linux.yml

name: Nightly builds on linux
on:
  push:
    paths:
      - '.github/workflows/linux.yml'
      - 'scripts/**'
  pull_request:
    paths:
      - '.github/workflows/linux.yml'
      - 'scripts/**'
  schedule:
    - cron: "0 2 * * *" # Every night at 2 AM UTC (9 PM EST; 10 PM EDT)
  workflow_dispatch:
    inputs:
      LIBTILEDB_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB
        default: dev
      TILEDB_PY_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-Py
        default: dev
      TILEDB_R_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-R
        default: master
      TILEDB_VCF_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout
          TileDB-Inc/TileDB-VCF
        default: main
      TILEDB_SOMA_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout
          single-cell-data/TileDB-SOMA
        default: main
      TILEDB_MARIADB_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-MariaDB
        default: master
      TILEDB_GO_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-Go
        default: master
      TILEDB_CLOUD_PY_REF:
        description: >-
          The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-Cloud-Py
        default: main
jobs:
  libtiledb:
    runs-on: ubuntu-latest
    steps:
      - name: Clone TileDB
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB
          ref: ${{ github.event.inputs.LIBTILEDB_REF || 'dev' }}
      # Use recent release tarball on branches for quicker feedback
      - name: Download release tarball
        if: github.ref_name != 'main'
        run: wget https://github.com/TileDB-Inc/TileDB/releases/download/2.26.0/tiledb-linux-x86_64-2.26.0-983b716.tar.gz
      - name: Unpack release tarball
        if: github.ref_name != 'main'
        run: |
          mkdir install-libtiledb
          tar xzf tiledb-linux-x86_64-*.tar.gz -C install-libtiledb
          ls -R install-libtiledb/
      - name: Patch tiledb.pc from release tarball
        if: github.ref_name != 'main'
        run: |
          new_prefix=prefix=\"$(pwd)/install-libtiledb\"
          echo $new_prefix
          sed -i "1 s+.*+$new_prefix+" install-libtiledb/lib/pkgconfig/tiledb.pc
          cat install-libtiledb/lib/pkgconfig/tiledb.pc
      - name: Configure TileDB
        if: github.ref_name == 'main'
        run: |
          cmake -B build-libtiledb \
            -D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/install-libtiledb/ \
            -D TILEDB_WERROR=ON \
            -D TILEDB_SERIALIZATION=ON \
            -D CMAKE_BUILD_TYPE=Release \
            -D TILEDB_S3=ON \
            -D VCPKG_TARGET_TRIPLET=x64-linux-release
      - name: Build TileDB
        if: github.ref_name == 'main'
        run: cmake --build build-libtiledb -j $(nproc) --config Release
      - name: Install TileDB
        if: github.ref_name == 'main'
        run: cmake --build build-libtiledb --config Release --target install-tiledb
      - name: Upload libtiledb as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: |
            install-libtiledb/*
          retention-days: 14
          if-no-files-found: error
      # Unable to run the test suite with `TILEDB_S3=ON` (required for
      # tiledbvcf-py tests) without configuring S3 credentials
      # - name: Test TileDB
      #   if: github.ref_name == 'main'
      #   run: |
      #     make -C build-libtiledb/tiledb tests -j $(nproc)
      #     ./build-libtiledb/tiledb/test/tiledb_unit --vfs native
  tiledb-py:
    runs-on: ubuntu-latest
    needs: libtiledb
    env:
      LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib
      PKG_CONFIG_PATH: ${{ github.workspace }}/install-libtiledb/lib/pkgconfig
    steps:
      - name: Clone TileDB-Py
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB-Py
          ref: ${{ github.event.inputs.TILEDB_PY_REF || 'dev' }}
          fetch-depth: 0 # fetch everything for python setuptools_scm
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Build TileDB-Py
        run: |
          echo $LD_LIBRARY_PATH
          export TILEDB_PATH=$(pwd)/install-libtiledb/
          python -m pip install -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v --editable .[test]
      - name: Import TileDB-Py
        run: |
          python -c "import tiledb; print('successful import')"
          python -c "import tiledb; print(tiledb.libtiledb.version())"
          python -c "import tiledb; print(tiledb.version())"
      - name: Test TileDB-Py
        run: pytest -vv
      - name: Create a wheel
        run: |
          export TILEDB_PATH=$(pwd)/install-libtiledb/
          python -m pip wheel -Cskbuild.cmake.define.TILEDB_REMOVE_DEPRECATIONS=OFF -v --wheel-dir=dist .
      - name: Upload Python wheel as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-tiledb-py-linux
          path: dist/tiledb-*-linux_x86_64.whl
          retention-days: 14
          if-no-files-found: error
  tiledb-r:
    runs-on: ubuntu-latest
    needs: libtiledb
    env:
      _R_CHECK_FORCE_SUGGESTS_: "FALSE"
    steps:
      - name: Clone TileDB-R
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB-R
          ref: ${{ github.event.inputs.TILEDB_R_REF || 'master' }}
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Bootstrap
        run: ./.github/r-ci.sh bootstrap
      - name: Dependencies
        run: ./.github/r-ci.sh install_all
      - name: Build
        run: R CMD build --no-manual --no-build-vignettes .
      - name: Install
        run: |
          R CMD INSTALL --configure-args=--with-tiledb=$(pwd)/install-libtiledb --build tiledb_*.tar.gz
      - name: Upload R binary tarball as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-tiledb-r-linux
          path: tiledb_*_R_x86_64-pc-linux-gnu.tar.gz
          retention-days: 14
          if-no-files-found: error
      - name: Test
        run: R -e 'tinytest::test_package("tiledb")'
  libtiledbvcf:
    runs-on: ubuntu-latest
    needs: libtiledb
    env:
      LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib
    steps:
      - name: Clone TileDB-VCF
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB-VCF
          ref: ${{ github.event.inputs.TILEDB_VCF_REF || 'main' }}
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Setup
        run: |
          sudo apt-get update
          sudo apt-get install --yes cmake
      - name: Configure libtiledbvcf
        run: |
          cmake -S libtiledbvcf -B build-libtiledbvcf \
            -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_PREFIX_PATH=$(pwd)/install-libtiledb/ \
            -D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/install-libtiledbvcf/ \
            -D OVERRIDE_INSTALL_PREFIX=OFF \
            -D TILEDB_WERROR=OFF
      - name: Build libtiledbvcf
        run: cmake --build build-libtiledbvcf -j $(nproc) --config Release
      - name: Install libtiledbvcf
        run: |
          cmake --build build-libtiledbvcf --config Release --target install-libtiledbvcf
          ls -R install-libtiledbvcf/
      - name: Upload libtiledbvcf as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-libtiledbvcf-linux
          path: |
            install-libtiledbvcf/*
          retention-days: 14
          if-no-files-found: error
      - name: libtiledbvcf version
        run: ./install-libtiledbvcf/bin/tiledbvcf version
      - name: Confirm linking
        run: ldd install-libtiledbvcf/lib/libtiledbvcf.so
      - name: Install bcftools (for tests)
        run: sudo apt-get install --yes bcftools
      - name: Test libtiledbvcf
        run: |
          make -j $(nproc) -C build-libtiledbvcf/libtiledbvcf tiledb_vcf_unit
          ./build-libtiledbvcf/libtiledbvcf/test/tiledb_vcf_unit

          # cli tests (require bcftools)
          # USAGE: run-cli-tests.sh <build-dir> <inputs-dir>
          libtiledbvcf/test/run-cli-tests.sh build-libtiledbvcf libtiledbvcf/test/inputs
  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@v4
        with:
          repository: TileDB-Inc/TileDB-VCF
          ref: ${{ github.event.inputs.TILEDB_VCF_REF || 'main' }}
          fetch-depth: 0 # fetch everything for python setuptools_scm
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Download nightly-libtiledbvcf
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledbvcf-linux
          path: install-libtiledbvcf
      - name: Download nightly-tiledb-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-py-linux
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install dependencies
        run: python -m pip install --prefer-binary \
          pyarrow==11
      - name: Install nightly tiledb-py
        run: |
          pip install --prefer-binary tiledb-*-linux_x86_64.whl
          pip list
      - name: Build tiledbvcf-py
        run: |
          export LIBTILEDBVCF_PATH=$(pwd)/install-libtiledbvcf/lib/
          export TileDB_DIR=$(pwd)/install-libtiledb/lib/cmake/TileDB
          python -m pip install -v apis/python[test]
      - name: Confirm linking
        run: |
          echo "Shared objects in build directory"
          find apis/python -name '*.so*'
          echo "Installed shared objects"
          find $pythonLocation/lib/python*/site-packages/tiledbvcf -name '*.so*'
          echo "Run ldd on installed shared objects"
          find $pythonLocation/lib/python*/site-packages/tiledbvcf -name '*.so*' | xargs ldd
          echo "Check RPATH of installed shared object"
          readelf -d  $pythonLocation/lib/python*/site-packages/tiledbvcf/libtiledbvcf.cpython-*-x86_64-linux-gnu.so | grep R*PATH
          echo "Check RPATH of shared object in build directory"
          readelf -d apis/python/build/cp311-cp311-linux_x86_64/libtiledbvcf.cpython-311-x86_64-linux-gnu.so | grep R*PATH
      - name: Install bcftools (for tests)
        run: |
          sudo apt-get update
          sudo apt-get install --yes bcftools
      - name: Test tiledbvcf-py
        run: |
          python -c "import tiledbvcf; print(tiledbvcf.version)"
          cd apis/python
          pytest
      - name: Create a wheel
        run: |
          export LIBTILEDBVCF_PATH=$(pwd)/install-libtiledbvcf/lib/
          export TileDB_DIR=$(pwd)/install-libtiledb/lib/cmake/TileDB
          python -m pip wheel -v --wheel-dir=apis/python/dist apis/python
      - name: Upload Python wheel as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-tiledbvcf-py-linux
          path: apis/python/dist/tiledbvcf-*-linux_x86_64.whl
          retention-days: 14
          if-no-files-found: error
  libtiledbsoma:
    runs-on: ubuntu-latest
    needs: [libtiledb]
    env:
      TileDB_DIR: ${{ github.workspace }}/install-libtiledb
      LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib
    steps:
      - name: Clone TileDB-SOMA
        uses: actions/checkout@v4
        with:
          repository: single-cell-data/TileDB-SOMA
          ref: ${{ github.event.inputs.TILEDB_SOMA_REF || 'main' }}
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Setup
        run: |
          sudo apt-get update
          sudo apt-get install --yes cmake
      - name: Configure libtiledbsoma
        run: |
          cmake -S libtiledbsoma -B build-libtiledbsoma \
            -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_PREFIX_PATH=$(pwd)/install-libtiledb/ \
            -D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/install-libtiledbsoma/ \
            -D OVERRIDE_INSTALL_PREFIX=OFF \
            -D DOWNLOAD_TILEDB_PREBUILT=OFF \
            -D FORCE_BUILD_TILEDB=OFF
      - name: Build libtiledbsoma
        run: cmake --build build-libtiledbsoma -j $(nproc)
      - name: Install libtiledbsoma
        run: |
          cmake --build build-libtiledbsoma --target install-libtiledbsoma
          ls -R $(pwd)/install-libtiledb/
      - name: Upload libtiledbsoma as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-libtiledbsoma-linux
          path: |
            install-libtiledbsoma/*
      - name: Confirm linking
        run: ldd install-libtiledbsoma/lib/libtiledbsoma.so
      - name: Test libtiledbsoma
        run: |
          cmake --build build-libtiledbsoma/libtiledbsoma --target build_tests -j $(nproc)
          ctest --test-dir build-libtiledbsoma/libtiledbsoma -C Release --verbose --rerun-failed --output-on-failure
  tiledbsoma-py:
    runs-on: ubuntu-latest
    needs: [libtiledb, libtiledbsoma, tiledb-py]
    env:
      LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib:${{ github.workspace }}/install-libtiledbsoma/lib"
      TILEDB_PATH: ${{ github.workspace }}/install-libtiledb
      TILEDBSOMA_PATH: ${{ github.workspace }}/install-libtiledbsoma
      PKG_CONFIG_PATH: "${{ github.workspace }}/install-libtiledb/lib/pkgconfig:${{ github.workspace }}/install-libtiledbsoma/lib/pkgconfig"
    steps:
      - name: Clone TileDB-SOMA
        uses: actions/checkout@v4
        with:
          repository: single-cell-data/TileDB-SOMA
          ref: ${{ github.event.inputs.TILEDB_SOMA_REF || 'main' }}
          fetch-depth: 0 # fetch everything for python setuptools_scm
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Download nightly-libtiledbsoma
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledbsoma-linux
          path: install-libtiledbsoma
      - name: Download nightly-tiledb-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-py-linux
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      # https://github.com/single-cell-data/TileDB-SOMA/blob/main/apis/python/pyproject.toml
      - name: Install dependencies
        run: |
          python -m pip install \
            -r apis/python/requirements_dev.txt \
            "pybind11[global]>=2.10.0" \
            "setuptools>=65.5.1" \
            "wheel>=0.37.1" \
            "cmake>=3.21"
      - name: Install nightly tiledb-py
        run: |
          pip install tiledb-*-linux_x86_64.whl
          pip list
      - name: Install tiledbsoma-py
        run: |
          python -m pip -v install --no-build-isolation -e apis/python
          pip list
      - name: Confirm linking
        run: |
          find apis/python -name '*.so*'
          find apis/python -name '*.so*' | xargs ldd
          readelf -d apis/python/src/tiledbsoma/pytiledbsoma.*.so  | grep R*PATH
      - name: Fail if unnecessary libtiledbsoma.so is created
        # https://github.com/single-cell-data/TileDB-SOMA/pull/1937
        run: |
          if [[ -f apis/python/src/tiledbsoma/libtiledbsoma.so ]]
          then
            echo "An unnecessary libtiledbsoma.so was created during the package build"
            exit 1
          fi
      - name: Test tiledbsoma-py
        run: |
          python -c "import tiledbsoma; print('successful import')"
          python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
          python -c "import tiledbsoma; print(f'tiledbsoma-py={tiledbsoma.__version__}')"
          # Obtain test data
          cd test
          tar zxf soco.tgz
          cd ..
          # Run test suite
          PYTHONPATH=$(pwd)/apis/python/src python -m pytest apis/python/tests
      - name: Create a wheel
        run: |
          cd apis/python
          python setup.py bdist_wheel
      - name: Upload Python wheel as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-tiledbsoma-py-linux
          path: apis/python/dist/tiledbsoma-*-linux_x86_64.whl
          retention-days: 14
          if-no-files-found: error
  tiledbsoma-r:
    runs-on: ubuntu-latest
    needs: [libtiledb, libtiledbsoma, tiledb-r]
    env:
      LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib:${{ github.workspace }}/install-libtiledbsoma/lib"
      PKG_CONFIG_PATH: "${{ github.workspace }}/install-libtiledb/lib/pkgconfig:${{ github.workspace }}/install-libtiledbsoma/lib/pkgconfig"
    steps:
      - name: Clone TileDB-SOMA
        uses: actions/checkout@v4
        with:
          repository: single-cell-data/TileDB-SOMA
          ref: ${{ github.event.inputs.TILEDB_SOMA_REF || 'main' }}
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Download nightly-libtiledbsoma
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledbsoma-linux
          path: install-libtiledbsoma
      - name: Download nightly-tiledb-r
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-r-linux
      - name: Bootstrap
        run: cd apis/r && tools/r-ci.sh bootstrap
      - name: Install nightly tiledb-r (and its dependencies)
        shell: Rscript {0}
        run: |
          install.packages("remotes")
          library("remotes")
          binary_tarball <- Sys.glob("tiledb_*_R_x86_64-pc-linux-gnu.tar.gz")
          message(binary_tarball)
          install_deps(binary_tarball, dependencies = TRUE, upgrade = "never")
          install.packages(binary_tarball, repos = NULL)
      - name: Dependencies
        run: cd apis/r && tools/r-ci.sh install_all
      - name: Build
        run: |
          export CXX17FLAGS="-Wno-deprecated-declarations -Wno-deprecated"
          cd apis/r && R CMD build --no-manual --no-build-vignettes .
      - name: Install
        run:
          cd apis/r && R CMD INSTALL --install-tests --build tiledbsoma_*.tar.gz
      - name: Upload R binary tarball as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-tiledbsoma-r-linux
          path: apis/r/tiledbsoma_*_R_x86_64-pc-linux-gnu.tar.gz
          retention-days: 14
          if-no-files-found: error
      - name: Test
        run:
          Rscript -e 'testthat::test_package("tiledbsoma")'
  tiledb-mariadb:
    runs-on: ubuntu-latest
    needs: [libtiledb]
    env:
      CFLAGS: -Wno-error=deprecated-declarations -Wno-error=missing-braces
      CXXFLAGS: -Wno-error=deprecated-declarations -Wno-error=missing-braces
      LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib
    steps:
      - name: Clone MariaDB
        uses: actions/checkout@v4
        with:
          repository: MariaDB/server.git
          ref: mariadb-11.0.2
      - name: Clone TileDB-MariaDB into MariaDB
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB-MariaDB
          ref: ${{ github.event.inputs.TILEDB_MARIADB_REF || 'master' }}
          path: storage/mytile
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Configure TileDB-MariaDB
        run: |
          cmake \
            -S . -B builddir \
            -D CMAKE_PREFIX_PATH=$(pwd)/install-libtiledb/ \
            -D PLUGIN_OQGRAPH=NO \
            -D WITH_MARIABACKUP=OFF \
            -D PLUGIN_TOKUDB=NO \
            -D PLUGIN_ROCKSDB=NO \
            -D PLUGIN_MROONGA=NO \
            -D PLUGIN_SPIDER=NO \
            -D PLUGIN_SPHINX=NO \
            -D PLUGIN_FEDERATED=NO \
            -D PLUGIN_FEDERATEDX=NO \
            -D PLUGIN_CONNECT=NO \
            -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_INCLUDE_PATH="/usr/local/include" \
            -D TILEDB_FORCE_ALL_DEPS=${TILEDB_FORCE_ALL_DEPS-OFF}
      - name: Build TileDB-MariaDB
        run: |
          cd builddir
          make -j $(nproc)
      - name: Confirm linking
        run: |
          du -sh builddir
          du -sh builddir/storage/mytile
          ldd builddir/storage/mytile/ha_mytile.so
          # Fail if not properly linked to nightly libtiledb.so
          ldd builddir/storage/mytile/ha_mytile.so | \
            grep -q $(pwd)/install-libtiledb/lib/libtiledb.so
      - name: Test TileDB-MariaDB
        run: |
          cd builddir
          ./mysql-test/mysql-test-run.pl --suite=mytile
  tiledb-go:
    runs-on: ubuntu-latest
    needs: [libtiledb]
    steps:
      - name: Clone TileDB-Go
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB-Go
          ref: ${{ github.event.inputs.TILEDB_GO_REF || 'master' }}
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Install dependencies
        run: go get -t .
      - name: Test TileDB-Go
        run: |
          export CPATH=$(pwd)/install-libtiledb/include
          export LIBRARY_PATH=$(pwd)/install-libtiledb/lib
          export LD_LIBRARY_PATH=$(pwd)/install-libtiledb/lib
          go test -v ./...
  tiledb-cloud-py:
    runs-on: ubuntu-latest
    needs: [libtiledb, tiledb-py]
    env:
      LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib"
    steps:
      - name: Clone TileDB-Cloud-Py
        uses: actions/checkout@v4
        with:
          repository: TileDB-Inc/TileDB-Cloud-Py
          ref: ${{ github.event.inputs.TILEDB_CLOUD_PY_REF || 'main' }}
          fetch-depth: 0 # fetch everything for python setuptools_scm
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Download nightly-tiledb-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-py-linux
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install dependencies
        run: python -m pip install \
               "attrs>=21.4.0" \
               "certifi" \
               "cloudpickle>=1.4.1,<3" \
               "importlib-metadata" \
               "packaging" \
               "pandas>=1.2.4" \
               "pyarrow>=3.0.0" \
               "python-dateutil" \
               "six>=1.10" \
               "tblib~=1.7" \
               "tiledb>=0.15.2" \
               "typing-extensions" \
               "urllib3>=1.26" \
               "wheel"
      - name: Install nightly tiledb-py
        run: |
          pip install tiledb-*-linux_x86_64.whl
          pip list
      - name: Build tiledb-cloud
        run: |
          echo $LD_LIBRARY_PATH
          pip install --no-build-isolation .
      - name: Create a wheel
        run: python setup.py bdist_wheel
      - name: Upload Python wheel as artifact
        uses: actions/upload-artifact@v4
        with:
          name: nightly-tiledb-cloud-py-linux
          path: dist/tiledb_cloud-*-none-any.whl
          retention-days: 14
          if-no-files-found: error
  build-all:
    # this is simply a target to build everything locally with `act` without
    # creating a new release
    name: Build everything
    runs-on: ubuntu-latest
    needs: [libtiledb, tiledb-py, tiledb-r, libtiledbvcf, tiledbvcf-py, libtiledbsoma,
            tiledbsoma-py, tiledbsoma-r, tiledb-mariadb, tiledb-go, tiledb-cloud-py]
    steps:
      - run: echo "Success! Everything was built"
  create-release:
    name: Create a new release
    if: github.ref_name == 'main' && github.repository_owner == 'jdblischak' && github.event_name != 'pull_request'
    runs-on: ubuntu-latest
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Create release
        run: |
          the_date=$(date +%Y-%m-%d)
          if ! gh release list | cut -f3 | grep -q $the_date
          then
            echo "Creating new release: $the_date"
            gh release create $the_date --notes "Nightly binaries created on $the_date"
          else
            echo "Release already exists: $the_date"
          fi
  upload-libtiledb:
    runs-on: ubuntu-latest
    needs: [create-release, libtiledb]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-libtiledb
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledb-linux
          path: install-libtiledb
      - name: Upload libtiledb to release
        run: |
          the_date=$(date +%Y-%m-%d)
          tar -C install-libtiledb -cvzf libtiledb-${the_date}.tar.gz ./
          gh release upload ${the_date} libtiledb-${the_date}.tar.gz --clobber
  upload-tiledb-py:
    runs-on: ubuntu-latest
    needs: [create-release, tiledb-py]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-tiledb-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-py-linux
      - name: Upload tiledb-py to release
        run: |
          the_date=$(date +%Y-%m-%d)
          unzip -l tiledb-*-linux_x86_64.whl
          gh release upload ${the_date} tiledb-*-linux_x86_64.whl --clobber
  upload-tiledb-r:
    runs-on: ubuntu-latest
    needs: [create-release, tiledb-r]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-tiledb-r
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-r-linux
      - name: Upload tiledb-r to release
        run: |
          the_date=$(date +%Y-%m-%d)
          tar --list -f tiledb_*_R_x86_64-pc-linux-gnu.tar.gz
          gh release upload ${the_date} tiledb_*_R_x86_64-pc-linux-gnu.tar.gz --clobber
  upload-libtiledbvcf:
    runs-on: ubuntu-latest
    needs: [create-release, libtiledbvcf]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-libtiledbvcf
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledbvcf-linux
          path: install-libtiledbvcf
      - name: Upload libtiledbvcf to release
        run: |
          the_date=$(date +%Y-%m-%d)
          tar -C install-libtiledbvcf -cvzf libtiledbvcf-${the_date}.tar.gz ./
          gh release upload ${the_date} libtiledbvcf-${the_date}.tar.gz --clobber
  upload-tiledbvcf-py:
    runs-on: ubuntu-latest
    needs: [create-release, tiledbvcf-py]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-tiledbvcf-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledbvcf-py-linux
      - name: Upload tiledbvcf-py to release
        run: |
          the_date=$(date +%Y-%m-%d)
          unzip -l tiledbvcf-*-linux_x86_64.whl
          gh release upload ${the_date} tiledbvcf-*-linux_x86_64.whl --clobber
  upload-libtiledbsoma:
    runs-on: ubuntu-latest
    needs: [create-release, libtiledbsoma]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-libtiledbsoma
        uses: actions/download-artifact@v4
        with:
          name: nightly-libtiledbsoma-linux
          path: install-libtiledbsoma
      - name: Upload libtiledbsoma to release
        run: |
          the_date=$(date +%Y-%m-%d)
          tar -C install-libtiledbsoma -cvzf libtiledbsoma-${the_date}.tar.gz ./
          gh release upload ${the_date} libtiledbsoma-${the_date}.tar.gz --clobber
  upload-tiledbsoma-py:
    runs-on: ubuntu-latest
    needs: [create-release, tiledbsoma-py]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-tiledbsoma-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledbsoma-py-linux
      - name: Upload tiledbsoma-py to release
        run: |
          the_date=$(date +%Y-%m-%d)
          unzip -l tiledbsoma-*-linux_x86_64.whl
          gh release upload ${the_date} tiledbsoma-*-linux_x86_64.whl --clobber
  upload-tiledbsoma-r:
    runs-on: ubuntu-latest
    needs: [create-release, tiledbsoma-r]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-tiledbsoma-r
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledbsoma-r-linux
      - name: Upload tiledbsoma-r to release
        run: |
          the_date=$(date +%Y-%m-%d)
          tar --list -f tiledbsoma_*_R_x86_64-pc-linux-gnu.tar.gz
          gh release upload ${the_date} tiledbsoma_*_R_x86_64-pc-linux-gnu.tar.gz --clobber
  upload-tiledb-cloud-py:
    runs-on: ubuntu-latest
    needs: [create-release, tiledb-cloud-py]
    permissions:
      contents: write
    env:
      GH_TOKEN: ${{ github.token }}
      TZ: "America/New_York"
    steps:
      - uses: actions/checkout@v4
      - name: Download nightly-tiledb-cloud-py
        uses: actions/download-artifact@v4
        with:
          name: nightly-tiledb-cloud-py-linux
      - name: Upload tiledb-cloud-py to release
        run: |
          the_date=$(date +%Y-%m-%d)
          unzip -l tiledb_cloud-*-none-any.whl
          gh release upload ${the_date} tiledb_cloud-*-none-any.whl --clobber
  issue:
    permissions:
      issues: write
    runs-on: ubuntu-latest
    needs: [build-all]
    if: ( failure() || cancelled() ) && github.repository_owner == 'jdblischak' && github.event_name == 'schedule'
    steps:
      - uses: actions/checkout@v4
      - name: Open Issue
        uses: TileDB-Inc/github-actions/open-issue@main
        with:
          name: centralized nightlies
          label: nightly-failure
          assignee: jdblischak
        env:
          TZ: "America/New_York"