, name.lstrip("_"), property(lambda self, name=name: self._get_list_from_mro(name))) diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py index a30410dd0207..80dd3789ef1b 100644 --- a/test/unit/data/model/test_model_store.py +++ b/test/unit/data/model/test_model_store.py @@ -1215,7 +1215,6 @@ def import_archive(archive_path, app, user, import_options=None): dest_dir = CompressedFile(archive_path).extract(dest_parent) import_options = import_options or store.ImportOptions() - new_history = None model_store = store.get_import_model_store_for_directory( dest_dir, app=app, From 135f47f37ebc4642c549df79b42bb1488cfb52f2 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 3 Jul 2024 18:07:28 +0100 Subject: [PATCH 5/5] Fix unit test --- lib/galaxy/tool_util/verify/asserts/hdf5.py | 2 +- test/unit/tool_util/verify/test_asserts.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tool_util/verify/asserts/hdf5.py b/lib/galaxy/tool_util/verify/asserts/hdf5.py index e94c61c3af04..ddbbcdd35cda 100644 --- a/lib/galaxy/tool_util/verify/asserts/hdf5.py +++ b/lib/galaxy/tool_util/verify/asserts/hdf5.py @@ -21,7 +21,7 @@ def assert_has_h5_attribute(output_bytes: bytes, key: str, value: str) -> None: local_attrs = h5py.File(output_temp, "r").attrs assert ( key in local_attrs and str(local_attrs[key]) == value - ), f"Not a HDF5 file or H5 attributes do not match:\n\t{list(local_attrs.items())}\n\n\t({key} : {value})" + ), f"Not a HDF5 file or H5 attributes do not match:\n\t{[(key, str(value)) for key, value in local_attrs.items()]}\n\n\t({key} : {value})" # TODO the function actually queries groups. so the function and argument name are misleading diff --git a/test/unit/tool_util/verify/test_asserts.py b/test/unit/tool_util/verify/test_asserts.py index a7f419fa4a32..af357871ccad 100644 --- a/test/unit/tool_util/verify/test_asserts.py +++ b/test/unit/tool_util/verify/test_asserts.py @@ -1315,7 +1315,7 @@ def test_has_h5_attribute_failure(): """test has_attribute .. negative""" a = run_assertions(H5_HAS_ATTRIBUTE_NEGATIVE, H5BYTES) assert ( - "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', 1)]\n\n\t(myfileattr : wrong)" + "Not a HDF5 file or H5 attributes do not match:\n\t[('myfileattr', 'myfileattrvalue'), ('myfileattrint', '1')]\n\n\t(myfileattr : wrong)" in a ) assert len(a) == 1