From fd11019becee7ba8d399685966d7d5b898e94200 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 15 Jun 2024 03:23:58 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 12 ++++++------ .../dependencies/pinned-lint-requirements.txt | 2 +- lib/galaxy/dependencies/pinned-requirements.txt | 16 ++++++++-------- .../pinned-typecheck-requirements.txt | 8 ++++---- 4 files changed, 19 insertions(+), 19 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 37cfc753bfd8..f7ce4c3b230c 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -33,7 +33,7 @@ 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==3.15.1 ; 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" @@ -71,7 +71,7 @@ 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" @@ -81,7 +81,7 @@ 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" 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" @@ -114,7 +114,7 @@ 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-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" +pytest==8.2.2 ; 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==2.0.1 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -126,13 +126,13 @@ 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" +rucio-clients==34.4.3 ; python_version >= "3.9" 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" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 9cd22f68931b..454e8157257e 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==0.4.8 +ruff==0.4.9 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 7a0e084d61a0..f1b86dde35c9 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -67,7 +67,7 @@ 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-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==3.15.1 ; 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" @@ -105,10 +105,10 @@ 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" markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" -mercurial==6.7.3 ; 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==1.28.1 ; 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" @@ -117,9 +117,9 @@ 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" 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==3.10.5 ; 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" @@ -127,7 +127,7 @@ 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" 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" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" @@ -135,8 +135,8 @@ 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-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.7.3 ; 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" 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" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 7f5ddd202f6e..44db9ab4d1f0 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,6 +1,6 @@ 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]==1.34.127 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.34.127 ; 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" @@ -9,9 +9,9 @@ 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==2.18.4 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.7.4 ; 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"