Add tiledbvcf-py

.github/workflows/linux.yml

@@ -87,14 +87,13 @@ jobs:
  - name: Build TileDB-Py
  run: |
  echo $LD_LIBRARY_PATH
- python setup.py install --tiledb="$GITHUB_WORKSPACE/install-libtiledb/"
+ python setup.py install --tiledb=$GITHUB_WORKSPACE/install-libtiledb/
  # - name: Test TileDB-Py
  # run: |
  # python -c "import tiledb; print(tiledb.libtiledb.version())"
  # pytest -vv
  - name: Create a wheel
- run: |
- python setup.py bdist_wheel --tiledb="$GITHUB_WORKSPACE/install-libtiledb/"
+ run: python setup.py bdist_wheel --tiledb=$GITHUB_WORKSPACE/install-libtiledb/
  - name: Upload Python wheel as artifact
  uses: actions/upload-artifact@v3
  with:
@@ -187,12 +186,61 @@ jobs:
  tiledbvcf-py:
  runs-on: ubuntu-latest
  needs: [libtiledb, libtiledbvcf, tiledb-py]
+ env:
+ LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib:${{ github.workspace }}/install-libtiledbvcf/lib"
  steps:
  - name: Clone TileDB-VCF
  uses: actions/checkout@v3
  with:
  repository: TileDB-Inc/TileDB-VCF
  ref: main
+ fetch-depth: 0 # fetch everything for python setuptools_scm
+ - name: Download nightly-libtiledb
+ uses: actions/download-artifact@v3
+ with:
+ name: nightly-libtiledb-linux
+ path: install-libtiledb
+ - name: Download nightly-libtiledbvcf
+ uses: actions/download-artifact@v3
+ with:
+ name: nightly-libtiledbvcf-linux
+ path: install-libtiledbvcf
+ - name: Download nightly-tiledb-py
+ uses: actions/download-artifact@v3
+ with:
+ name: nightly-tiledb-py-linux
+ - name: Set up Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: "3.11"
+ - name: Install dependencies
+ run: python -m pip install pyarrow wheel
+ - name: Install nightly tiledb-py
+ run: |
+ ls -R
+ pip install tiledb-*-linux_x86_64.whl
+ - name: Build tiledbvcf-py
+ run: |
+ echo $LD_LIBRARY_PATH
+ cd apis/python
+ python setup.py install --libtiledbvcf=$GITHUB_WORKSPACE/install-libtiledbvcf/
+ - name: Install bcftools (for tests)
+ run: sudo apt install bcftools
+ - name: Test tiledbvcf-py
+ run: |
+ python -c "import tiledbvcf; print(tiledbvcf.version)"
+ cd apis/python
+ pytest
+ - name: Create a wheel
+ run: |
+ cd apis/python
+ python setup.py bdist_wheel --libtiledbvcf=$GITHUB_WORKSPACE/install-libtiledbvcf/
+ - name: Upload Python wheel as artifact
+ uses: actions/upload-artifact@v3
+ with:
+ name: nightly-tiledbvcf-py-linux
+ path: dist/tiledbvcf-*-linux_x86_64.whl
+ retention-days: 14
  libtiledbsoma:
  runs-on: ubuntu-latest
  needs: [libtiledb]