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 <kerl.john.@gmail.com>

.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:

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

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

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

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

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

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

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

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"
   (