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johnkerljohnkerl
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Support Python 3.13 (#257)
* Support Python 3.13 * run ./python-spec/update-requirements-txt
1 parent c3262e1 commit 878134a

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+112
-69
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‎.github/workflows/python-somacore.yaml

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

‎python-spec/requirements-py3.10.txt

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@@ -1,19 +1,18 @@
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anndata==0.10.7
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array_api_compat==1.7.1
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attrs==23.2.0
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exceptiongroup==1.2.1
5-
h5py==3.11.0
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llvmlite==0.43.0
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anndata==0.11.3
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array_api_compat==1.11.1
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attrs==25.1.0
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exceptiongroup==1.2.2
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h5py==3.13.0
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natsort==8.4.0
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numpy==2.0.0
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packaging==24.1
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pandas==2.2.2
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pyarrow==16.1.0
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numpy==2.2.3
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packaging==24.2
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pandas==2.2.3
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pyarrow==19.0.1
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pyarrow-hotfix==0.6
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python-dateutil==2.9.0.post0
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pytz==2024.1
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scipy==1.13.1
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shapely==2.0.4
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six==1.16.0
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pytz==2025.1
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scipy==1.15.2
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shapely==2.0.7
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six==1.17.0
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typing_extensions==4.12.2
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tzdata==2024.1
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tzdata==2025.1

‎python-spec/requirements-py3.11.txt

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

‎python-spec/requirements-py3.12.txt

Lines changed: 15 additions & 16 deletions
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@@ -1,20 +1,19 @@
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anndata==0.10.7
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array_api_compat==1.7.1
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attrs==23.2.0
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h5py==3.11.0
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llvmlite==0.43.0
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anndata==0.11.3
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array_api_compat==1.11.1
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attrs==25.1.0
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h5py==3.13.0
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natsort==8.4.0
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numpy==2.0.0
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packaging==24.1
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pandas==2.2.2
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pyarrow==16.1.0
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numpy==2.2.3
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packaging==24.2
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pandas==2.2.3
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pyarrow==19.0.1
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pyarrow-hotfix==0.6
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python-dateutil==2.9.0.post0
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pytz==2024.1
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scipy==1.13.1
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setuptools==70.0.0
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shapely==2.0.4
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six==1.16.0
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pytz==2025.1
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scipy==1.15.2
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setuptools==75.8.2
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shapely==2.0.7
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six==1.17.0
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typing_extensions==4.12.2
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tzdata==2024.1
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wheel==0.43.0
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tzdata==2025.1
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wheel==0.45.1

‎python-spec/requirements-py3.13.txt

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

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

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

‎python-spec/requirements-py3.9.txt

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@@ -1,23 +1,18 @@
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anndata==0.10.7
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array_api_compat==1.7.1
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attrs==23.2.0
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docutils==0.16
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exceptiongroup==1.2.1
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h5py==3.11.0
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jmespath==1.0.1
8-
llvmlite==0.43.0
1+
anndata==0.10.9
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array_api_compat==1.11.1
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attrs==25.1.0
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exceptiongroup==1.2.2
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h5py==3.13.0
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natsort==8.4.0
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numpy==2.0.0
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packaging==24.1
12-
pandas==2.2.2
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pyarrow==16.1.0
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numpy==2.0.2
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packaging==24.2
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pandas==2.2.3
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pyarrow==19.0.1
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pyarrow-hotfix==0.6
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python-dateutil==2.8.2
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pytz==2024.1
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rsa==4.7.2
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s3transfer==0.6.0
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python-dateutil==2.9.0.post0
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pytz==2025.1
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scipy==1.13.1
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shapely==2.0.4
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six==1.16.0
15+
shapely==2.0.7
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six==1.17.0
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typing_extensions==4.12.2
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tzdata==2024.1
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tzdata==2025.1

‎python-spec/update-requirements-txt

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

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