feat: add variant region condition for dups ending in 3' UTR (#192) (… #433
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| components: rustfmt | |
| - name: Check format | |
| run: | | |
| cargo fmt -- --check | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| components: clippy | |
| - name: Lint with clippy | |
| uses: actions-rs/clippy-check@v1 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| Testing: | |
| needs: Formatting | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - label: fast | |
| - label: full | |
| services: | |
| # The tests need a postgres server; the data will be loaded later | |
| # after checkout. | |
| postgres: | |
| image: postgres | |
| env: | |
| POSTGRES_DB: uta | |
| POSTGRES_USER: uta_admin | |
| POSTGRES_PASSWORD: uta_admin | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Import test database. | |
| run: | | |
| set -euo pipefail | |
| zcat tests/data/data/uta_20210129-subset.pgd.gz \ | |
| | psql -v ON_ERROR_STOP=1 -U uta_admin -h 0.0.0.0 -d uta | |
| shell: bash | |
| env: | |
| PGPASSWORD: uta_admin | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - uses: Swatinem/rust-cache@v2.7.3 | |
| - name: Run cargo-tarpaulin with fast tests | |
| uses: actions-rs/tarpaulin@v0.1 | |
| with: | |
| version: 0.21.0 | |
| args: "-- --test-threads 1" | |
| env: | |
| TEST_UTA_DATABASE_URL: postgres://uta_admin:uta_admin@0.0.0.0/uta | |
| TEST_UTA_DATABASE_SCHEMA: uta_20210129 | |
| TEST_SEQREPO_CACHE_MODE: read | |
| TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta | |
| if: ${{ matrix.label == 'fast' }} | |
| - name: Run cargo-test with full tests | |
| uses: actions-rs/cargo@v1 | |
| with: | |
| command: test | |
| args: "--release -- --include-ignored" | |
| env: | |
| TEST_UTA_DATABASE_URL: postgres://uta_admin:uta_admin@0.0.0.0/uta | |
| TEST_UTA_DATABASE_SCHEMA: uta_20210129 | |
| TEST_SEQREPO_CACHE_MODE: read | |
| TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta | |
| if: ${{ matrix.label == 'full' }} | |
| - name: Codecov submission of fast test results | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| if: ${{ matrix.label == 'fast' }} |