Feature-substrate Python boundary + reproducibility demo #62
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| name: CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| jobs: | |
| rust: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo- | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| profile: minimal | |
| override: true | |
| - name: Cargo fmt | |
| run: cargo fmt --all -- --check | |
| - name: Cargo test | |
| run: cargo test | |
| - name: Build examples | |
| run: cargo build --examples | |
| - name: Build docs | |
| run: cargo doc --no-deps | |
| python: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo- | |
| - name: Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install maturin and cffi | |
| run: pip install maturin cffi | |
| - name: Build python bindings | |
| run: maturin build --features python-bindings | |
| cli-e2e: | |
| runs-on: ubuntu-latest | |
| env: | |
| PYO3_PYTHON: python3 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo- | |
| - name: Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| profile: minimal | |
| override: true | |
| - name: Generate toy dataset | |
| run: python3 scripts/generate_toy_data.py examples/data/illumina_toy | |
| - name: Verify checksums | |
| run: sha256sum --check SHA256SUMS | |
| working-directory: examples/data/illumina_toy | |
| - name: Align to SAM | |
| run: | | |
| cargo run --release -- align \ | |
| --reference examples/data/illumina_toy/reference.fa \ | |
| --reads examples/data/illumina_toy/reads_R1.fastq \ | |
| --format sam \ | |
| --output examples/data/illumina_toy/alignments.sam | |
| - name: Align to BAM | |
| run: | | |
| cargo run --release -- align \ | |
| --reference examples/data/illumina_toy/reference.fa \ | |
| --reads examples/data/illumina_toy/reads_R1.fastq \ | |
| --format bam \ | |
| --output examples/data/illumina_toy/alignments.bam | |
| - name: Call variants | |
| run: | | |
| cargo run --release -- variants \ | |
| --reference examples/data/illumina_toy/reference.fa \ | |
| --alignments examples/data/illumina_toy/alignments.sam \ | |
| --mapq-threshold 5 \ | |
| --output examples/data/illumina_toy/variants.vcf | |
| - name: Sanity-check outputs | |
| run: | | |
| test -s examples/data/illumina_toy/alignments.sam | |
| test -s examples/data/illumina_toy/alignments.bam | |
| grep -q '^#CHROM' examples/data/illumina_toy/variants.vcf | |
| grep -q -v '^#' examples/data/illumina_toy/variants.vcf || echo \"warning: no variant lines emitted\" | |
| - name: Build index for the bounded contract path | |
| run: | | |
| cargo run --release -- index \ | |
| --reference examples/data/illumina_toy/reference.fa \ | |
| --output examples/data/illumina_toy/reference.idx | |
| - name: Sort the BAM for the contract path | |
| run: | | |
| cargo run --release -- sort \ | |
| --input examples/data/illumina_toy/alignments.bam \ | |
| --output examples/data/illumina_toy/sorted.bam | |
| - name: Contract gate — fits / verify / refuse (bounded --index path) | |
| run: | | |
| set -e | |
| # (1) Generous budget fits -> exit 0 + "contract: OK". | |
| cargo run --release -- variants --index examples/data/illumina_toy/reference.idx \ | |
| --alignments examples/data/illumina_toy/sorted.bam \ | |
| --memory-budget-mb 4096 --enforce \ | |
| -o examples/data/illumina_toy/contract.vcf 2> ok.log | |
| grep -q "contract: OK" ok.log | |
| # (2) Verify the receipt without re-running -> exit 0. | |
| cargo run --release -- verify \ | |
| --manifest examples/data/illumina_toy/contract.vcf.manifest.json | grep -q "verify: OK" | |
| # (3) 1 MiB budget refuses up front -> exit 3, and writes no VCF. | |
| rm -f examples/data/illumina_toy/refused.vcf | |
| set +e | |
| cargo run --release -- variants --index examples/data/illumina_toy/reference.idx \ | |
| --alignments examples/data/illumina_toy/sorted.bam \ | |
| --memory-budget-mb 1 --enforce \ | |
| -o examples/data/illumina_toy/refused.vcf 2> refuse.log | |
| code=$? | |
| set -e | |
| test "$code" -eq 3 | |
| grep -q "REFUSE" refuse.log | |
| test ! -f examples/data/illumina_toy/refused.vcf | |
| - name: Exercise the rosalind-budget Action (local, from-source binary) | |
| uses: ./ | |
| with: | |
| index: examples/data/illumina_toy/reference.idx | |
| alignments: examples/data/illumina_toy/sorted.bam | |
| budget-mb: 4096 | |
| binary-path: target/release/rosalind | |
| output: examples/data/illumina_toy/action.vcf |