Test on Python 3.12 - but only on NumPy 2 due to cbgen version constraints

Author: tomwhite

.github/workflows/build-numpy-2.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -22,8 +22,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt
-        pip install -U 'numpy<2.1'
+        pip install -r requirements-numpy2.txt -r requirements-numpy2-dev.txt
     - name: Run pre-commit
       uses: pre-commit/[email protected]
     - name: Test with pytest (numba jit disabled)

requirements-numpy2-dev.txt

@@ -0,0 +1,24 @@
+callee
+pre-commit
+pytest
+pytest-cov
+pytest-datadir
+pytest-mock
+hypothesis
+scikit-allel
+statsmodels
+msprime>=1.0
+scikit-learn
+partd
+bed-reader
+rechunker
+cbgen > 1.0.5; platform_system != "Windows"
+cbgen == 1.0.1; platform_system == "Windows"
+cyvcf2; platform_system != "Windows"
+yarl
+matplotlib
+asv
+networkx
+aiohttp
+requests
+graphviz

requirements-numpy2.txt

@@ -0,0 +1,12 @@
+numpy < 2.1
+xarray
+dask[array] >= 2023.01.0, <= 2024.8.0
+distributed >= 2023.01.0, <= 2024.8.0
+dask-ml
+scipy
+typing-extensions
+numba
+zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3
+fsspec != 2021.6.*
+scikit-learn
+pandas