Remove vcf_to_zarr usage

Author: tomwhite

.github/scripts/test_sgkit_vcf.py

@@ -38,14 +38,14 @@ jobs:
       with:
         path: dist
 
-  unix-test:
+  test:
     # This workflow only runs on the origin org
     if: github.repository_owner == 'sgkit-dev'
     needs: ['build']
     strategy:
       matrix:
         # don't use macos-latest as it uses M1 which doesn't work
-        os: [ubuntu-latest, macos-12]
+        os: [ubuntu-latest, macos-12, windows-latest]
         python-version: ["3.9", "3.10", "3.11"]
     runs-on: ${{ matrix.os }}
     steps:
@@ -64,46 +64,16 @@ jobs:
           python -VV
           # Install the local wheel
           wheel=$(ls artifact/sgkit-*.whl)
-          pip install ${wheel} ${wheel}[bgen] ${wheel}[plink] ${wheel}[vcf]
+          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
-          python sgkit-copy/.github/scripts/test_sgkit_vcf.py
 
-  # Windows doesn't support vcf
-  windows-test:
-    # This workflow only runs on the origin org
-    if: github.repository_owner == 'sgkit-dev'
-    runs-on: windows-latest
-    needs: ['build']
-    strategy:
-      matrix:
-        python-version: ["3.9"]
-    steps:
-      # checkout repo to subdirectory to get access to scripts
-      - uses: actions/checkout@v2
-        with:
-          path: sgkit-copy
-      - name: Download artifacts
-        uses: actions/[email protected]
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - 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
 
   pypi-upload:
     if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
-    needs: ['unix-test', 'windows-test']
+    needs: ['test']
     steps:
       - name: Download all
         uses: actions/[email protected]