fix: add variant region condition for dups ending in 3' UTR (#192) #428
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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' }} |