Nightly #50
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| name: Nightly | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - '*' | |
| release: | |
| types: [published] | |
| schedule: | |
| - cron: '0 0 * * *' | |
| env: | |
| GITHUB_USERNAME: ${{ github.actor }} | |
| GITHUB_TOKEN: ${{ github.token }} | |
| RUN_CMD: "./rebar" | |
| jobs: | |
| # --------------------------------------------------------------------------- | |
| # Latest is a model/algorithm test, only needs the linux version compiled | |
| compile: | |
| uses: ./.github/workflows/compile.yaml | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Linux | |
| - arch: x86_64-unknown-linux-musl | |
| os: ubuntu-latest | |
| binary: rebar | |
| with: | |
| arch: ${{ matrix.arch }} | |
| os: ${{ matrix.os }} | |
| binary: ${{ matrix.binary }} | |
| # --------------------------------------------------------------------------- | |
| latest: | |
| needs: compile | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Linux | |
| - arch: x86_64-unknown-linux-musl | |
| os: ubuntu-latest | |
| binary: rebar | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: download binary from build | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: rebar-${{ matrix.arch }} | |
| path: target/${{ matrix.arch }}/release | |
| - name: install | |
| run: | | |
| chmod +x target/${{ matrix.arch }}/release/${{ matrix.binary }} | |
| cp target/${{ matrix.arch }}/release/${{ matrix.binary }} . | |
| ${{ env.RUN_CMD }} --help | |
| - name: dataset download | |
| run: | | |
| ${{ env.RUN_CMD }} dataset download --name sars-cov-2 --tag nightly --output-dir dataset/sars-cov-2/nightly | |
| - name: run | |
| run: | | |
| ${{ env.RUN_CMD }} run --dataset-dir dataset/sars-cov-2/nightly --output-dir output/sars-cov-2/nightly/validate --populations "*" --threads 2 | |
| - name: plot | |
| run: | | |
| ${{ env.RUN_CMD }} plot --annotations dataset/sars-cov-2/nightly/annotations.tsv --run-dir output/sars-cov-2/nightly/validate | |
| - name: validate | |
| run: | | |
| if [[ $(grep "fail" output/sars-cov-2/nightly/validate/linelist.tsv) ]]; then exit 1; fi | |
| - name: upload | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: validate-${{ matrix.arch }} | |
| path: output/sars-cov-2/nightly/validate | |
| if-no-files-found: error | |
| retention-days: 7 |