chore(deps): bump tracing from 0.1.41 to 0.1.44 #159
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| name: CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| jobs: | |
| rust: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo- | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: stable | |
| - name: Cargo fmt | |
| run: cargo fmt --all -- --check | |
| - name: Cargo test | |
| run: cargo test --workspace | |
| - name: Synthetic chr20 GIAB smoke | |
| run: | | |
| benchmarks/giab/smoke.sh | |
| python3 -m unittest discover -s benchmarks/giab -p 'test_*.py' | |
| - name: Build examples | |
| run: cargo build --examples | |
| - name: Build docs | |
| run: cargo doc --workspace --no-deps | |
| - name: Compile receipt parser fuzz targets | |
| run: cargo check --manifest-path fuzz/Cargo.toml --bins | |
| - name: Package publishable crates and embedded assets | |
| run: | | |
| cargo package -p rosalind-build-info --allow-dirty | |
| cargo package -p rosalind-receipt --allow-dirty | |
| cargo package -p rosalind-bio --allow-dirty \ | |
| --config 'patch.crates-io.rosalind-receipt.path="crates/receipt"' \ | |
| --config 'patch.crates-io.rosalind-build-info.path="crates/build-info"' | |
| cargo package -p rosalind-bio --allow-dirty --list \ | |
| --config 'patch.crates-io.rosalind-receipt.path="crates/receipt"' \ | |
| --config 'patch.crates-io.rosalind-build-info.path="crates/build-info"' > package-files.txt | |
| grep -q '^web/verify/pkg/rosalind_verify_bg.wasm$' package-files.txt | |
| grep -q '^assets/demo/reference.fa$' package-files.txt | |
| grep -q '^assets/scaffold/Cargo.toml.template$' package-files.txt | |
| python: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # 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@0057852bfaa89a56745cba8c7296529d2fc39830 # v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('.github/workflows/ci.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: stable | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install numpy | |
| run: pip install numpy | |
| - name: Build the rosalind binary | |
| run: cargo build --release --bin rosalind | |
| - name: Exercise the Python boundary (bit-reproducible feature substrate) | |
| # Runs the documented entry point (python/rosalind.py) end-to-end: builds a | |
| # toy index + BAM, extracts features twice, and proves the inputs are | |
| # byte-identical with matching BLAKE3 receipts. | |
| run: python3 examples/reproducible_features_demo.py target/release/rosalind | |
| cli-e2e: | |
| runs-on: ubuntu-latest | |
| env: | |
| PYO3_PYTHON: python3 | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # 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@0057852bfaa89a56745cba8c7296529d2fc39830 # v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('.github/workflows/ci.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: '3.11' | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: stable | |
| - 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: Reproduce fence — a stranger re-derives the result on this runner | |
| # The contract.vcf + its receipt were produced above; reproduce re-derives it | |
| # byte-for-byte from content-located inputs on THIS runner (a different machine | |
| # than the author's), writes a chainable certificate, and a byte-changed input | |
| # is correctly reported INCONCLUSIVE (exit 7) — never a false DIVERGED. | |
| run: | | |
| set -e | |
| D=examples/data/illumina_toy | |
| cargo run --release -- reproduce \ | |
| --manifest $D/contract.vcf.manifest.json \ | |
| --inputs $D/ | tee reproduce.log | |
| grep -q "REPRODUCED" reproduce.log | |
| test -f $D/contract.vcf.manifest.json.repro.json | |
| # Negative: a byte-changed input can no longer be content-located -> exit 7. | |
| mkdir -p tamper && cp $D/reference.idx tamper/ && cp $D/sorted.bam tamper/ | |
| printf 'x' >> tamper/sorted.bam | |
| set +e | |
| cargo run --release -- reproduce \ | |
| --manifest $D/contract.vcf.manifest.json --inputs tamper/ > /dev/null 2>&1 | |
| code=$? | |
| set -e | |
| test "$code" -eq 7 | |
| - name: Emit a self-hosted reproducibility badge | |
| run: | | |
| D=examples/data/illumina_toy | |
| cargo run --release -- badge \ | |
| --manifest $D/contract.vcf.manifest.json \ | |
| --repro $D/contract.vcf.manifest.json.repro.json \ | |
| -o badge.json | |
| cat badge.json | |
| - name: Upload the reproducibility badge | |
| if: always() | |
| uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 | |
| with: | |
| name: rosalind-reproducibility-badge | |
| path: badge.json | |
| if-no-files-found: ignore | |
| - 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 | |
| msrv: | |
| name: MSRV (1.83) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-msrv-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo-msrv- | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: 1.83.0 | |
| - name: cargo check on the declared MSRV | |
| run: cargo check --all-targets | |
| clippy: | |
| name: Clippy (-D warnings) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-clippy-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo-clippy- | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: stable | |
| components: clippy | |
| - name: Clippy as a gate | |
| run: cargo clippy --all-targets -- -D warnings | |
| benchmarks: | |
| name: Claims harness | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - name: Cache cargo artifacts | |
| uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4 | |
| with: | |
| path: | | |
| ~/.cargo/registry | |
| ~/.cargo/git | |
| target | |
| key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-cargo- | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: stable | |
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Run the claims harness (a standing regression gate on the contract + reproducibility) | |
| run: bash benchmarks/run.sh | |
| studio-assets: | |
| name: Receipt Studio generated assets | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| with: | |
| toolchain: 1.83.0 | |
| targets: wasm32-unknown-unknown | |
| - uses: taiki-e/install-action@c7eb1735f09259a5035e8e5d44b1406b1cddc0fb # v2 | |
| with: | |
| tool: wasm-pack@0.14.0 | |
| - name: Rebuild committed client-only WASM | |
| env: | |
| RUSTUP_TOOLCHAIN: 1.83.0 | |
| run: scripts/build-wasm-verifier.sh | |
| - name: Generated assets are reproducible | |
| run: git diff --exit-code -- web/verify/pkg crates/receipt-wasm/Cargo.lock | |
| - name: WASM unit tests | |
| run: cargo test --manifest-path crates/receipt-wasm/Cargo.toml | |
| release-automation: | |
| name: Maintainer automation dry run | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4 | |
| - uses: dtolnay/rust-toolchain@4be7066ada62dd38de10e7b70166bc74ed198c30 # stable | |
| - name: Install pinned workflow linters | |
| run: | | |
| curl -fsSLO https://github.com/rhysd/actionlint/releases/download/v1.7.7/actionlint_1.7.7_linux_amd64.tar.gz | |
| echo '023070a287cd8cccd71515fedc843f1985bf96c436b7effaecce67290e7e0757 actionlint_1.7.7_linux_amd64.tar.gz' | sha256sum --check | |
| tar -xzf actionlint_1.7.7_linux_amd64.tar.gz actionlint | |
| sudo install actionlint /usr/local/bin/actionlint | |
| curl -fsSLO https://github.com/koalaman/shellcheck/releases/download/v0.10.0/shellcheck-v0.10.0.linux.x86_64.tar.xz | |
| echo '6c881ab0698e4e6ea235245f22832860544f17ba386442fe7e9d629f8cbedf87 shellcheck-v0.10.0.linux.x86_64.tar.xz' | sha256sum --check | |
| tar -xJf shellcheck-v0.10.0.linux.x86_64.tar.xz | |
| sudo install shellcheck-v0.10.0/shellcheck /usr/local/bin/shellcheck | |
| python3 -m pip install 'jsonschema==4.23.0' | |
| - name: Maintainer CLI fake-remote integration suite | |
| run: cargo test -p xtask --locked | |
| - name: Validate schemas, workflows, and shell entry points | |
| run: | | |
| set +e | |
| cargo xtask doctor --json > maintainer-report.json | |
| doctor_code=$? | |
| set -e | |
| if [ "$doctor_code" -ne 0 ] && [ "$doctor_code" -ne 3 ]; then exit "$doctor_code"; fi | |
| cargo xtask partners init --persona analyzer-builder --output partner-packet | |
| python3 - <<'PY' | |
| import json | |
| from pathlib import Path | |
| from jsonschema import Draft202012Validator, validate | |
| for path in Path("release/schemas").glob("*.json"): | |
| Draft202012Validator.check_schema(json.load(open(path))) | |
| validate(json.load(open("maintainer-report.json")), json.load(open("release/schemas/maintainer-report-v1.schema.json"))) | |
| validate(json.load(open("partner-packet/feedback.json")), json.load(open("release/schemas/design-partner-v1.schema.json"))) | |
| PY | |
| scripts/verify-release-automation.py | |
| actionlint | |
| shellcheck scripts/release-publish.sh scripts/post-publish-smoke.sh \ | |
| scripts/stage-release.sh benchmarks/giab/prepare.sh benchmarks/giab/run.sh \ | |
| benchmarks/giab/happy/run.sh assets/scaffold/scripts/contract-check.sh | |
| bash -n scripts/release-publish.sh scripts/post-publish-smoke.sh \ | |
| scripts/stage-release.sh benchmarks/giab/prepare.sh benchmarks/giab/run.sh \ | |
| benchmarks/giab/happy/run.sh assets/scaffold/scripts/contract-check.sh |