From e6b7b4c099ce54e2e1798e58ee2467216989bdf6 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 4 May 2024 03:13:39 +0000 Subject: [PATCH] Update Python dependencies --- lib/galaxy/dependencies/dev-requirements.txt | 20 ++++++++--------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 22 +++++++++---------- .../pinned-typecheck-requirements.txt | 2 +- 4 files changed, 23 insertions(+), 23 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 59178ed6dc9d..57a4854417dc 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -19,8 +19,8 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13" codespell==2.2.6 ; 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]==7.5.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13" +coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.6 ; 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" darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13" @@ -31,11 +31,11 @@ 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==3.13.4 ; python_version >= "3.8" and python_version < "3.13" +filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13" fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" -galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13" +galaxy-release-util==0.1.9 ; python_version >= "3.8" and python_version < "3.13" graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13" greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" @@ -72,7 +72,7 @@ more-itertools==10.2.0 ; 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==3.0.0 ; 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" @@ -93,11 +93,11 @@ psycopg==3.1.18 ; 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" -pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13" +pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13" pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" 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==1.0.0 ; 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-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13" @@ -112,14 +112,14 @@ 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" python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13" -python-irodsclient==2.0.0 ; python_version >= "3.8" and python_version < "3.13" +python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9" pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13" -referencing==0.35.0 ; python_version >= "3.9" 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==2.31.0 ; python_version >= "3.8" and python_version < "3.13" responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13" @@ -152,7 +152,7 @@ sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_versio statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13" stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13" tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13" -testfixtures==8.1.0 ; python_version >= "3.8" and python_version < "3.13" +testfixtures==8.2.0 ; python_version >= "3.8" and python_version < "3.13" text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13" 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" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 951a6bf4792f..22dfc1d78b88 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.4.26 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.4.2 +ruff==0.4.3 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 007384ec0854..d70a81459cd9 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -25,7 +25,7 @@ backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" 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==4.1.2 ; 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" 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" @@ -51,7 +51,7 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.6 ; 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" @@ -66,8 +66,8 @@ 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" exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11" -fastapi==0.110.2 ; python_version >= "3.8" and python_version < "3.13" -filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13" +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==2023.12.2 ; python_version >= "3.8" and python_version < "3.13" @@ -117,12 +117,12 @@ nodeenv==1.8.0 ; 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" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" -orjson==3.10.1 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.10.3 ; 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" 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==3.10.0 ; 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" @@ -140,7 +140,7 @@ pydantic[email]==2.7.1 ; 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" -pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13" +pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13" pyjwt==2.8.0 ; python_version >= "3.8" and python_version < "3.13" pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13" @@ -155,11 +155,11 @@ python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13" python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13" pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" -pyzmq==26.0.2 ; python_version >= "3.8" and python_version < "3.13" +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==0.35.0 ; 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==2024.4.16 ; python_version >= "3.8" and python_version < "3.13" +regex==2024.4.28 ; 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" @@ -194,7 +194,7 @@ 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" tornado==6.4 ; python_version >= "3.8" and python_version < "3.13" -tqdm==4.66.2 ; python_version >= "3.8" and python_version < "3.13" +tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.11.0 ; 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 99e1264d74fd..2de65943a6be 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,6 +1,6 @@ annotated-types==0.6.0 ; 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==42.0.5 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13" lxml-stubs==0.5.1 ; 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"