Migrate development and CI to uv and remove Upstream checks

.github/workflows/build-gpu.yml

@@ -34,6 +34,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
           miniconda-version: "latest"
 
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.0.1
+        with:
+          version: "0.12.10"
+          enable-cache: true
+
       - name: Conda info
         run: |
           conda info
@@ -42,7 +48,8 @@ jobs:
       - name: Installing cudatoolkit and dependencies
         run: |
           conda install -c nvidia cudatoolkit
-          pip install -r requirements.txt -r requirements-dev.txt
+          # Avoid building SciPy from source in CI.
+          uv pip install --only-binary scipy --python "$CONDA_PREFIX/bin/python" -e ".[bgen,plink]" --group test
 
       - name: Numba Information
         run: |

.github/workflows/build.yml

@@ -22,15 +22,20 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.0.1
+      with:
+        version: "0.12.10"
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt
+        uv sync --locked --all-extras --group test --group lint --no-default-groups --python "${{ matrix.python-version }}"
     - name: Run pre-commit
-      uses: pre-commit/action@v3.0.1
+      run: uv run --no-sync pre-commit run --all-files
     - name: Test with pytest and coverage
       run: |
-        pytest -v --cov=sgkit --cov-report=term-missing
+        uv run --no-sync pytest -v --cov=sgkit --cov-report=term-missing
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v7
       with:
@@ -49,14 +54,19 @@ jobs:
       - uses: actions/setup-python@v7
         with:
           python-version: '3.11'
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.0.1
+        with:
+          version: "0.12.10"
+          python-version: '3.11'
+          enable-cache: true
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt -r requirements-dev.txt
+          uv sync --locked --all-extras --group test --no-default-groups --python 3.11
       - name: Install zarr${{ matrix.zarr }}
         run: |
-          python -m pip install --pre 'zarr${{ matrix.zarr }}'
-          python -m pip uninstall -y bio2zarr  # TODO: remove when bio2zarr supports Zarr Python 3
+          uv pip install --python .venv/bin/python --pre 'zarr${{ matrix.zarr }}'
+          uv pip uninstall --python .venv/bin/python bio2zarr  # TODO: remove when bio2zarr supports Zarr Python 3
       - name: Run tests
         run: |
-          pytest
+          uv run --no-sync pytest

.github/workflows/check-docs.yml

@@ -22,19 +22,25 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.0.1
+      with:
+        version: "0.12.10"
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
     - name: Install dependencies
       run: |
         sudo apt update -y
         sudo apt install graphviz  # Needed for documentation
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
-        pip install -U dask distributed  # need latest versions to successully build docs
+        uv sync --locked --all-extras --group docs --group lint --no-default-groups --python "${{ matrix.python-version }}"
+        # Use newer Dask for task-graph rendering with NumPy 2.
+        uv pip uninstall --python .venv/bin/python dask-expr
+        uv pip install --python .venv/bin/python 'dask==2026.8.0'
     - name: Run pre-commit
-      uses: pre-commit/action@v3.0.1
+      run: uv run --no-sync pre-commit run --all-files
     - name: Check for Sphinx doc warnings
       run: |
-        cd docs
-        make html SPHINXOPTS="-W --keep-going -n"
+        make -C docs html SPHINXOPTS="-W --keep-going -n"
     - uses: actions/upload-artifact@v7
       if: failure()
       with:

.github/workflows/cubed.yml

@@ -21,16 +21,24 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.0.1
+      with:
+        version: "0.12.10"
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
 
     - name: Install deps and sgkit
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install -r requirements.txt -r requirements-dev.txt
-        python -m pip install -U git+https://github.com/cubed-dev/cubed.git -U git+https://github.com/cubed-dev/cubed-xarray.git -U git+https://github.com/pydata/xarray.git
+        uv sync --locked --all-extras --group test --no-default-groups --python "${{ matrix.python-version }}"
+        # Update the experimental packages without upgrading unrelated dependencies.
+        uv pip install --python .venv/bin/python \
+          --upgrade-package cubed --upgrade-package cubed-xarray --upgrade-package xarray \
+          git+https://github.com/cubed-dev/cubed.git git+https://github.com/cubed-dev/cubed-xarray.git git+https://github.com/pydata/xarray.git
 
     - name: Test with pytest
       run: |
-        pytest -v sgkit/tests/test_{aggregation,association,hwe,pca,window}.py \
+        uv run --no-sync pytest -v sgkit/tests/test_{aggregation,association,hwe,pca,window}.py \
           -k "test_count_call_alleles or \
               test_gwas_linear_regression or \
               test_hwep or \

.github/workflows/docs.yml

@@ -12,21 +12,27 @@ jobs:
 
     steps:
     - uses: actions/checkout@v7
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python 3.11
       uses: actions/setup-python@v7
       with:
         python-version: "3.11"
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.0.1
+      with:
+        version: "0.12.10"
+        python-version: "3.11"
+        enable-cache: true
     - name: Install dependencies
       run: |
         sudo apt update -y
         sudo apt install graphviz  # Needed for documentation
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
-        pip install -U dask distributed  # need latest versions to successully build docs
+        uv sync --locked --all-extras --group docs --no-default-groups --python "3.11"
+        # Use newer Dask for task-graph rendering with NumPy 2.
+        uv pip uninstall --python .venv/bin/python dask-expr
+        uv pip install --python .venv/bin/python 'dask==2026.8.0'
     - name: Build Sphinx documentation
       run: |
-        cd docs
-        make html SPHINXOPTS="-W --keep-going -n"
+        make -C docs html SPHINXOPTS="-W --keep-going -n"
     - name: Commit documentation changes to gh-pages branch
       run: |
         git clone https://github.com/sgkit-dev/sgkit.git --branch gh-pages --single-branch gh-pages

.github/workflows/wheels.yml

@@ -22,18 +22,25 @@ jobs:
 
     steps:
     - uses: actions/checkout@v7
+      with:
+        fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.0.1
+      with:
+        version: "0.12.10"
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install setuptools twine wheel build
+        uv sync --locked --only-group packaging --python "${{ matrix.python-version }}"
     - name: Build a source distribution and a wheel
       run: |
-        python -m build --sdist --wheel
-        python -m twine check --strict dist/*
+        uv build --no-sources --python "${{ matrix.python-version }}"
+        uv run --locked --only-group packaging twine check --strict dist/*
     - name: Upload artifacts
       uses: actions/upload-artifact@v7
       with:
@@ -62,15 +69,22 @@ jobs:
         uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.0.1
+        with:
+          version: "0.12.10"
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
       - name: Install wheel and test
         run: |
           python -VV
-          # Install the local wheel
+          # Avoid building SciPy from source in CI.
           wheel=$(ls artifact/sgkit-*.whl)
-          pip install ${wheel} ${wheel}[bgen] ${wheel}[plink]
-          python sgkit-copy/.github/scripts/test_sgkit.py
-          python sgkit-copy/.github/scripts/test_sgkit_bgen.py
-          python sgkit-copy/.github/scripts/test_sgkit_plink.py
+          uv venv --python "${{ matrix.python-version }}"
+          uv pip install --python .venv/bin/python --only-binary scipy "${wheel}[bgen,plink]"
+          .venv/bin/python sgkit-copy/.github/scripts/test_sgkit.py
+          .venv/bin/python sgkit-copy/.github/scripts/test_sgkit_bgen.py
+          .venv/bin/python sgkit-copy/.github/scripts/test_sgkit_plink.py
 
   windows-test:
     # This workflow only runs on the origin org
@@ -94,15 +108,22 @@ jobs:
         uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.0.1
+        with:
+          version: "0.12.10"
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
       - name: Install wheel and test
         run: |
           python -VV
-          # Install the local wheel
-          $env:wheel = $(ls artifact/sgkit-*.whl)
-          pip install $env:wheel "$env:wheel[bgen]" "$env:wheel[plink]"
-          python sgkit-copy/.github/scripts/test_sgkit.py
-          python sgkit-copy/.github/scripts/test_sgkit_bgen.py
-          python sgkit-copy/.github/scripts/test_sgkit_plink.py
+          # Avoid building SciPy from source in CI.
+          $wheel = (Get-ChildItem artifact/sgkit-*.whl).FullName
+          uv venv --python "${{ matrix.python-version }}"
+          uv pip install --python .venv/Scripts/python.exe --only-binary scipy "${wheel}[bgen,plink]"
+          .venv/Scripts/python.exe sgkit-copy/.github/scripts/test_sgkit.py
+          .venv/Scripts/python.exe sgkit-copy/.github/scripts/test_sgkit_bgen.py
+          .venv/Scripts/python.exe sgkit-copy/.github/scripts/test_sgkit_plink.py
 
 
   pypi-upload:
@@ -118,14 +139,14 @@ jobs:
       - name: Move to dist
         run: |
           mkdir dist
-          cp */*.{whl,gz} dist/.
+          cp ./*/*.{whl,gz} dist/.
       - name: Publish package to TestPyPI
         if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
       - name: Publish package to PyPI
         if: github.event_name == 'release'
         uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/windows.yml

@@ -22,13 +22,18 @@ jobs:
       uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v10.0.1
+      with:
+        version: "0.12.10"
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt
+        uv sync --locked --all-extras --group test --no-default-groups --python "${{ matrix.python-version }}"
     - name: Test with pytest
       # To avoid: 'UserWarning: KMeans is known to have a memory leak on Windows with MKL, when there are less chunks than available threads. You can avoid it by setting the environment variable OMP_NUM_THREADS=1'
       env:
         OMP_NUM_THREADS: 1
       run: |
-        pytest -v
+        uv run --no-sync pytest -v