rosalind/.github/workflows/ci.yml at bb69982856c4cd347971cc64e4889c338371da98 · logannye/rosalind · GitHub

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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: Verify the committed toy reference is intact (pinned hash)
        # A real anti-corruption gate, not the old self-referential check: pin the
        # COMMITTED reference.fa (the one the release bundle + every other job
        # ships) to a known hash. The previous step regenerated reference.fa at
        # 1 Mbp without --length, overwriting the committed 4 kbp fixture and
        # checking freshly-generated files against freshly-generated sums (a
        # tautology that also tested a different reference than ships).
        run: |
          echo "ce8a6df801e836f4eda0b7661a68dcd7b7a9ab247c66d4582a89dbc207554efa  examples/data/illumina_toy/reference.fa" \
            | sha256sum --check
      - name: Generate reads from the committed toy reference
        # --reference simulates reads FROM the committed reference (does not invent
        # or overwrite one), so cli-e2e exercises exactly the fixture that ships.
        run: python3 scripts/generate_toy_data.py examples/data/illumina_toy --reference examples/data/illumina_toy/reference.fa
      - 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