Support Python 3.13

.github/workflows/python-somacore.yaml

@@ -45,7 +45,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
         with:

python-spec/requirements-py3.10.txt

@@ -1,19 +1,18 @@
-anndata==0.10.7
-array_api_compat==1.7.1
-attrs==23.2.0
-exceptiongroup==1.2.1
-h5py==3.11.0
-llvmlite==0.43.0
+anndata==0.11.3
+array_api_compat==1.11.1
+attrs==25.1.0
+exceptiongroup==1.2.2
+h5py==3.13.0
 natsort==8.4.0
-numpy==2.0.0
-packaging==24.1
-pandas==2.2.2
-pyarrow==16.1.0
+numpy==2.2.3
+packaging==24.2
+pandas==2.2.3
+pyarrow==19.0.1
 pyarrow-hotfix==0.6
 python-dateutil==2.9.0.post0
-pytz==2024.1
-scipy==1.13.1
-shapely==2.0.4
-six==1.16.0
+pytz==2025.1
+scipy==1.15.2
+shapely==2.0.7
+six==1.17.0
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2025.1

python-spec/requirements-py3.11.txt

@@ -1,18 +1,17 @@
-anndata==0.10.7
-array_api_compat==1.7.1
-attrs==23.2.0
-h5py==3.11.0
-llvmlite==0.43.0
+anndata==0.11.3
+array_api_compat==1.11.1
+attrs==25.1.0
+h5py==3.13.0
 natsort==8.4.0
-numpy==2.0.0
-packaging==24.1
-pandas==2.2.2
-pyarrow==16.1.0
+numpy==2.2.3
+packaging==24.2
+pandas==2.2.3
+pyarrow==19.0.1
 pyarrow-hotfix==0.6
 python-dateutil==2.9.0.post0
-pytz==2024.1
-shapely==2.0.4
-scipy==1.13.1
-six==1.16.0
+pytz==2025.1
+scipy==1.15.2
+shapely==2.0.7
+six==1.17.0
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2025.1

python-spec/requirements-py3.12.txt

@@ -1,20 +1,19 @@
-anndata==0.10.7
-array_api_compat==1.7.1
-attrs==23.2.0
-h5py==3.11.0
-llvmlite==0.43.0
+anndata==0.11.3
+array_api_compat==1.11.1
+attrs==25.1.0
+h5py==3.13.0
 natsort==8.4.0
-numpy==2.0.0
-packaging==24.1
-pandas==2.2.2
-pyarrow==16.1.0
+numpy==2.2.3
+packaging==24.2
+pandas==2.2.3
+pyarrow==19.0.1
 pyarrow-hotfix==0.6
 python-dateutil==2.9.0.post0
-pytz==2024.1
-scipy==1.13.1
-setuptools==70.0.0
-shapely==2.0.4
-six==1.16.0
+pytz==2025.1
+scipy==1.15.2
+setuptools==75.8.2
+shapely==2.0.7
+six==1.17.0
 typing_extensions==4.12.2
-tzdata==2024.1
-wheel==0.43.0
+tzdata==2025.1
+wheel==0.45.1

python-spec/requirements-py3.13.txt

@@ -0,0 +1,17 @@
+anndata==0.11.3
+array_api_compat==1.11.1
+attrs==25.1.0
+h5py==3.13.0
+natsort==8.4.0
+numpy==2.2.3
+packaging==24.2
+pandas==2.2.3
+pyarrow==19.0.1
+pyarrow-hotfix==0.6
+python-dateutil==2.9.0.post0
+pytz==2025.1
+scipy==1.15.2
+shapely==2.0.7
+six==1.17.0
+typing_extensions==4.12.2
+tzdata==2025.1

python-spec/requirements-py3.9-lint.txt

@@ -1,3 +1,37 @@
-mypy==1.11.2
-pandas-stubs==2.2.2.240807  # last version which supports Python 3.9
-pre-commit==3.8.0
+anndata==0.10.9
+array_api_compat==1.11.1
+attrs==25.1.0
+black==25.1.0
+cfgv==3.4.0
+click==8.1.8
+distlib==0.3.9
+exceptiongroup==1.2.2
+filelock==3.17.0
+h5py==3.13.0
+identify==2.6.8
+isort==6.0.1
+mypy==1.15.0
+mypy-extensions==1.0.0
+natsort==8.4.0
+nodeenv==1.9.1
+numpy==2.0.2
+packaging==24.2
+pandas==2.2.3
+pandas-stubs==2.2.2.240807
+pathspec==0.12.1
+platformdirs==4.3.6
+pre_commit==4.1.0
+pyarrow==19.0.1
+pyarrow-hotfix==0.6
+python-dateutil==2.9.0.post0
+pytz==2025.1
+PyYAML==6.0.2
+ruff==0.9.9
+scipy==1.13.1
+shapely==2.0.7
+six==1.17.0
+tomli==2.2.1
+types-pytz==2025.1.0.20250204
+typing_extensions==4.12.2
+tzdata==2025.1
+virtualenv==20.29.2

python-spec/requirements-py3.9.txt

@@ -1,23 +1,18 @@
-anndata==0.10.7
-array_api_compat==1.7.1
-attrs==23.2.0
-docutils==0.16
-exceptiongroup==1.2.1
-h5py==3.11.0
-jmespath==1.0.1
-llvmlite==0.43.0
+anndata==0.10.9
+array_api_compat==1.11.1
+attrs==25.1.0
+exceptiongroup==1.2.2
+h5py==3.13.0
 natsort==8.4.0
-numpy==2.0.0
-packaging==24.1
-pandas==2.2.2
-pyarrow==16.1.0
+numpy==2.0.2
+packaging==24.2
+pandas==2.2.3
+pyarrow==19.0.1
 pyarrow-hotfix==0.6
-python-dateutil==2.8.2
-pytz==2024.1
-rsa==4.7.2
-s3transfer==0.6.0
+python-dateutil==2.9.0.post0
+pytz==2025.1
 scipy==1.13.1
-shapely==2.0.4
-six==1.16.0
+shapely==2.0.7
+six==1.17.0
 typing_extensions==4.12.2
-tzdata==2024.1
+tzdata==2025.1

python-spec/update-requirements-txt

@@ -12,7 +12,7 @@ trap "trash $TEMPDIR" EXIT
 # The version of Python we want to run lints under.
 LINTVER=3.9
 
-for PYVER in 3.9 3.10 3.11 3.12; do
+for PYVER in 3.9 3.10 3.11 3.12 3.13; do
   CONDIR="$TEMPDIR/py-$PYVER"
   conda create -y -p "$CONDIR" "python=$PYVER"
   (