From 76b2d2bbca7c8baf543b5cc9cf71fc5c9138a39a Mon Sep 17 00:00:00 2001 From: John Kerl Date: Tue, 13 Feb 2024 17:58:18 -0500 Subject: [PATCH] Support Python 3.12 (#186) * Run python-spec/update-requirements-txt * more * more * Use files from pfish/python-3.12 branch --------- Co-authored-by: John Kerl --- .github/workflows/python-somacore.yaml | 2 +- python-spec/requirements-py3.10.txt | 30 +++++++++-------- python-spec/requirements-py3.11.txt | 18 ++++++++++ python-spec/requirements-py3.12.txt | 20 +++++++++++ python-spec/requirements-py3.7.txt | 8 ++--- python-spec/requirements-py3.8-lint.txt | 44 ++++++++++++------------- python-spec/requirements-py3.8.txt | 22 ++++++------- python-spec/requirements-py3.9.txt | 30 +++++++++-------- python-spec/update-requirements-txt | 2 +- 9 files changed, 109 insertions(+), 67 deletions(-) create mode 100644 python-spec/requirements-py3.11.txt create mode 100644 python-spec/requirements-py3.12.txt diff --git a/.github/workflows/python-somacore.yaml b/.github/workflows/python-somacore.yaml index 3c9553e3..12ffcf12 100644 --- a/.github/workflows/python-somacore.yaml +++ b/.github/workflows/python-somacore.yaml @@ -45,7 +45,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.7", "3.8", "3.9", "3.10"] + python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 with: diff --git a/python-spec/requirements-py3.10.txt b/python-spec/requirements-py3.10.txt index 8958867a..ec1f979b 100644 --- a/python-spec/requirements-py3.10.txt +++ b/python-spec/requirements-py3.10.txt @@ -1,17 +1,19 @@ -anndata==0.9.2 -attrs==23.1.0 -h5py==3.9.0 -llvmlite==0.41.0 +anndata==0.10.5.post1 +array_api_compat==1.4.1 +attrs==23.2.0 +exceptiongroup==1.2.0 +h5py==3.10.0 +llvmlite==0.42.0 natsort==8.4.0 -numba==0.58.0 -numpy==1.25.2 -packaging==23.1 -pandas==2.1.1 -pyarrow==13.0.0 -pyarrow_hotfix==0.6.0 +numba==0.59.0 +numpy==1.26.4 +packaging==23.2 +pandas==2.2.0 +pyarrow==15.0.0 +pyarrow-hotfix==0.6 python-dateutil==2.8.2 -pytz==2023.3.post1 -scipy==1.11.3 +pytz==2024.1 +scipy==1.12.0 six==1.16.0 -typing_extensions==4.8.0 -tzdata==2023.3 +typing_extensions==4.9.0 +tzdata==2024.1 diff --git a/python-spec/requirements-py3.11.txt b/python-spec/requirements-py3.11.txt new file mode 100644 index 00000000..771c7e81 --- /dev/null +++ b/python-spec/requirements-py3.11.txt @@ -0,0 +1,18 @@ +anndata==0.10.5.post1 +array_api_compat==1.4.1 +attrs==23.2.0 +h5py==3.10.0 +llvmlite==0.42.0 +natsort==8.4.0 +numba==0.59.0 +numpy==1.26.4 +packaging==23.2 +pandas==2.2.0 +pyarrow==15.0.0 +pyarrow-hotfix==0.6 +python-dateutil==2.8.2 +pytz==2024.1 +scipy==1.12.0 +six==1.16.0 +typing_extensions==4.9.0 +tzdata==2024.1 diff --git a/python-spec/requirements-py3.12.txt b/python-spec/requirements-py3.12.txt new file mode 100644 index 00000000..b23699fc --- /dev/null +++ b/python-spec/requirements-py3.12.txt @@ -0,0 +1,20 @@ +anndata==0.10.5.post1 +array_api_compat==1.4.1 +attrs==23.2.0 +h5py==3.10.0 +llvmlite==0.42.0 +natsort==8.4.0 +numba==0.59.0 +numpy==1.26.4 +packaging==23.2 +pandas==2.2.0 +pyarrow==15.0.0 +pyarrow-hotfix==0.6 +python-dateutil==2.8.2 +pytz==2024.1 +scipy==1.12.0 +setuptools==69.0.3 +six==1.16.0 +typing_extensions==4.9.0 +tzdata==2024.1 +wheel==0.42.0 diff --git a/python-spec/requirements-py3.7.txt b/python-spec/requirements-py3.7.txt index cd13e212..fcdd4b3d 100644 --- a/python-spec/requirements-py3.7.txt +++ b/python-spec/requirements-py3.7.txt @@ -1,17 +1,17 @@ anndata==0.8.0 -attrs==23.1.0 +attrs==23.2.0 h5py==3.8.0 importlib-metadata==6.7.0 llvmlite==0.39.1 natsort==8.4.0 numba==0.56.4 numpy==1.21.6 -packaging==23.1 +packaging==23.2 pandas==1.3.5 pyarrow==12.0.1 -pyarrow_hotfix==0.6.0 +pyarrow-hotfix==0.6 python-dateutil==2.8.2 -pytz==2023.3.post1 +pytz==2024.1 scipy==1.7.3 six==1.16.0 typing_extensions==4.7.1 diff --git a/python-spec/requirements-py3.8-lint.txt b/python-spec/requirements-py3.8-lint.txt index d20d9883..682e9913 100644 --- a/python-spec/requirements-py3.8-lint.txt +++ b/python-spec/requirements-py3.8-lint.txt @@ -1,36 +1,36 @@ anndata==0.9.2 -attrs==23.1.0 -black==23.9.1 +attrs==23.2.0 +black==24.2.0 cfgv==3.4.0 click==8.1.7 -distlib==0.3.7 -filelock==3.12.4 -h5py==3.9.0 -identify==2.5.29 -importlib-metadata==6.8.0 -isort==5.12.0 -llvmlite==0.41.0 -mypy==1.5.1 +distlib==0.3.8 +filelock==3.13.1 +h5py==3.10.0 +identify==2.5.34 +importlib-metadata==7.0.1 +isort==5.13.2 +llvmlite==0.41.1 +mypy==1.8.0 mypy-extensions==1.0.0 natsort==8.4.0 nodeenv==1.8.0 -numba==0.58.0 +numba==0.58.1 numpy==1.24.4 -packaging==23.1 +packaging==23.2 pandas==2.0.3 -pathspec==0.11.2 -platformdirs==3.10.0 -pre-commit==3.4.0 -pyarrow==13.0.0 -pyarrow_hotfix==0.6.0 +pathspec==0.12.1 +platformdirs==4.2.0 +pre-commit==3.5.0 +pyarrow==15.0.0 +pyarrow-hotfix==0.6 python-dateutil==2.8.2 -pytz==2023.3.post1 +pytz==2024.1 PyYAML==6.0.1 -ruff==0.0.291 +ruff==0.2.1 scipy==1.10.1 six==1.16.0 tomli==2.0.1 -typing_extensions==4.8.0 -tzdata==2023.3 -virtualenv==20.24.5 +typing_extensions==4.9.0 +tzdata==2024.1 +virtualenv==20.25.0 zipp==3.17.0 diff --git a/python-spec/requirements-py3.8.txt b/python-spec/requirements-py3.8.txt index e44bafe3..8fe62e73 100644 --- a/python-spec/requirements-py3.8.txt +++ b/python-spec/requirements-py3.8.txt @@ -1,19 +1,19 @@ anndata==0.9.2 -attrs==23.1.0 -h5py==3.9.0 -importlib-metadata==6.8.0 -llvmlite==0.41.0 +attrs==23.2.0 +h5py==3.10.0 +importlib-metadata==7.0.1 +llvmlite==0.41.1 natsort==8.4.0 -numba==0.58.0 +numba==0.58.1 numpy==1.24.4 -packaging==23.1 +packaging==23.2 pandas==2.0.3 -pyarrow==13.0.0 -pyarrow_hotfix==0.6.0 +pyarrow==15.0.0 +pyarrow-hotfix==0.6 python-dateutil==2.8.2 -pytz==2023.3.post1 +pytz==2024.1 scipy==1.10.1 six==1.16.0 -typing_extensions==4.8.0 -tzdata==2023.3 +typing_extensions==4.9.0 +tzdata==2024.1 zipp==3.17.0 diff --git a/python-spec/requirements-py3.9.txt b/python-spec/requirements-py3.9.txt index e2e95445..726bdc0b 100644 --- a/python-spec/requirements-py3.9.txt +++ b/python-spec/requirements-py3.9.txt @@ -1,21 +1,23 @@ -anndata==0.9.2 -attrs==23.1.0 +anndata==0.10.5.post1 +array_api_compat==1.4.1 +attrs==23.2.0 docutils==0.16 -h5py==3.9.0 +exceptiongroup==1.2.0 +h5py==3.10.0 jmespath==1.0.1 -llvmlite==0.41.0 +llvmlite==0.42.0 natsort==8.4.0 -numba==0.58.0 -numpy==1.25.2 -packaging==23.1 -pandas==2.1.1 -pyarrow==13.0.0 -pyarrow_hotfix==0.6.0 +numba==0.59.0 +numpy==1.26.4 +packaging==23.2 +pandas==2.2.0 +pyarrow==15.0.0 +pyarrow-hotfix==0.6 python-dateutil==2.8.2 -pytz==2023.3.post1 +pytz==2024.1 rsa==4.7.2 s3transfer==0.6.0 -scipy==1.11.3 +scipy==1.12.0 six==1.16.0 -typing_extensions==4.8.0 -tzdata==2023.3 +typing_extensions==4.9.0 +tzdata==2024.1 diff --git a/python-spec/update-requirements-txt b/python-spec/update-requirements-txt index e9d8052b..59ca65e5 100755 --- a/python-spec/update-requirements-txt +++ b/python-spec/update-requirements-txt @@ -12,7 +12,7 @@ trap "trash $TEMPDIR" EXIT # The version of Python we want to run lints under. LINTVER=3.8 -for PYVER in 3.7 3.8 3.9 3.10; do +for PYVER in 3.7 3.8 3.9 3.10 3.11 3.12; do CONDIR="$TEMPDIR/py-$PYVER" conda create -y -p "$CONDIR" "python=$PYVER" (