fix(quant): include fragment-length probability in equivalence-class weights #62
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| pull_request: | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| env: | |
| CARGO_TERM_COLOR: always | |
| # Unified MSRV across the salmon workspace and its COMBINE-lab deps (see plan R2). | |
| RUST_TOOLCHAIN: "1.91.1" | |
| jobs: | |
| build-test: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: ubuntu-22.04 | |
| target_id: linux-x86_64 | |
| - os: ubuntu-24.04-arm | |
| target_id: linux-aarch64 | |
| - os: macos-15-intel | |
| target_id: macos-x86_64 | |
| - os: macos-14 | |
| target_id: macos-arm64 | |
| steps: | |
| - name: Checkout salmon | |
| uses: actions/checkout@v4 | |
| - name: Install Rust ${{ env.RUST_TOOLCHAIN }} | |
| uses: dtolnay/rust-toolchain@master | |
| with: | |
| toolchain: ${{ env.RUST_TOOLCHAIN }} | |
| components: rustfmt, clippy | |
| - name: Cache cargo | |
| uses: Swatinem/rust-cache@v2 | |
| - name: Format check | |
| run: cargo fmt --all -- --check | |
| - name: Clippy | |
| run: cargo clippy --workspace --all-targets -- -D warnings | |
| - name: Build (release, portable floor) | |
| # .cargo/config.toml pins the x86-64-v2 / NEON SIMD floor; ksw2rs picks | |
| # AVX2/SSE4.1/NEON at runtime. | |
| run: cargo build --workspace --release | |
| - name: Test | |
| run: cargo test --workspace --release | |
| - name: CLI smoke | |
| run: ./target/release/salmon --help | |
| - name: Sample data smoke (mapping) | |
| shell: bash | |
| run: | | |
| set -euo pipefail | |
| [[ -d sample_data ]] || tar -xzf sample_data.tgz | |
| ./target/release/salmon index \ | |
| -t sample_data/transcripts.fasta \ | |
| -i target/sample_index | |
| ./target/release/salmon quant \ | |
| -l A -i target/sample_index \ | |
| -1 sample_data/reads_1.fastq \ | |
| -2 sample_data/reads_2.fastq \ | |
| -o target/sample_quant_mapping | |
| test -s target/sample_quant_mapping/quant.sf | |
| - name: Sample data smoke (alignment) | |
| shell: bash | |
| run: | | |
| set -euo pipefail | |
| ./target/release/salmon quant \ | |
| -l A -t sample_data/transcripts.fasta \ | |
| -a sample_data/sample_alignments.bam \ | |
| -o target/sample_quant_alignment | |
| test -s target/sample_quant_alignment/quant.sf |