Nightly #436
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name: Nightly | |
# High-level notes: | |
# * Installs libtiledb and libtiledbvcf into ./install/ | |
# * Manually updates library path so that tiledbvcf-py can link to | |
# the shared objects in ./install/ | |
on: | |
push: | |
paths: | |
- '.github/workflows/nightly.yml' | |
- 'ci/nightly/**' | |
pull_request: | |
paths: | |
- '.github/workflows/nightly.yml' | |
- 'ci/nightly/**' | |
schedule: | |
- cron: "0 3 * * *" # Every night at 3 AM UTC (10 PM EST; 11 PM EDT) | |
workflow_dispatch: | |
jobs: | |
nightly: | |
runs-on: ${{ matrix.os }} | |
name: ${{ matrix.os }}-libtiledb-${{ matrix.branches.libtiledb }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [macos-12, ubuntu-latest] | |
branches: | |
- {libtiledb: release-2.24, tiledb-py: 0.30.1} | |
- {libtiledb: dev, tiledb-py: dev} | |
env: | |
MACOSX_DEPLOYMENT_TARGET: 10.15 | |
steps: | |
- name: Clone TileDB | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB | |
ref: ${{ matrix.branches.libtiledb }} | |
path: TileDB | |
- name: Clone TileDB-Py | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-Py | |
ref: ${{ matrix.branches.tiledb-py }} | |
path: TileDB-Py | |
- name: Clone TileDB-VCF | |
uses: actions/checkout@v4 | |
with: | |
path: TileDB-VCF | |
fetch-depth: 0 # fetch everything for python setuptools_scm | |
- name: Build libtiledb | |
run: bash TileDB-VCF/ci/nightly/build-libtiledb.sh | |
- name: Setup to build htslib from source (macOS) | |
if: runner.os == 'macOS' | |
run: brew install autoconf automake | |
- name: Build libtiledbvcf | |
run: bash TileDB-VCF/ci/nightly/build-libtiledbvcf.sh | |
- name: Confirm linking (Linux) | |
if: runner.os == 'Linux' | |
run: | | |
ldd install/lib/libtiledb.so | |
ldd install/lib/libtiledbvcf.so | |
- name: Confirm linking (macOS) | |
if: runner.os == 'macOS' | |
run: | | |
otool -L install/lib/libtiledb.dylib | |
otool -L install/lib/libtiledbvcf.dylib | |
- name: Install bcftools (for tests) (Linux) | |
if: runner.os == 'Linux' | |
run: sudo apt install bcftools | |
- name: Install bcftools (for tests) (macOS) | |
if: runner.os == 'macOS' | |
run: brew install bcftools | |
- name: Test libtiledbvcf | |
run: bash TileDB-VCF/ci/nightly/test-libtiledbvcf.sh | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
- name: Install dependencies for tiledb-py build | |
run: | | |
python -m pip install --prefer-binary \ | |
-r TileDB-VCF/ci/nightly/requirements.txt | |
pip list | |
- name: Build tiledb-py from source | |
run: | | |
cd TileDB-Py/ | |
python setup.py develop --tiledb=../install/ | |
python -c "import tiledb; print('successful import')" | |
python -c "import tiledb; print(tiledb.libtiledb.version())" | |
python -c "import tiledb; print(tiledb.version())" | |
- name: Build (and test) tiledbvcf-py | |
run: bash TileDB-VCF/ci/nightly/build-tiledbvcf-py.sh | |
issue: | |
permissions: | |
issues: write | |
runs-on: ubuntu-latest | |
needs: nightly | |
if: ( failure() || cancelled() ) && github.repository_owner == 'TileDB-Inc' && github.event_name == 'schedule' | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Open Issue | |
uses: TileDB-Inc/github-actions/open-issue@main | |
with: | |
name: nightly build | |
label: nightly-failure | |
assignee: awenocur,gspowley,ihnorton,Shelnutt2,jdblischak | |
env: | |
TZ: "America/New_York" |