diff --git a/pyproject.toml b/pyproject.toml index ef3ad17..f8ecb82 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ dependencies = [ "cloudpathlib", "docker", "pandas", - "polars>=1.17.1,<1.29.0", + "polars>=1.17.1,<1.37.0", "pyarrow", "requests>=2.32.0", "rich", diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt index f4c5f9a..8c125d4 100644 --- a/requirements/requirements-dev.txt +++ b/requirements/requirements-dev.txt @@ -1,50 +1,50 @@ # This file was autogenerated by uv via the following command: # uv pip compile pyproject.toml --extra dev -o requirements/requirements-dev.txt -awscli==1.40.17 +awscli==1.43.15 # via cladetime (pyproject.toml) biobear==0.23.7 # via cladetime (pyproject.toml) -biopython==1.85 +biopython==1.86 # via cladetime (pyproject.toml) -boto3==1.38.18 +boto3==1.42.9 # via # cladetime (pyproject.toml) # moto -boto3-stubs==1.38.18 +boto3-stubs==1.42.9 # via cladetime (pyproject.toml) -botocore==1.38.18 +botocore==1.42.9 # via # awscli # boto3 # moto # s3transfer -botocore-stubs==1.38.18 +botocore-stubs==1.42.9 # via boto3-stubs -certifi==2025.4.26 +certifi==2025.11.12 # via requests -cffi==1.17.1 +cffi==2.0.0 # via cryptography -charset-normalizer==3.4.2 +charset-normalizer==3.4.4 # via requests -cloudpathlib==0.21.1 +cloudpathlib==0.23.0 # via cladetime (pyproject.toml) colorama==0.4.6 # via awscli -coverage==7.8.0 +coverage==7.13.0 # via cladetime (pyproject.toml) -cryptography==44.0.3 +cryptography==46.0.3 # via moto docker==7.1.0 # via cladetime (pyproject.toml) -docutils==0.19 +docutils==0.22.3 # via awscli -freezegun==1.5.1 +freezegun==1.5.5 # via cladetime (pyproject.toml) -idna==3.10 +idna==3.11 # via requests -iniconfig==2.1.0 +iniconfig==2.3.0 # via pytest -jellyfish==1.2.0 +jellyfish==1.2.1 # via us jinja2==3.1.6 # via @@ -54,49 +54,49 @@ jmespath==1.0.1 # via # boto3 # botocore -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via rich -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # werkzeug mdurl==0.1.2 # via markdown-it-py -moto==5.1.4 +moto==5.1.18 # via cladetime (pyproject.toml) -mypy==1.15.0 +mypy==1.19.0 # via cladetime (pyproject.toml) -mypy-boto3-s3==1.38.0 +mypy-boto3-s3==1.42.3 # via boto3-stubs mypy-extensions==1.1.0 # via mypy -numpy==2.2.5 +numpy==2.3.5 # via # biopython # pandas packaging==25.0 # via pytest -pandas==2.2.3 +pandas==2.3.3 # via cladetime (pyproject.toml) pluggy==1.6.0 # via pytest -polars==1.28.1 +polars==1.36.1 # via cladetime (pyproject.toml) -pyarrow==20.0.0 +pyarrow==22.0.0 # via # cladetime (pyproject.toml) # biobear pyasn1==0.6.1 # via rsa -pycparser==2.22 +pycparser==2.23 # via cffi -pygments==2.19.1 +pygments==2.19.2 # via rich -pytest==8.3.5 +pytest==9.0.2 # via # cladetime (pyproject.toml) # pytest-mock -pytest-mock==3.14.0 +pytest-mock==3.15.1 # via cladetime (pyproject.toml) python-dateutil==2.9.0.post0 # via @@ -106,50 +106,50 @@ python-dateutil==2.9.0.post0 # pandas pytz==2025.2 # via pandas -pyyaml==6.0.2 +pyyaml==6.0.3 # via # awscli # responses -requests==2.32.3 +requests==2.32.5 # via # cladetime (pyproject.toml) # docker # moto # responses -responses==0.25.7 +responses==0.25.8 # via moto -rich==14.0.0 +rich==14.2.0 # via cladetime (pyproject.toml) -rsa==4.7.2 +rsa==4.9.1 # via awscli -ruff==0.11.10 +ruff==0.14.9 # via cladetime (pyproject.toml) -s3transfer==0.12.0 +s3transfer==0.16.0 # via # awscli # boto3 six==1.17.0 # via python-dateutil -structlog==25.3.0 +structlog==25.5.0 # via cladetime (pyproject.toml) tqdm==4.67.1 # via cladetime (pyproject.toml) -types-awscrt==0.27.2 +types-awscrt==0.30.0 # via botocore-stubs types-python-dateutil==2.9.0.20250516 # via cladetime (pyproject.toml) -types-requests==2.32.0.20250515 +types-requests==2.32.4.20250913 # via cladetime (pyproject.toml) -types-s3transfer==0.12.0 +types-s3transfer==0.16.0 # via boto3-stubs -typing-extensions==4.13.2 +typing-extensions==4.15.0 # via # boto3-stubs # mypy # mypy-boto3-s3 -tzdata==2025.2 +tzdata==2025.3 # via pandas -urllib3==2.4.0 +urllib3==2.6.2 # via # cladetime (pyproject.toml) # botocore @@ -159,9 +159,9 @@ urllib3==2.4.0 # types-requests us==3.2.0 # via cladetime (pyproject.toml) -werkzeug==3.1.3 +werkzeug==3.1.4 # via moto -xmltodict==0.14.2 +xmltodict==1.0.2 # via moto -zstandard==0.23.0 +zstandard==0.25.0 # via cladetime (pyproject.toml) diff --git a/requirements/requirements-docs.txt b/requirements/requirements-docs.txt index cdca688..30f54fa 100644 --- a/requirements/requirements-docs.txt +++ b/requirements/requirements-docs.txt @@ -1,8 +1,8 @@ # This file was autogenerated by uv via the following command: # uv pip compile pyproject.toml --extra docs -o requirements/requirements-docs.txt -alabaster==0.7.16 +alabaster==1.0.0 # via sphinx -anyio==4.9.0 +anyio==4.12.0 # via # starlette # watchfiles @@ -12,40 +12,40 @@ apeye-core==1.1.5 # via apeye autodocsumm==0.2.14 # via sphinx-toolbox -awscli==1.40.17 +awscli==1.43.15 # via cladetime (pyproject.toml) babel==2.17.0 # via sphinx -beautifulsoup4==4.13.4 +beautifulsoup4==4.14.3 # via # furo # sphinx-toolbox biobear==0.23.7 # via cladetime (pyproject.toml) -biopython==1.85 +biopython==1.86 # via cladetime (pyproject.toml) -boto3==1.38.18 +boto3==1.42.9 # via cladetime (pyproject.toml) -botocore==1.38.18 +botocore==1.42.9 # via # awscli # boto3 # s3transfer -cachecontrol==0.14.3 +cachecontrol==0.14.4 # via sphinx-toolbox -certifi==2025.4.26 +certifi==2025.11.12 # via requests -charset-normalizer==3.4.2 +charset-normalizer==3.4.4 # via requests -click==8.2.0 +click==8.3.1 # via uvicorn -cloudpathlib==0.21.1 +cloudpathlib==0.23.0 # via cladetime (pyproject.toml) colorama==0.4.6 # via # awscli # sphinx-autobuild -contourpy==1.3.2 +contourpy==1.3.3 # via matplotlib cssutils==2.11.1 # via dict2css @@ -55,7 +55,7 @@ dict2css==0.3.0.post1 # via sphinx-toolbox docker==7.1.0 # via cladetime (pyproject.toml) -docutils==0.19 +docutils==0.22.3 # via # awscli # myst-parser @@ -69,26 +69,26 @@ domdf-python-tools==3.10.0 # apeye-core # dict2css # sphinx-toolbox -filelock==3.18.0 +filelock==3.20.0 # via # cachecontrol # sphinx-toolbox -fonttools==4.58.0 +fonttools==4.61.1 # via matplotlib -furo==2024.8.6 +furo==2025.9.25 # via cladetime (pyproject.toml) h11==0.16.0 # via uvicorn html5lib==1.1 # via sphinx-toolbox -idna==3.10 +idna==3.11 # via # anyio # apeye-core # requests imagesize==1.4.1 # via sphinx -jellyfish==1.2.0 +jellyfish==1.2.1 # via us jinja2==3.1.6 # via @@ -100,32 +100,32 @@ jmespath==1.0.1 # via # boto3 # botocore -kiwisolver==1.4.8 +kiwisolver==1.4.9 # via matplotlib -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via # mdit-py-plugins # myst-parser # rich -markupsafe==3.0.2 +markupsafe==3.0.3 # via # jinja2 # sphinx-jinja2-compat -matplotlib==3.10.3 +matplotlib==3.10.8 # via cladetime (pyproject.toml) -mdit-py-plugins==0.4.2 +mdit-py-plugins==0.5.0 # via myst-parser mdurl==0.1.2 # via markdown-it-py -more-itertools==10.7.0 +more-itertools==10.8.0 # via cssutils -msgpack==1.1.0 +msgpack==1.1.2 # via cachecontrol myst-parser==4.0.1 # via cladetime (pyproject.toml) natsort==8.4.0 # via domdf-python-tools -numpy==2.2.5 +numpy==2.3.5 # via # biopython # contourpy @@ -135,28 +135,28 @@ packaging==25.0 # via # matplotlib # sphinx -pandas==2.2.3 +pandas==2.3.3 # via cladetime (pyproject.toml) -pillow==11.2.1 +pillow==12.0.0 # via matplotlib -platformdirs==4.3.8 +platformdirs==4.5.1 # via apeye -polars==1.28.1 +polars==1.36.1 # via cladetime (pyproject.toml) -pyarrow==20.0.0 +pyarrow==22.0.0 # via # cladetime (pyproject.toml) # biobear pyasn1==0.6.1 # via rsa -pygments==2.19.1 +pygments==2.19.2 # via # furo # rich # sphinx # sphinx-prompt # sphinx-tabs -pyparsing==3.2.3 +pyparsing==3.2.5 # via matplotlib python-dateutil==2.9.0.post0 # via @@ -165,26 +165,26 @@ python-dateutil==2.9.0.post0 # pandas pytz==2025.2 # via pandas -pyyaml==6.0.2 +pyyaml==6.0.3 # via # awscli # myst-parser -requests==2.32.3 +requests==2.32.5 # via # cladetime (pyproject.toml) # apeye # cachecontrol # docker # sphinx -rich==14.0.0 +rich==14.2.0 # via cladetime (pyproject.toml) -rsa==4.7.2 +rsa==4.9.1 # via awscli -ruamel-yaml==0.18.10 +ruamel-yaml==0.18.16 # via sphinx-toolbox -ruamel-yaml-clib==0.2.12 +ruamel-yaml-clib==0.2.15 # via ruamel-yaml -s3transfer==0.12.0 +s3transfer==0.16.0 # via # awscli # boto3 @@ -196,9 +196,9 @@ sniffio==1.3.1 # via anyio snowballstemmer==3.0.1 # via sphinx -soupsieve==2.7 +soupsieve==2.8 # via beautifulsoup4 -sphinx==7.3.7 +sphinx==9.0.4 # via # cladetime (pyproject.toml) # autodocsumm @@ -213,9 +213,9 @@ sphinx==7.3.7 # sphinx-tabs # sphinx-toolbox # sphinxext-opengraph -sphinx-autobuild==2024.10.3 +sphinx-autobuild==2025.8.25 # via cladetime (pyproject.toml) -sphinx-autodoc-typehints==2.3.0 +sphinx-autodoc-typehints==3.6.0 # via sphinx-toolbox sphinx-basic-ng==1.0.0b2 # via furo @@ -223,13 +223,13 @@ sphinx-copybutton==0.5.2 # via cladetime (pyproject.toml) sphinx-github-style==1.2.2 # via cladetime (pyproject.toml) -sphinx-jinja2-compat==0.3.0 +sphinx-jinja2-compat==0.4.1 # via sphinx-toolbox -sphinx-prompt==1.8.0 +sphinx-prompt==1.10.2 # via sphinx-toolbox -sphinx-tabs==3.4.5 +sphinx-tabs==3.4.7 # via sphinx-toolbox -sphinx-toolbox==4.0.0 +sphinx-toolbox==4.1.0 # via cladetime (pyproject.toml) sphinxcontrib-applehelp==2.0.0 # via sphinx @@ -243,25 +243,25 @@ sphinxcontrib-qthelp==2.0.0 # via sphinx sphinxcontrib-serializinghtml==2.0.0 # via sphinx -sphinxext-opengraph==0.10.0 +sphinxext-opengraph==0.13.0 # via cladetime (pyproject.toml) -starlette==0.46.2 +starlette==0.50.0 # via sphinx-autobuild -structlog==25.3.0 +structlog==25.5.0 # via cladetime (pyproject.toml) tabulate==0.9.0 # via sphinx-toolbox tqdm==4.67.1 # via cladetime (pyproject.toml) -typing-extensions==4.13.2 +typing-extensions==4.15.0 # via # anyio # beautifulsoup4 # domdf-python-tools # sphinx-toolbox -tzdata==2025.2 +tzdata==2025.3 # via pandas -urllib3==2.4.0 +urllib3==2.6.2 # via # cladetime (pyproject.toml) # botocore @@ -269,13 +269,13 @@ urllib3==2.4.0 # requests us==3.2.0 # via cladetime (pyproject.toml) -uvicorn==0.34.2 +uvicorn==0.38.0 # via sphinx-autobuild -watchfiles==1.0.5 +watchfiles==1.1.1 # via sphinx-autobuild webencodings==0.5.1 # via html5lib websockets==15.0.1 # via sphinx-autobuild -zstandard==0.23.0 +zstandard==0.25.0 # via cladetime (pyproject.toml) diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 30399c6..a85c76e 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,57 +1,57 @@ # This file was autogenerated by uv via the following command: # uv pip compile pyproject.toml -o requirements/requirements.txt -awscli==1.40.17 +awscli==1.43.15 # via cladetime (pyproject.toml) biobear==0.23.7 # via cladetime (pyproject.toml) -biopython==1.85 +biopython==1.86 # via cladetime (pyproject.toml) -boto3==1.38.18 +boto3==1.42.9 # via cladetime (pyproject.toml) -botocore==1.38.18 +botocore==1.42.9 # via # awscli # boto3 # s3transfer -certifi==2025.4.26 +certifi==2025.11.12 # via requests -charset-normalizer==3.4.2 +charset-normalizer==3.4.4 # via requests -cloudpathlib==0.21.1 +cloudpathlib==0.23.0 # via cladetime (pyproject.toml) colorama==0.4.6 # via awscli docker==7.1.0 # via cladetime (pyproject.toml) -docutils==0.19 +docutils==0.22.3 # via awscli -idna==3.10 +idna==3.11 # via requests -jellyfish==1.2.0 +jellyfish==1.2.1 # via us jmespath==1.0.1 # via # boto3 # botocore -markdown-it-py==3.0.0 +markdown-it-py==4.0.0 # via rich mdurl==0.1.2 # via markdown-it-py -numpy==2.2.5 +numpy==2.3.5 # via # biopython # pandas -pandas==2.2.3 +pandas==2.3.3 # via cladetime (pyproject.toml) -polars==1.28.1 +polars==1.36.1 # via cladetime (pyproject.toml) -pyarrow==20.0.0 +pyarrow==22.0.0 # via # cladetime (pyproject.toml) # biobear pyasn1==0.6.1 # via rsa -pygments==2.19.1 +pygments==2.19.2 # via rich python-dateutil==2.9.0.post0 # via @@ -59,29 +59,29 @@ python-dateutil==2.9.0.post0 # pandas pytz==2025.2 # via pandas -pyyaml==6.0.2 +pyyaml==6.0.3 # via awscli -requests==2.32.3 +requests==2.32.5 # via # cladetime (pyproject.toml) # docker -rich==14.0.0 +rich==14.2.0 # via cladetime (pyproject.toml) -rsa==4.7.2 +rsa==4.9.1 # via awscli -s3transfer==0.12.0 +s3transfer==0.16.0 # via # awscli # boto3 six==1.17.0 # via python-dateutil -structlog==25.3.0 +structlog==25.5.0 # via cladetime (pyproject.toml) tqdm==4.67.1 # via cladetime (pyproject.toml) -tzdata==2025.2 +tzdata==2025.3 # via pandas -urllib3==2.4.0 +urllib3==2.6.2 # via # cladetime (pyproject.toml) # botocore @@ -89,5 +89,5 @@ urllib3==2.4.0 # requests us==3.2.0 # via cladetime (pyproject.toml) -zstandard==0.23.0 +zstandard==0.25.0 # via cladetime (pyproject.toml)