diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index cae757b95dd7..94efbf98aac2 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -2,7 +2,7 @@ aiohttp==3.8.4 ; python_version >= "3.7" and python_version < "3.12" aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12" alabaster==0.7.13 ; python_version >= "3.7" and python_version < "3.12" amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" -anyio==3.7.0 ; python_version >= "3.7" and python_version < "3.12" +anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12" ase==3.22.1 ; python_version >= "3.7" and python_version < "3.12" async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.12" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" @@ -18,15 +18,15 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12" cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -click==8.1.3 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.4 ; python_version >= "3.7" and python_version < "3.12" codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12" -cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" +cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux" cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12" cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12" darker==1.7.1 ; python_version >= "3.7" and python_version < "3.12" @@ -41,7 +41,7 @@ frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" galaxy-release-util==0.1.4 ; python_version >= "3.7" and python_version < "3.12" h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" -httpcore==0.17.2 ; python_version >= "3.7" and python_version < "3.12" +httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.12" httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12" idna==3.4 ; python_version >= "3.7" and python_version < "3.12" imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.12" @@ -57,12 +57,12 @@ junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12" keyring==24.1.1 ; python_version >= "3.7" and python_version < "3.12" kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12" kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" -lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12" +lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12" markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12" markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.12" markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12" matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.8" -matplotlib==3.7.1 ; python_version >= "3.8" and python_version < "3.12" +matplotlib==3.7.2 ; python_version >= "3.8" and python_version < "3.12" mdit-py-plugins==0.3.5 ; python_version >= "3.7" and python_version < "3.12" mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12" mirakuru==2.5.1 ; python_version >= "3.7" and python_version < "3.12" @@ -74,14 +74,14 @@ mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12" myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.12" numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.25.0 ; python_version >= "3.9" and python_version < "3.12" +numpy==1.25.1 ; python_version >= "3.9" and python_version < "3.12" outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12" packaging==23.1 ; python_version >= "3.7" and python_version < "3.12" pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12" pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12" pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12" pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12" -platformdirs==3.8.0 ; python_version >= "3.7" and python_version < "3.12" +platformdirs==3.8.1 ; python_version >= "3.7" and python_version < "3.12" pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12" port-for==0.7.0 ; python_version >= "3.7" and python_version < "3.12" prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12" @@ -93,7 +93,7 @@ pygithub==1.59.0 ; python_version >= "3.7" and python_version < "3.12" pygments==2.15.1 ; python_version >= "3.7" and python_version < "3.12" pyjwt[crypto]==2.7.0 ; python_version >= "3.7" and python_version < "3.12" pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" -pyparsing==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12" pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12" pytest-asyncio==0.21.0 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3efb83b9be4c..2371ba3ab8e2 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -9,7 +9,7 @@ aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12" aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12" alembic==1.11.1 ; python_version >= "3.7" and python_version < "3.12" amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" -anyio==3.7.0 ; python_version >= "3.7" and python_version < "3.12" +anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12" apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12" appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12" arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12" @@ -36,19 +36,19 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12" cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12" circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -click==8.1.3 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.4 ; python_version >= "3.7" and python_version < "3.12" cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12" cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12" conda-package-streaming==0.8.0 ; python_version >= "3.7" and python_version < "3.12" -cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12" +cryptography==41.0.2 ; python_version >= "3.7" and python_version < "3.12" cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12" cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12" cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12" @@ -92,13 +92,13 @@ jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.12" jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.12" kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" lagom==2.4.1 ; python_version >= "3.7" and python_version < "3.12" -lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12" +lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12" mako==1.2.4 ; python_version >= "3.7" and python_version < "3.12" markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12" markdown==3.4.3 ; python_version >= "3.7" and python_version < "3.12" markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12" mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12" -mercurial==6.4.5 ; python_version >= "3.7" and python_version < "3.12" +mercurial==6.5 ; python_version >= "3.7" and python_version < "3.12" mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12" mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12" msal==1.22.0 ; python_version >= "3.7" and python_version < "3.12" @@ -109,9 +109,9 @@ networkx==2.5 ; python_version >= "3.7" and python_version < "3.12" nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12" numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.25.0 ; python_version >= "3.9" and python_version < "3.12" +numpy==1.25.1 ; python_version >= "3.9" and python_version < "3.12" oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12" -orjson==3.9.1 ; python_version >= "3.7" and python_version < "3.12" +orjson==3.9.2 ; python_version >= "3.7" and python_version < "3.12" oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12" packaging==23.1 ; python_version >= "3.7" and python_version < "3.12" paramiko==3.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -139,7 +139,7 @@ pyjwt[crypto]==2.7.0 ; python_version >= "3.7" and python_version < "3.12" pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.12" pylibmagic==0.4.0 ; python_version >= "3.7" and python_version < "3.12" pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" -pyparsing==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12" pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7" pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.12" @@ -174,7 +174,7 @@ six==1.16.0 ; python_version >= "3.7" and python_version < "3.12" sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12" social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.7" and python_version < "3.12" sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" -sqlalchemy==1.4.48 ; python_version >= "3.7" and python_version < "3.12" +sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.12" sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12" sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.12" starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 12d411febef1..efeaa6e36878 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,5 +1,5 @@ cffi==1.15.1 -cryptography==41.0.1 +cryptography==41.0.2 mypy==1.4.1 mypy-extensions==1.0.0 pycparser==2.21 @@ -8,7 +8,7 @@ tomli==2.0.1 typed-ast==1.5.5 types-bleach==6.0.0.3 types-boto==2.49.18.8 -types-contextvars==2.4.7.2 +types-contextvars==2.4.7.3 types-dataclasses==0.6.6 types-docutils==0.20.0.1 types-Markdown==3.4.2.9 diff --git a/pyproject.toml b/pyproject.toml index bba81c7104df..0d96d9c75025 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -85,7 +85,7 @@ pydantic = {version = "<2", extras = ["email"]} PyJWT = "*" pykwalify = "*" pylibmagic = "*" -pyparsing = "*" +pyparsing = "<3.1" # Needed by matplotlib on Python >=3.8 https://github.com/matplotlib/matplotlib/issues/26152 pysam = ">=0.21" # for Python 3.11 support on macOS python = ">=3.7,<3.12" # Keep maximum version strict to appease numpy and scipy python-dateutil = "*"