diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index a6a92842ef80..3653ef9dcaf6 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -2,7 +2,7 @@ aiohttp==3.9.3 ; 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" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" -anyio==4.2.0 ; python_version >= "3.8" and python_version < "3.13" +anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -25,8 +25,8 @@ 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]==7.4.1 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13" +coverage[toml]==7.4.2 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.4 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13" @@ -36,13 +36,13 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13" -fonttools==4.48.1 ; python_version >= "3.8" and python_version < "3.13" +fonttools==4.49.0 ; 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==0.1.5 ; python_version >= "3.8" and python_version < "3.13" +galaxy-release-util==0.1.7 ; 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" -httpcore==1.0.2 ; python_version >= "3.8" and python_version < "3.13" -httpx==0.26.0 ; python_version >= "3.8" and python_version < "3.13" +httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13" +httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.6 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13" @@ -61,8 +61,8 @@ lxml==4.9.4 ; 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" -matplotlib==3.7.4 ; python_version >= "3.8" and python_version < "3.9" -matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13" +matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9" +matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13" mdit-py-plugins==0.4.0 ; 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" @@ -85,7 +85,7 @@ platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13" playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13" -prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13" +prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13" prompt-toolkit==3.0.43 ; 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==3.1.18 ; python_version >= "3.8" and python_version < "3.13" @@ -130,7 +130,7 @@ schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.12.0 ; 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==4.17.2 ; python_version >= "3.8" and python_version < "3.13" +selenium==4.18.1 ; python_version >= "3.8" and python_version < "3.13" seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13" setuptools==69.1.0 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" @@ -147,7 +147,7 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13" sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13" statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13" -testfixtures==7.2.2 ; python_version >= "3.8" and python_version < "3.13" +testfixtures==8.0.0 ; 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 6133df8e071f..fb9ff86ef79a 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.2.6 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.2.1 +ruff==0.2.2 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index a2f72da952c3..a32343d0d0db 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,4 +1,4 @@ -a2wsgi==1.10.0 ; python_version >= "3.8" and python_version < "3.13" +a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" aiobotocore==2.11.2 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -10,7 +10,7 @@ alembic==1.13.1 ; 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==0.6.0 ; python_version >= "3.8" and python_version < "3.13" -anyio==4.2.0 ; python_version >= "3.8" and python_version < "3.13" +anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" apispec==6.4.0 ; 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" @@ -49,7 +49,7 @@ 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==42.0.2 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.4 ; 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==0.32 ; python_version >= "3.8" and python_version < "3.13" cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13" @@ -57,7 +57,7 @@ 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" -dnspython==2.5.0 ; python_version >= "3.8" and python_version < "3.13" +dnspython==2.6.1 ; python_version >= "3.8" and python_version < "3.13" docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13" docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13" dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13" @@ -70,7 +70,7 @@ filelock==3.13.1 ; 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==2023.12.2 ; python_version >= "3.8" and python_version < "3.13" -future @ git+https://github.com/nsoranzo/python-future.git@9ef05b386ce45dd40d2dab5915aec3ed78d81ed9 ; 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" graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13" @@ -89,7 +89,7 @@ idna==3.6 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9" isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" -isal==1.5.3 ; python_version >= "3.8" and python_version < "3.13" +isal==1.6.0 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13" jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" @@ -116,7 +116,7 @@ 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==3.9.13 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.9.14 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" packaging==23.2 ; python_version >= "3.8" and python_version < "3.13" paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -169,7 +169,7 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.0 ; python_version >= "3.8" and python_version < "3.13" rocrate==0.9.0 ; python_version >= "3.8" and python_version < "3.13" routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13" -rpds-py==0.17.1 ; python_version >= "3.8" and python_version < "3.13" +rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13" rsa==4.9 ; 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" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 27e7dfdccf1a..07842cb52fa0 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==42.0.2 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.4 ; 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==1.8.0 ; python_version >= "3.8" and python_version < "3.13" @@ -8,11 +8,12 @@ pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platfo pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" -types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13" +types-bleach==6.1.0.20240222 ; 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" types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13" types-docutils==0.20.0.20240201 ; python_version >= "3.8" and python_version < "3.13" +types-html5lib==1.1.11.20240222 ; python_version >= "3.8" and python_version < "3.13" types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13" types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13" types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13" diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index e7b174ffbfc5..485149c7b0cd 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -52,7 +52,7 @@ jstree = dictobj template = Cheetah3!=3.2.6.post2 - future @ git+https://github.com/nsoranzo/python-future.git@python312-imp-module_past + future>=1.0.0 [options.packages.find] exclude = diff --git a/pyproject.toml b/pyproject.toml index 34faa14f63e6..ac8fc88c9522 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -59,7 +59,7 @@ dparse = "*" edam-ontology = "*" fastapi = ">=0.108" fs = "*" -future = { git = "https://github.com/nsoranzo/python-future.git", branch = "python312-imp-module_past" } +future = ">=1.0.0" # Python 3.12 support galaxy_sequence_utils = "*" graphene-sqlalchemy = "3.0.0rc1" # need a beta release to be compat. with starlette plugin gravity = ">=1.0.4"