General test workflow

.github/workflows/tests.yml

@@ -30,77 +30,92 @@ jobs:
       additional-apt-packages: libgsl-dev
     secrets: inherit
 
+
   test-python:
     name: Python
-    runs-on: ${{ matrix.os }}
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@main
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python }}
+      coverage-directory: msprime
+    secrets: inherit
     strategy:
-      fail-fast: false
       matrix:
-        python: [ 3.11, 3.14 ]
+        python: [ 3.11, 3.13 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
-    defaults:
-      run:
-        shell: bash
-    steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.13.0
-        with:
-          access_token: ${{ github.token }}
-
-      - name: Checkout
-        uses: actions/checkout@v6.0.2
-        with:
-          submodules: true
-
-      - name: Fix windows symlinks
-        # This is horrible, but the "git config core.symlinks true" didn't work.
-        if: matrix.os == 'windows-latest'
-        run: |
-          rm lwt_interface
-          cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface
-
-      - name: Install GSL (macOS)
-        if: matrix.os == 'macos-latest'
-        run: brew install gsl
-
-      - name: Install GSL (Windows)
-        if: matrix.os == 'windows-latest'
-        run: |
-          vcpkg install gsl:x64-windows
-          # Add GSL DLL directory to PATH for runtime
-          $vcpkgRoot = $env:VCPKG_INSTALLATION_ROOT
-          if (-not $vcpkgRoot) { $vcpkgRoot = "C:\vcpkg" }
-          $gslBinPath = Join-Path $vcpkgRoot "installed\x64-windows\bin"
-          echo "$gslBinPath" >> $env:GITHUB_PATH
-          Write-Output "Added to PATH: $gslBinPath"
-        shell: powershell
-
-      - name: Install GSL (Ubuntu)
-        if: matrix.os == 'ubuntu-24.04'
-        run: sudo apt-get update && sudo apt-get install -y libgsl-dev
-
-      - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v6
-        with:
-          python-version: ${{ matrix.python }}
-          version: "0.8.15"
-
-      - name: Install Python dependencies
-        run: uv sync --locked --group test --no-default-groups
-
-      - name: Build module
-        run: uv run --no-default-groups python setup.py build_ext --inplace
-
-      - name: Fix windows gsl dlls
-        if: matrix.os == 'windows-latest'
-        run: cp /c/vcpkg/installed/x64-windows/bin/gsl*.dll msprime/
-
-      - name: Run tests
-        run: uv run --no-default-groups pytest --cov=msprime --cov-report=xml --cov-branch -n2
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5.4.0
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          flags: python
-          fail_ci_if_error: true
+
+
+#   test-python:
+#     name: Python
+#     runs-on: ${{ matrix.os }}
+#     strategy:
+#       fail-fast: false
+#       matrix:
+#         python: [ 3.11, 3.14 ]
+#         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
+#     defaults:
+#       run:
+#         shell: bash
+#     steps:
+#       - name: Cancel Previous Runs
+#         uses: styfle/cancel-workflow-action@0.13.0
+#         with:
+#           access_token: ${{ github.token }}
+
+#       - name: Checkout
+#         uses: actions/checkout@v6.0.2
+#         with:
+#           submodules: true
+
+#       - name: Fix windows symlinks
+#         # This is horrible, but the "git config core.symlinks true" didn't work.
+#         if: matrix.os == 'windows-latest'
+#         run: |
+#           rm lwt_interface
+#           cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface
+
+#       - name: Install GSL (macOS)
+#         if: matrix.os == 'macos-latest'
+#         run: brew install gsl
+
+#       - name: Install GSL (Windows)
+#         if: matrix.os == 'windows-latest'
+#         run: |
+#           vcpkg install gsl:x64-windows
+#           # Add GSL DLL directory to PATH for runtime
+#           $vcpkgRoot = $env:VCPKG_INSTALLATION_ROOT
+#           if (-not $vcpkgRoot) { $vcpkgRoot = "C:\vcpkg" }
+#           $gslBinPath = Join-Path $vcpkgRoot "installed\x64-windows\bin"
+#           echo "$gslBinPath" >> $env:GITHUB_PATH
+#           Write-Output "Added to PATH: $gslBinPath"
+#         shell: powershell
+
+#       - name: Install GSL (Ubuntu)
+#         if: matrix.os == 'ubuntu-24.04'
+#         run: sudo apt-get update && sudo apt-get install -y libgsl-dev
+
+#       - name: Install uv and set the python version
+#         uses: astral-sh/setup-uv@v6
+#         with:
+#           python-version: ${{ matrix.python }}
+#           version: "0.8.15"
+
+#       - name: Install Python dependencies
+#         run: uv sync --locked --group test --no-default-groups
+
+#       - name: Build module
+#         run: uv run --no-default-groups python setup.py build_ext --inplace
+
+#       - name: Fix windows gsl dlls
+#         if: matrix.os == 'windows-latest'
+#         run: cp /c/vcpkg/installed/x64-windows/bin/gsl*.dll msprime/
+
+#       - name: Run tests
+#         run: uv run --no-default-groups pytest --cov=msprime --cov-report=xml --cov-branch -n2
+
+#       - name: Upload coverage to Codecov
+#         uses: codecov/codecov-action@v5.4.0
+#         with:
+#           token: ${{ secrets.CODECOV_TOKEN }}
+#           flags: python
+#           fail_ci_if_error: true