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17 00:00:00 2001 From: WassimG Date: Wed, 9 Oct 2024 17:48:10 +0000 Subject: [PATCH 2/2] fix requirements file --- requirements.txt | 73 ++++++++++++++++++++++++------------------------ 1 file changed, 36 insertions(+), 37 deletions(-) diff --git a/requirements.txt b/requirements.txt index 1a1b3d1..f78821a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,43 +2,43 @@ alabaster==0.7.16 ; python_version >= "3.9" and python_full_version < "3.11.0" alphatims==1.0.8 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" anndata==0.10.9 ; python_version >= "3.9" and python_full_version < "3.11.0" annotated-types==0.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -anyio==4.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +anyio==4.6.0 ; python_version >= "3.9" and python_full_version < "3.11.0" array-api-compat==1.7.1 ; python_version >= "3.9" and python_full_version < "3.11.0" attrs==24.2.0 ; python_full_version >= "3.9.0" and 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+docutils==0.21.2 ; python_version >= "3.9" and python_full_version < "3.11.0" dparse==0.6.4b0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" et-xmlfile==1.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" exceptiongroup==1.2.2 ; python_version >= "3.9" and python_version < "3.11" -filelock==3.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +filelock==3.16.1 ; python_version >= "3.9" and python_full_version < "3.11.0" flake8-bandit==4.1.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" flake8-bugbear==24.8.19 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" flake8-docstrings==1.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" flake8-rst-docstrings==0.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" flake8==7.1.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -fonttools==4.53.1 ; python_version >= "3.9" and python_full_version < "3.11.0" -grpcio==1.66.1 ; python_full_version >= "3.9.0" and python_version < "3.11" +fonttools==4.54.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +grpcio==1.66.2 ; python_full_version >= "3.9.0" and python_version < "3.11" h11==0.14.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -h5py==3.11.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -identify==2.6.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -idna==3.8 ; python_version >= "3.9" and python_full_version < "3.11.0" +h5py==3.12.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +identify==2.6.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +idna==3.10 ; python_version >= "3.9" and python_full_version < "3.11.0" imagesize==1.4.1 ; python_version >= "3.9" and python_full_version < "3.11.0" importlib-metadata==8.5.0 ; python_version >= "3.9" and python_full_version < "3.11.0" importlib-resources==6.4.5 ; python_version >= "3.9" and python_version < "3.10" @@ -51,7 +51,7 @@ koinapy==0.0.7 ; python_full_version >= "3.9.0" and python_full_version < "3.11. llvmlite==0.42.0 ; python_version >= "3.9" and python_full_version < "3.11.0" lxml==5.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" markdown-it-py==3.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -markupsafe==2.1.5 ; python_version >= "3.9" and python_full_version < "3.11.0" +markupsafe==3.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0" marshmallow==3.22.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" matplotlib==3.9.2 ; python_version >= "3.9" and python_full_version < "3.11.0" mccabe==0.7.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" @@ -67,29 +67,29 @@ numba==0.59.1 ; python_version >= "3.9" and python_full_version < "3.11.0" numpy==1.24.4 ; python_version >= "3.9" and python_version < "3.11" openpyxl==3.1.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" packaging==24.1 ; python_version >= "3.9" and python_version < "3.11" -pandas==2.2.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +pandas==2.2.3 ; python_version >= "3.9" and python_full_version < "3.11.0" pathspec==0.12.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pbr==6.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pep8-naming==0.14.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" picked-group-fdr==0.7.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pillow==10.4.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -platformdirs==4.3.2 ; python_version >= "3.9" and python_full_version < "3.11.0" +platformdirs==4.3.6 ; python_version >= "3.9" and python_full_version < "3.11.0" pluggy==1.5.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -pre-commit-hooks==4.6.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -pre-commit==3.8.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -protobuf==4.25.4 ; python_full_version >= "3.9.0" and python_version < "3.11" +pre-commit-hooks==5.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pre-commit==4.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +protobuf==4.25.5 ; python_full_version >= "3.9.0" and python_version < "3.11" psutil==6.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pyarrow==17.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pycodestyle==2.12.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pycparser==2.22 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" and platform_python_implementation != "PyPy" -pydantic-core==2.23.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -pydantic==2.9.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pydantic-core==2.23.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pydantic==2.9.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pydocstyle==6.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pyflakes==3.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pygments==2.18.0 ; python_version >= "3.9" and python_full_version < "3.11.0" pymzml==2.5.10 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pyparsing==3.1.4 ; python_version >= "3.9" and python_full_version < "3.11.0" -pyteomics==4.7.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +pyteomics==4.7.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" pytest==8.3.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_full_version < "3.11.0" python-rapidjson==1.20 ; python_full_version >= "3.9.0" and python_version < "3.11" @@ -100,7 +100,7 @@ pyzstd==0.16.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11. regex==2024.9.11 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" requests==2.32.3 ; python_version >= "3.9" and python_full_version < "3.11.0" restructuredtext-lint==1.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -rich==13.8.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +rich==13.9.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_full_version < "3.11.0" and python_full_version >= "3.9.0" ruamel-yaml==0.18.6 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" safety-schemas==0.0.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" @@ -108,18 +108,17 @@ safety==3.2.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0 scikit-learn==1.5.2 ; python_version >= "3.9" and python_full_version < "3.11.0" scipy==1.13.1 ; python_version >= "3.9" and python_full_version < "3.11.0" seaborn==0.13.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -setuptools==74.1.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +setuptools==75.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" shellingham==1.5.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" six==1.16.0 ; python_version >= "3.9" and python_full_version < "3.11.0" sniffio==1.3.1 ; python_version >= "3.9" and python_full_version < "3.11.0" snowballstemmer==2.2.0 ; python_version >= "3.9" and python_full_version < "3.11.0" sortedcontainers==2.4.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -spectrum-fundamentals==0.7.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -spectrum-io==0.6.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -sphinx-autobuild==2024.9.3 ; python_version >= "3.9" and python_full_version < "3.11.0" +spectrum-fundamentals==0.7.4 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +spectrum-io==0.6.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" sphinx-autodoc-typehints==2.3.0 ; python_version >= "3.9" and python_full_version < "3.11.0" sphinx-click==6.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -sphinx-rtd-theme==2.0.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +sphinx-rtd-theme==3.0.1 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" sphinx==7.4.7 ; python_version >= "3.9" and python_full_version < "3.11.0" sphinxcontrib-applehelp==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0" sphinxcontrib-devhelp==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0" @@ -128,25 +127,25 @@ sphinxcontrib-jquery==4.1 ; python_full_version >= "3.9.0" and python_full_versi sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0" sphinxcontrib-qthelp==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0" sphinxcontrib-serializinghtml==2.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -starlette==0.38.5 ; python_version >= "3.9" and python_full_version < "3.11.0" +starlette==0.39.2 ; python_version >= "3.9" and python_full_version < "3.11.0" stevedore==5.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" threadpoolctl==3.5.0 ; python_version >= "3.9" and python_full_version < "3.11.0" tokenize-rt==6.0.0 ; python_version >= "3.9" and python_full_version < "3.11.0" toml==0.10.2 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -tomli==2.0.1 ; python_version >= "3.9" and python_version < "3.11" +tomli==2.0.2 ; python_version >= "3.9" and python_version < "3.11" tqdm==4.66.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" triqler==0.7.3 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -tritonclient[grpc]==2.49.0 ; python_full_version >= "3.9.0" and python_version < "3.11" +tritonclient[grpc]==2.50.0 ; python_full_version >= "3.9.0" and python_version < "3.11" typeguard==4.3.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" typer==0.12.5 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" types-attrs==19.1.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -types-requests==2.32.0.20240907 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" +types-requests==2.32.0.20240914 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.11" -tzdata==2024.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +tzdata==2024.2 ; python_version >= "3.9" and python_full_version < "3.11.0" urllib3==2.2.3 ; python_version >= "3.9" and python_version < "3.11" -uvicorn==0.30.6 ; python_version >= "3.9" and python_full_version < "3.11.0" -virtualenv==20.26.4 ; python_version >= "3.9" and python_full_version < "3.11.0" +uvicorn==0.31.0 ; python_version >= "3.9" and python_full_version < "3.11.0" +virtualenv==20.26.6 ; python_version >= "3.9" and python_full_version < "3.11.0" watchfiles==0.24.0 ; python_version >= "3.9" and python_full_version < "3.11.0" -websockets==13.0.1 ; python_version >= "3.9" and python_full_version < "3.11.0" -xdoctest[colors]==1.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3.11.0" -zipp==3.20.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +websockets==13.1 ; python_version >= "3.9" and python_full_version < "3.11.0" +xdoctest[colors]==1.2.0 ; python_full_version >= "3.9.0" and python_full_version < "3sph.11.0" +zipp==3.20.2 ; python_version >= "3.9" and python_full_version < "3.11.0"