omics-rust / rsomics-common

No fue posible recopilar el conjunto de dependencias resuelto para este informe: GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository

{
  "data": {
    "repo": {
      "topics": [],
      "is_fork": false,
      "size_kb": 177,
      "has_wiki": true,
      "homepage": null,
      "languages": {
        "Rust": 43294
      },
      "pushed_at": "2026-07-30T05:47:45Z",
      "created_at": "2026-05-21T15:26:00Z",
      "owner_type": "Organization",
      "updated_at": "2026-07-30T05:48:05Z",
      "description": "Shared primitives for every rsomics-* crate (errors, CLI scaffold, runner, progress, exit codes).",
      "is_archived": false,
      "is_disabled": false,
      "license_spdx": "Apache-2.0",
      "default_branch": "main",
      "license_spdx_raw": "Apache-2.0",
      "primary_language": "Rust",
      "significant_languages": [
        "Rust"
      ]
    },
    "owner": {
      "blog": null,
      "name": null,
      "type": "Organization",
      "login": "omics-rust",
      "company": null,
      "location": null,
      "followers": 10,
      "avatar_url": "https://avatars.githubusercontent.com/u/286340406?v=4",
      "created_at": "2026-05-20T12:50:20Z",
      "is_verified": null,
      "public_repos": 17,
      "account_age_days": 71
    },
    "license": {
      "state": "standard",
      "spdx_id": "Apache-2.0",
      "raw_spdx": "Apache-2.0",
      "file_present": true,
      "scorecard_found": true,
      "profile_has_license": true
    },
    "activity": {
      "releases": [],
      "recent_commits": [
        {
          "oid": "1c51f7d0b356683697942d9c6a0f60585e0dc8a9",
          "body": "Add fallible JSON emitters and route the shared runner through them so serialization, write, newline, and flush failures return the existing I/O exit code. Preserve legacy emitter signatures as deprecated fail-loud wrappers and keep the public error vocabulary compatible.",
          "is_bot": false,
          "headline": "fix(common): propagate JSON output failures",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-30T05:47:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ed02bcb9f813ef65d47ed6374f71ca9c77f6eb4a",
          "body": null,
          "is_bot": false,
          "headline": "feat(common): share output path opening",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T17:14:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8f2f192b24c819f643347dce77aa57e03b739e99",
          "body": null,
          "is_bot": false,
          "headline": "test(common): exercise piped stdin input",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T14:29:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ce418f56c9a3a2f34b7f2361fa53f9940c05ddb0",
          "body": null,
          "is_bot": false,
          "headline": "chore(common): prepare 0.6.2 release",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T14:23:44Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0ac8663f7684b0787ba04bb3c5e9171b1db78544",
          "body": null,
          "is_bot": false,
          "headline": "chore(common): ignore local build artifacts",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T14:22:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7af59edf09981709eff99d91048c596ea369cdac",
          "body": null,
          "is_bot": false,
          "headline": "chore(common): correct package repository",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T14:22:08Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec7054e5a19fb49afc1aad696c5e8c87556bea2b",
          "body": null,
          "is_bot": false,
          "headline": "ci(common): validate supported targets",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T14:21:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a56514368b5b4e4d2b79491b497fa64fe1872539",
          "body": null,
          "is_bot": false,
          "headline": "feat(common): share path or stdin input",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-29T14:20:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7686b2683a4b1e344869211f7bca01088272b900",
          "body": "…ter (0.6.1)\n\nSeveral tool crates carried private format_g6 copies; a differential test vs C\nprintf %g found three of them buggy (log10-based exponent misses power-of-ten\nrounding; unguarded trailing-zero strip drops significant zeros). Promote one\ncorrect implementation (rounding-aware {:.5e} exponent, .-guarded strip, nan/inf)\nwith a printf-%g battery test, so consumers can dedup onto it. Additive patch.",
          "is_bot": false,
          "headline": "feat(rsomics-common): add fmt::format_g6, canonical C %g 6-sig format…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-07-09T11:09:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5c9bda1713a880d28242c97e706001a83996268b",
          "body": null,
          "is_bot": false,
          "headline": "refactor(rsomics-common): humanize comments and naming",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-30T08:15:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "513623dccd0a5373b7ab252705eec4640b02aeae",
          "body": null,
          "is_bot": false,
          "headline": "chore: make Cargo.toml standalone",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-21T16:25:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6654bd76de6f6c87bb91941e48f2c78188ecec22",
          "body": null,
          "is_bot": false,
          "headline": "ci: add GitHub Actions workflow",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-21T15:26:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3f346efd391bddff6a95244a67dcbb58dbf060db",
          "body": "New public API: rsomics_common::Tool trait with meta(), common(),\nexecute(), and default run() method. All 62 dependent crates updated\nto require version 0.6.",
          "is_bot": false,
          "headline": "chore: bump rsomics-common to 0.6.0 (adds Tool trait)",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-21T07:23:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7f066b910bb8f2a4724d5967f058571104f5bbbe",
          "body": "Every tool crate now implements `rsomics_common::Tool` which enforces\na uniform contract: `meta()`, `common()`, `execute(self) -> Result<()>`.\n\n- New `rsomics_common::tool::Tool` trait with default `run()` method\n- All 43 cli.rs files: added `impl Tool for Cli` block\n- All 43 main.rs files: replaced\n[…]\nventing silent divergence at 200+ crate scale\n\nThe 5 utils crates (bed/fasta/fastq/gff/vcf-utils) still use inline\nmain.rs pattern — they will be migrated to cli.rs+rsomics-help in a\nfollow-up commit.",
          "is_bot": false,
          "headline": "refactor: add Tool trait to rsomics-common, migrate all 43 CLI crates",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-21T02:07:52Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "949363ecbafdc7d8cf68cd24c34e436860605869",
          "body": "Bring every tracked crate's comments to the project's human standard\n(the bcmr reference): names + types carry meaning; the only survivors\nare clap --help text, one-line load-bearing \"why\" not recoverable from\ncode, byte-compat invariants, and terse upstream/paper citations.\n\n- removed every //! mod\n[…]\nd-done diff; the one\nreal over-deletion (rsomics-seqstats shared-primitive byte-compat\nrationale) was restored as a terse //. cargo fmt + cargo clippy\n--workspace --all-targets -D warnings both green.",
          "is_bot": false,
          "headline": "refactor: humanize comments to bcmr density across the workspace",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-17T15:54:44Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "1841d850f49776f5c7b2907f4ffe3505660f04ab",
          "body": "Comments-only across 43 files: delete what-comments, control-flow\nnarration, restated-code, ASCII separators, redundant struct-field /\nconstant / private-fn doc, test-arithmetic walkthroughs; condense\nverbose //! and pub-item doc to the minimum. SAFETY, toolchain-forced\n#Errors/#Panics, citations, a\n[…]\nheck = 0;\nworkspace clippy -D warnings = 0 (igzip CI-authoritative, comments-only).\nFirst strict pass; the authoritative //!→README + remaining tightening\nis tracked under the quality-bar remediation.",
          "is_bot": false,
          "headline": "chore: strict comment sweep — foundation + formats (bcmr bar)",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-16T11:30:03Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "d564b60da7e0bf148cb8b3d67ba8e5077b6cf70f",
          "body": "G1 common+help, G2 intervals(skip bed.rs)/stats/kmer/debruijn, G3\nfm-index/align-core/hmm/phylo-tree, G5 all tool crates(skip bed-merge).\nDeleted what-comments, section banners, multi-sentence prose inferable\nfrom the code; converted single-line block comments to terse trailing\ninline; kept clap/Hel\n[…]\ncontracts. ~285 net comment lines removed\nhere (G4 taxonomy/popgen/pgen/models committed separately, same\nconcern). fmt + clippy -D warnings + 56 test suites green; behaviour\nunchanged (comment-only).",
          "is_bot": false,
          "headline": "refactor(workspace): aggressive comment-density cleanup to bcmr standard",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-15T13:48:06Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "d6a9cece9ce421d0261718f2f911afc04d10480c",
          "body": "Hypothesis tests, FDR control, p-value combination — covers the 12\ndeclared Layer-B consumers (rsomics-de, rsomics-vcf-popgen,\nrsomics-vcf-call, rsomics-vcf-stats, rsomics-rmats, rsomics-suppa,\nrsomics-leafcutter, rsomics-bisulfite-dmr, rsomics-dada2, rsomics-macs,\nrsomics-plink-assoc, rsomics-popge\n[…]\n\nshift-by-2 example, BH step-up against the closed-form expectation.\n\nGLM / IRLS / NB regression and Storey q-value are explicitly out of\nscope for 0.1.0 — defer to 0.2 once a B consumer demands them.",
          "is_bot": false,
          "headline": "feat(rsomics-stats): scaffold Layer A 0.1.0",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-15T05:00:13Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "d18ba4ce24e4714320030a28f06b39c116a30847",
          "body": "User flagged that the workspace was systematically over-documented:\nmodule-level //! \"## Why / ## Approach\" paragraphs, per-fn /// docs\nthat just restate the name, # Errors / # Panics sections on every\npublic Result-returning fn. Reference: /Users/snaix/Documents/bcmr —\nits config.rs and output.rs s\n[…]\nonale)\n- upstream-source citations\n- platform-quirk explanations in tests\n\nAll 27+13+28+10+32 = 110 unit tests + 6 integration tests pass\nunchanged. clippy --workspace --all-targets -D warnings clean.",
          "is_bot": false,
          "headline": "docs: workspace comment-density sweep — bcmr style",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-15T04:34:48Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "dbd7a16b777030db8df59fb7ecf9a3280835db3e",
          "body": "🟡 Drops audit-flagged loose ends:\n\n- rsomics-common/flags.rs: rewrite seed-zero docstring without\n  temporal reference (\"no longer\", \"prior\").\n- rsomics-common/Cargo.toml: stale comment named retired rsomics-fastp\n  and rsomics-bam crates as default-rayon's consumers.\n- rsomics-fastq-trim: remove `b\n[…]\nas\n  missing.\n\nVersion bumps (all patch — additive / docs-only):\n- rsomics-common  0.5.0 → 0.5.1\n- rsomics-help    0.3.0 → 0.3.1\n- rsomics-fasta-stats 0.4.2 → 0.4.3\n- rsomics-fastq-trim  0.4.3 → 0.4.4",
          "is_bot": false,
          "headline": "chore: audit-followup cleanup batch",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-15T02:33:19Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "305a840762290c8c12c52a2c1bf7d4e865e59c93",
          "body": "Audit found `rsomics_common::writers::open_output` has zero consumers\nand `rsomics_common::fastq` has only the one-line `write_record` helper\nused by rsomics-fastq-trim's `parallel_gz`. CLAUDE.md's \"2+ B-crate\nconsumer\" rule says a foundation module with <2 consumers should live\nin the one consumer \n[…]\n writer extracted\nfrom parallel_gz — not the serial GzEncoder enum we just removed.\n\nrsomics-common  0.4.0 → 0.5.0  (breaking — removed pub items)\npilots          0.4.1 → 0.4.2  (track new common dep)",
          "is_bot": false,
          "headline": "refactor(rsomics-common)!: drop unused fastq + writers modules",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-15T02:03:39Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "e4f2dba4ddcd3d2408e8c633850cce6a3a1c813b",
          "body": "…HelpMode\n\nAdding `#[non_exhaustive]` to public extensible enums prevents the next\nvariant addition (e.g. `NetworkError` for HTTP-based tools, `Pager` for\nhelp routing) from becoming a workspace-wide breaking change. Strictly\nbreaking per semver, so:\n\n- rsomics-common  0.3.0 → 0.4.0\n- rsomics-help  \n[…]\n no-construction restriction would force a const-fn\nconstructor refactor across every future tool crate. Future field\nadditions on those types will be tracked as minor bumps as a documented\ntrade-off.",
          "is_bot": false,
          "headline": "feat(rsomics-common,rsomics-help)!: non_exhaustive on RsomicsError + …",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-15T01:59:35Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "824f52c45feb461db90cf21eb8db847fe07739a9",
          "body": "Pre-audit rsomics-common 0.2.0 was published to crates.io without the\n`fastq` module. The audit session added `rsomics_common::fastq::Writer`\nand `write_record` for sibling-crate reuse, but the local 0.2.0 still\nhad the same version number as the registry — so publishing\nrsomics-fastq-trim 0.2.0 (wh\n[…]\n `u64` but seqkit can emit fractional\n  quartiles on small inputs — switched to `f64` with `<0.5` epsilon\n  in the equality assertions (we round to %.0f for tabular but seqkit\n  prints the raw float).",
          "is_bot": false,
          "headline": "chore: bump rsomics-common 0.3.0 + pilots track new dep",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T22:43:11Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "49c411ef39e2874ca353baec600db2f88e06b438",
          "body": "…eshEye comment audit\n\nPer the 4-model L3 comment audit (Sonnet × 2 + Gemini-flash):\n\nHIGH deletes (TEMPORAL / WHAT, 100% auditor agreement):\n- adapter.rs / overlap.rs `//!`: \"0.1.0 implementation\" and \"deferred\n  to a later minor\" temporal language → restated as timeless capability\n  statements (\"A\n[…]\nting openings cut.\n- rsomics-common/fastq.rs `Writer` / `write_record` — same.\n- fasta-stats lib.rs — module docstring tightened.\n\nTests: 31 + 13 + 27 + 3 across foundation and both pilots, all green.",
          "is_bot": false,
          "headline": "docs(rsomics-fastq-trim,rsomics-fasta-stats,rsomics-common): apply Fr…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T22:12:26Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "42c2b7aa28384e72d0362064a7604ad5f45878a7",
          "body": "…-threads)\n\n`CommonFlags::threads` reserves `-t` globally for the whole crate\nfamily. fastp's `-t` / `-T` for `--trim_tail1` / `--trim_tail2` cannot\ncoexist; clap's debug_assert! catches the collision but only fires in\ndebug builds, so my `cargo test --release` local pass missed it. CI on\nLinux ran \n[…]\nne. The\ncompat test that used `-t 2` updated to `--trim_tail1 2`.\n\nAlso wraps the `Box::new(GzEncoder::new(...))` line in `rsomics-common`\nto placate rustfmt — local mac rustfmt was happier than CI's.",
          "is_bot": false,
          "headline": "fix(rsomics-fastq-trim): drop short `-t`/`-T` aliases (collide with -…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T21:13:28Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "2297f561b0e1aa717a46674fd0b85260ad10c15c",
          "body": "…xed trim\n\nSecond per-function crate landing under the new layout. Scope is the\ntrim subset of fastp's surface: 3' static adapter, PE overlap-based\nadapter detect, polyG / polyX, fixed-length 5'/3'. Quality / UMI / stats\ndeliberately out of scope — those land in sibling crates.\n\nCompat (byte-equal `\n[…]\n5-15.toml\n\nAlso lands rsomics-common::fastq with the shared gzip-aware Writer +\nwrite_record format helper, used by this crate and earmarked for the\nupcoming `rsomics-fastq-quality` / `-umi` siblings.",
          "is_bot": false,
          "headline": "feat(rsomics-fastq-trim): pilot #2 — adapter / polyG/X / overlap / fi…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T21:08:09Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "fdd6d9efe587bd7d1bb81083ba8088fc615193e0",
          "body": "User's selling point: agentic-era CLI must speak machine-readable\noutput as well as human. Today the CommonFlags::json bool was dead\nin every tool. This commit makes it actually do something.\n\nNew: rsomics_common::json module + ToolMeta type. Every tool's\nmain() declares a const META { name: env!(\"C\n[…]\n  $ rsomics-bam view -c --json input.bam\n  {\"schema_version\":\"1.0\",\"tool\":\"rsomics-bam\",\"tool_version\":\"0.2.0\",\n   \"status\":\"ok\",\"result\":{\"subcommand\":\"view\",\"records\":100000,\n   \"mode\":\"count\",...}}",
          "is_bot": false,
          "headline": "feat: AI-friendly --json envelope across the family + bump to 0.2.0",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T17:26:35Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "7894994da2009537e576b9cbd3eb76fdf3e64e94",
          "body": "Adds the macro tier2_manifest_path!() that resolves the workspace-root\ntests/fixtures-manifest.toml from any rsomics-* crate's compile site.\nRequired by both rsomics-fastp and rsomics-bam's Tier-2 compat tests.\n\nAlso picks up rustfmt's preferred ordering of the cfg-gated\nuse crate::error::Result vs \n[…]\nwas failing on this) and a width-driven .ok_or_else\nindent fix in tier2.rs.\n\n.gitignore: tests/fixtures-staging/ — local-only fixture build dir,\nsources for the fixtures-v0.1 GitHub release artifacts.",
          "is_bot": false,
          "headline": "feat(rsomics-common): tier2_manifest_path! macro + fmt sweep",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T17:12:41Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "2e58837ba44ca99c2bd9e94df52d44a3247607f8",
          "body": "Phase 4b infrastructure. Real-world FASTQ/BAM/VCF fixtures that\nexceed Tier-1's \"< 100 MB inside git\" budget now have a declarative\nhome at tests/fixtures-manifest.toml + a runtime fetcher under\nrsomics_common::test_support::tier2 (behind the new `tier2` Cargo\nfeature so production binaries don't ca\n[…]\nad cannot poison the cache.\n\n7 unit tests cover sha256 vs known vector, manifest round-trip,\nunknown-name error, and all three cache-dir precedence arms.\n\nFixture URLs follow in 4c (real-data compat).",
          "is_bot": false,
          "headline": "feat(rsomics-common): Tier-2 fixture manifest + on-demand fetcher",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T16:53:51Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "8be9beddba65ef06d3989b2df6697186a49f809a",
          "body": null,
          "is_bot": false,
          "headline": "docs(rsomics-common): flatten-placement rule on CommonFlags",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T16:41:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "00212d3fb19f4ad55d74556967050be8cc64e02d",
          "body": "Future single-threaded FFI-wrapper tools (Quadrant ② tools that don't\ntouch the global thread pool) can opt out of rayon's transitive deps\nand binary-size impact with default-features = false.\n\nDefault-on preserves the current API for rsomics-fastp and rsomics-bam\nwithout changes. install_rayon_pool keeps its signature in both\nflavors so crate::run can call it unconditionally; the no-feature arm\nis a stub returning Ok(()).\n\nSonnet structural-lens audit #5.",
          "is_bot": false,
          "headline": "feat(rsomics-common): rayon behind default-on Cargo feature",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T16:40:00Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "99e811fc95fbe77e4a907f5fe46ba283363d532a",
          "body": "…ce.lints]\n\nThree crates carried identical lint blocks. Future tools cloning the\ntemplate would either copy-paste them (sync hazard) or omit (lint\ngap). Promote to workspace level; each crate inherits via\n[lints] workspace = true.\n\nrsomics-bam keeps a per-crate comment noting the FFI-quadrant\nnuance (the workspace forbid applies to our Rust only, not to\nrust-htslib's internal unsafe).\n\nSonnet structural-lens audit #6.",
          "is_bot": false,
          "headline": "refactor(workspace): promote unsafe_code+clippy::pedantic to [workspa…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T16:38:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5dce41834167482c7de047d84dd49cec2b154c1c",
          "body": null,
          "is_bot": false,
          "headline": "style: rustfmt wrap on assert! line",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T14:11:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "156378990f84c28e32fb3bad287fbfb49eceb9a3",
          "body": "Ubuntu's /bin/sh is dash, which exits non-zero on --version. The unit\ntest was probing sh (worked on macOS where sh = bash) and failed on\nall 4 Linux CI runners with 'test result: FAILED. 26 passed; 1 failed'.\n\ncargo is universally present during `cargo test` and follows the\n--version convention that tool_on_path is designed for. Switch the\nprobe target; expand the comment to document why the predicate\nimplicitly requires --version-respecting tools (samtools, fastp,\nbcftools fit; dash does not).",
          "is_bot": false,
          "headline": "fix(rsomics-common): tool_on_path unit test uses cargo not sh",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T14:08:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1702a92a1cf2b1095890506303ef0ebfab36314d",
          "body": "…, writers)\n\n0.1.1 contains:\n\n- pub mod test_support (Cargo feature \"test-support\")\n- pub mod writers + pub use writers::open_output\n- expanded doc comment on RsomicsError::UpstreamError\n\nNo breaking changes; SemVer-minor bump is correct.\n\nNot published in this session — the user runs the tag push when\nready. See .autopilot/gates/gate-phase2-publish-ready-2026-05-14.md\nfor the publish sequence (analogous flow for rsomics-common-v0.1.1).",
          "is_bot": false,
          "headline": "chore(rsomics-common): bump to 0.1.1 — additive surface (test_support…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T13:38:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b8218025da01ede1c50620f97a5f7285dedd584b",
          "body": "…s dual-use\n\nL3 audit Opus #2 flagged that UpstreamError covers two distinct\nfailure shapes (FFI return code, subprocess exit non-zero) that share\nthe ExitCode mapping but differ at the operator-debug level. Document\nthe dual-use in the variant's doc comment now so the next consumer\n(rsomics-bam, wh\n[…]\nh will hit both shapes regularly) reads the\nintended semantics.\n\nNo code change. Splitting into FfiError + UpstreamProcessError is\ndeferred to a future minor bump if rsomics-bam reveals real friction.",
          "is_bot": false,
          "headline": "docs(rsomics-common): UpstreamError variant clarifies FFI + subproces…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T13:37:50Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "f5969757141a95866b63c4d45a1c399bc0899dcd",
          "body": "Template audit (Sonnet structural + Opus abstraction lenses) flagged\ntwo HIGH-severity gaps before rsomics-bam scaffolding starts:\n\n- The fixture_path + tool_on_path + run_tool helpers are duplicated\n  across rsomics-fastp's tests/compat.rs, golden_se.rs, golden_pe.rs,\n  and benches/fastp.rs. rsomic\n[…]\nth>; None means buffered stdout.\n\nFive additive unit tests on the new surface (3 test_support + 2\nwriters). No changes to existing exports.\n\nSynthesis at .autopilot/state/template-audit-2026-05-14.md.",
          "is_bot": false,
          "headline": "feat(rsomics-common): test_support module + writers::open_output",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T13:37:33Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "d5c547e98b917879bbaeca66708063699523fc86",
          "body": "0.0.x signals \"the shape is so unstable I'd rather not be depended on\nat all\" — even more extreme than 0.1.0-alpha. The Rust ecosystem\nconvention for first published version is 0.1.0 (real but unstable\nAPI). Adopt it.\n\nUpdate rsomics-fastp's path-dep pin to version = \"0.1.0\" so cargo\npublish resolve\n[…]\np rsomics-fastp --dry-run: fails with the expected\n  \"no matching package named rsomics-common\" — resolves once\n  rsomics-common is published.\n\nPublish order: rsomics-common first, then rsomics-fastp.",
          "is_bot": false,
          "headline": "chore: bump rsomics-common + rsomics-fastp to 0.1.0 for first publish",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:50:42Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "04f3486dc84d40e0e61c1dc09db4aec0e42fc0d4",
          "body": "L3 FreshEye (Opus, robustness lens) flagged that --threads >1 was\nsilently accepted while the SE/PE pipeline runs sequentially — the\nworst option per CLAUDE.md's fail-loud rule. Per-tool runtime notice\nis the right level: the flag DOES install the rayon global pool\n(other paths and future tools will\n[…]\ninfo() so --quiet still suppresses\nit; a user passing --quiet --threads N is opting out of all\ndiagnostics deliberately.\n\nAlso tighten CommonFlags::threads doc to be honest about per-tool\nconsumption.",
          "is_bot": false,
          "headline": "fix(rsomics-fastp): emit honest --threads notice on sequential pipeline",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:49:06Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "af4d28d5deea3632c31fc7a4eacdeac8ad060bc2",
          "body": "L3 FreshEye (Sonnet) flagged the prior AtomicU64::new(0) + \"0 means\nunset\" sentinel as fragile: any future refactor that changes how the\ncached seed is read can silently turn an explicit --seed 0 into a\nfresh OS-derived seed. The if-let-Some guard fired first today, so\n--seed 0 was safe in practice,\n[…]\nu64>. \"Initialised\" vs \"not\"\nbecomes the type's job. fresh_os_seed no longer needs to avoid 0\n(the prior invariant collapses to nothing). Add a regression test\nasserting --seed 0 round-trips verbatim.",
          "is_bot": false,
          "headline": "fix(rsomics-common): seed_rng uses OnceLock instead of zero-sentinel",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:44:58Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "384bf41a9e0fe1a1acb1eee081b1bf06e792df0a",
          "body": "L3 FreshEye review (Sonnet, API stability lens) flagged that the\nContext trait only impl'd over io::Error sources. Tools holding a\nResult<T, RsomicsError> — the dominant type in pipeline code —\ncouldn't chain rs_context() onto it. The workaround in rsomics-fastp\nwas to define a local parse_err helpe\n[…]\nntext impl for Result<T, RsomicsError>. Prefixes the\nexisting variant's message while preserving the variant — so\nExitCode mapping stays correct. Two tests cover Io- and\nInvalidInput-variant chaining.",
          "is_bot": false,
          "headline": "fix(rsomics-common): Context impl for Result<T, RsomicsError>",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:42:47Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "ca8e8dd50088e7cf1bf1917a6db2e50d0dff6944",
          "body": "…ult chaining",
          "is_bot": false,
          "headline": "feat(rsomics-common): Context extension trait for path-preserving Res…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:15:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f2edd04d820436ff9459c04b256bd830dce12bfd",
          "body": "…d rayon idempotency\n\nFreshEye L2 review surfaced three pre-adoption fixes:\n\n- The info!/error!/debug! macros at crate root via #[macro_export]\n  would collide with the well-known log crate's macros on every\n  downstream that adopts both. Drop the macros — callers can write\n  log.info(format_args!(\\\n[…]\ness; if not, fail loud with the actual counts.\n\nAlso document the io::Error -> IoError exit-code mapping ambiguity\n('bad user path' routes to exit 4, not 1) and the FRESH_SEED == 0\nsentinel invariant.",
          "is_bot": false,
          "headline": "refactor(rsomics-common): drop macro exports, drop is_* methods, type…",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:12:18Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "7102207870c3fec647cf1afcb0f6f899fd5aadbf",
          "body": null,
          "is_bot": false,
          "headline": "docs(rsomics-common): crate-level rustdoc and usage example",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:07:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bef3d79150ac02c21e36991ab364cf5a64023c73",
          "body": null,
          "is_bot": false,
          "headline": "feat(rsomics-common): tool entry helper that maps Result to ExitCode",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:06:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1536ba9016e96dd839142b9cc65b3b2b8d557e44",
          "body": null,
          "is_bot": false,
          "headline": "feat(rsomics-common): quiet-aware stderr writer",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:05:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "aa0be5a928c4ad1de903db8be5881e5817883afb",
          "body": null,
          "is_bot": false,
          "headline": "feat(rsomics-common): CommonFlags clap-derive scaffold",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:04:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "faf9489f4591ef14510128a0d19ad2406e813b5c",
          "body": null,
          "is_bot": false,
          "headline": "feat(rsomics-common): ExitCode enum mapping RsomicsError to process exit",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:03:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3badf51f3aa23094df9fe1050136e310200c5458",
          "body": null,
          "is_bot": false,
          "headline": "feat(rsomics-common): RsomicsError type + Result alias",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-14T01:02:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "122a795f440003d68a4b2342a05de5697002b492",
          "body": "rustfmt treats a 0-byte file as needing a terminating newline; cargo fmt\n--check rejected it. Keep the file 'effectively empty' per the directive\nbut POSIX-text-file-shaped (single \\n) so the fmt gate passes.",
          "is_bot": false,
          "headline": "fix(rsomics-common): newline-terminate empty lib.rs",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-13T17:28:53Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "72764637284d9fbd31c8a71ed65b8b5ffa28ec5b",
          "body": "rsomics-common's planned scope (CLI scaffold, errors, runner, JSON, progress,\nexit codes) needs std. Putting no_std on the seed would only be reverted\nwhen the first real module lands. Keep the file empty rather than carrying\na placeholder that misrepresents the intended shape.",
          "is_bot": false,
          "headline": "feat(rsomics-common): drop no_std attribute",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-13T17:25:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4abc2675129c5ce3cf03c675bda9a64e75161c19",
          "body": "Newer cargo (>=1.84) errors out on a virtual workspace with zero members,\nso .gitkeep alone is not enough to keep CI green. Seed rsomics-common —\nthe first foundation crate per CLAUDE.md's Layer A list — with empty\nno_std lib + manifest inheriting workspace package metadata. Forbids\nunsafe_code by default and turns on clippy::pedantic at warn level.",
          "is_bot": false,
          "headline": "feat(rsomics-common): seed Layer A foundation crate",
          "author_name": "Bengerthelorf",
          "author_login": "Bengerthelorf",
          "committed_at": "2026-05-13T15:21:30Z",
          "body_truncated": false,
          "is_coding_agent": false
        }
      ],
      "releases_count": 0,
      "commits_last_year": 51,
      "latest_release_at": null,
      "latest_release_tag": null,
      "releases_from_tags": false,
      "days_since_last_push": 0,
      "active_weeks_last_year": 6,
      "days_since_latest_release": null,
      "mean_days_between_releases": null
    },
    "community": {
      "has_readme": true,
      "has_license": true,
      "has_description": true,
      "has_contributing": false,
      "health_percentage": 50,
      "has_issue_template": false,
      "has_code_of_conduct": false,
      "has_pull_request_template": false
    },
    "ecosystem": {
      "packages": [
        {
          "name": "rsomics-common",
          "exists": true,
          "license": "MIT OR Apache-2.0",
          "keywords": [],
          "ecosystem": "crates",
          "matches_repo": true,
          "registry_url": "https://crates.io/crates/rsomics-common",
          "is_deprecated": false,
          "latest_version": "0.6.3",
          "repository_url": "https://github.com/omics-rust/rsomics-common",
          "versions_count": 9,
          "total_downloads": 8865,
          "dependents_count": null,
          "deprecation_note": null,
          "maintainers_count": null,
          "monthly_downloads": 2955,
          "first_published_at": "2026-05-14T13:03:48.733886Z",
          "latest_published_at": "2026-07-29T17:17:14.844825Z",
          "latest_version_yanked": false,
          "days_since_latest_publish": 0
        }
      ]
    },
    "popularity": {
      "forks": 0,
      "stars": 0,
      "watchers": 0,
      "fork_history": {
        "days": [],
        "complete": true,
        "collected": 0,
        "total_forks": 0
      },
      "star_history": {
        "days": [],
        "complete": true,
        "collected": 0,
        "total_stars": 0,
        "collected_at": null
      },
      "open_issues_and_prs": 0
    },
    "ai_readiness": {
      "has_nix": false,
      "example_dirs": [],
      "has_llms_txt": false,
      "has_dockerfile": false,
      "has_mcp_signal": false,
      "bootstrap_files": [],
      "api_schema_files": [],
      "has_devcontainer": false,
      "typecheck_configs": [],
      "toolchain_manifests": [
        "Cargo.toml"
      ],
      "largest_source_bytes": 9472,
      "source_files_sampled": 14,
      "oversized_source_files": 0,
      "agent_instruction_files": [],
      "agent_instruction_max_bytes": null
    },
    "dependencies": {
      "manifests": [
        "Cargo.toml"
      ],
      "advisories": {
        "error": null,
        "scope": null,
        "source": null,
        "findings": [],
        "collected": false,
        "malicious": [],
        "truncated": false,
        "by_severity": {},
        "advisory_count": 0,
        "affected_count": 0,
        "assessed_count": 0,
        "malicious_count": 0,
        "assessed_package": null,
        "unassessed_count": 0,
        "direct_affected_count": 0
      },
      "ecosystems": [
        "crates"
      ],
      "dependencies": [
        {
          "name": "thiserror",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "2"
        },
        {
          "name": "clap",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "4"
        },
        {
          "name": "serde",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "1"
        },
        {
          "name": "serde_json",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "1"
        },
        {
          "name": "flate2",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "1"
        },
        {
          "name": "rayon",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "1"
        },
        {
          "name": "toml",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "0.9"
        },
        {
          "name": "sha2",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "0.10"
        },
        {
          "name": "ureq",
          "manifest": "Cargo.toml",
          "ecosystem": "crates",
          "version_constraint": "3"
        }
      ],
      "all_dependencies": {
        "error": "GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository",
        "source": null,
        "packages": [],
        "collected": false,
        "truncated": false,
        "total_count": null,
        "direct_count": null,
        "indirect_count": null
      }
    },
    "maintainership": {
      "issues": {
        "open_prs": 0,
        "merged_prs": 0,
        "open_issues": 0,
        "closed_ratio": null,
        "closed_issues": 0,
        "closed_unmerged_prs": 0
      },
      "bus_factor": 1,
      "bot_contributors": 0,
      "top_contributors": [
        {
          "type": "User",
          "login": "Bengerthelorf",
          "commits": 52,
          "avatar_url": "https://avatars.githubusercontent.com/u/92011459?v=4"
        }
      ],
      "contributors_sampled": 1,
      "top_contributor_share": 1
    },
    "quality_signals": {
      "has_ci": true,
      "has_tests": true,
      "ci_workflows": [
        "ci.yml"
      ],
      "has_docs_dir": false,
      "linter_configs": [],
      "has_editorconfig": false,
      "has_linter_config": false,
      "has_precommit_config": false
    },
    "security_signals": {
      "lockfiles": [
        "Cargo.lock"
      ],
      "scorecard": {
        "checks": [
          {
            "name": "Binary-Artifacts",
            "score": 10,
            "reason": "no binaries found in the repo",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
          },
          {
            "name": "Branch-Protection",
            "score": 0,
            "reason": "branch protection not enabled on development/release branches",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
          },
          {
            "name": "CI-Tests",
            "score": null,
            "reason": "no pull request found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
          },
          {
            "name": "CII-Best-Practices",
            "score": 0,
            "reason": "no effort to earn an OpenSSF best practices badge detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#cii-best-practices"
          },
          {
            "name": "Code-Review",
            "score": 0,
            "reason": "Found 0/30 approved changesets -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
          },
          {
            "name": "Contributors",
            "score": 10,
            "reason": "project has 5 contributing companies or organizations",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
          },
          {
            "name": "Dangerous-Workflow",
            "score": 10,
            "reason": "no dangerous workflow patterns detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
          },
          {
            "name": "Dependency-Update-Tool",
            "score": 0,
            "reason": "no update tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
          },
          {
            "name": "Fuzzing",
            "score": 0,
            "reason": "project is not fuzzed",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
          },
          {
            "name": "License",
            "score": 10,
            "reason": "license file detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
          },
          {
            "name": "Maintained",
            "score": 0,
            "reason": "project was created within the last 90 days. Please review its contents carefully",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#maintained"
          },
          {
            "name": "Packaging",
            "score": null,
            "reason": "packaging workflow not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
          },
          {
            "name": "Pinned-Dependencies",
            "score": 0,
            "reason": "dependency not pinned by hash detected -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
          },
          {
            "name": "SAST",
            "score": 0,
            "reason": "no SAST tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
          },
          {
            "name": "Security-Policy",
            "score": 0,
            "reason": "security policy file not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
          },
          {
            "name": "Signed-Releases",
            "score": null,
            "reason": "no releases found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
          },
          {
            "name": "Token-Permissions",
            "score": 0,
            "reason": "detected GitHub workflow tokens with excessive permissions",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
          },
          {
            "name": "Vulnerabilities",
            "score": 8,
            "reason": "2 existing vulnerabilities detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
          }
        ],
        "commit": "1c51f7d0b356683697942d9c6a0f60585e0dc8a9",
        "ran_at": "2026-07-30T15:42:32Z",
        "aggregate_score": 3.2,
        "scorecard_version": "v5.5.0"
      },
      "has_codeql_workflow": false,
      "has_security_policy": false,
      "has_dependabot_config": false
    },
    "contribution_flow": {
      "collected": true,
      "ci_last_run_at": "2026-07-30T05:48:37Z",
      "oldest_open_prs": [],
      "last_merged_pr_at": null,
      "ci_last_conclusion": "SUCCESS",
      "oldest_open_issues": []
    }
  },
  "config": {
    "disabled_metrics": [],
    "disabled_categories": [],
    "disabled_components": {}
  },
  "source": {
    "url": "https://github.com/omics-rust/rsomics-common",
    "host": "github.com",
    "name": "rsomics-common",
    "owner": "omics-rust"
  },
  "metrics": {
    "overall": {
      "key": "overall",
      "band": "at_risk",
      "name": "Overall health",
      "note": null,
      "notes": [],
      "value": 39,
      "inputs": {
        "security": 32,
        "vitality": 34,
        "community": 32,
        "governance": 38,
        "engineering": 56
      },
      "components": []
    },
    "categories": [
      {
        "key": "vitality",
        "band": "at_risk",
        "name": "Vitality",
        "value": 34,
        "weight": 0.22,
        "metrics": [
          {
            "key": "development_activity",
            "band": "moderate",
            "name": "Development activity",
            "note": null,
            "notes": [],
            "value": 56,
            "inputs": {
              "commits_last_year": 51,
              "human_commit_share": 1,
              "days_since_last_push": 0,
              "active_weeks_last_year": 6
            },
            "components": [
              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 0 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "push_recency",
                    "params": {
                      "days": 0
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_cadence",
                "name": "Commit cadence",
                "detail": "6/52 weeks with commits",
                "points": 4.2,
                "status": "partial",
                "details": [
                  {
                    "code": "commit_cadence_weeks",
                    "params": {
                      "weeks": 6
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_volume",
                "name": "Commit volume",
                "detail": "51 commits in the last year",
                "points": 15.4,
                "status": "partial",
                "details": [
                  {
                    "code": "commits_last_year",
                    "params": {
                      "count": 51
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "project was created within the last 90 days. Please review its contents carefully",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "release_discipline",
            "band": "critical",
            "name": "Release discipline",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "openssf_scorecard_signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 1,
            "inputs": {
              "releases_count": 0
            },
            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "no releases published",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_releases_published",
                    "params": {}
                  }
                ],
                "max_points": 27
              },
              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "no releases",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_releases",
                    "params": {}
                  }
                ],
                "max_points": 36
              },
              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "no releases",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_releases",
                    "params": {}
                  }
                ],
                "max_points": 27
              },
              {
                "key": "openssf_scorecard_signed_releases",
                "name": "OpenSSF Scorecard: Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              }
            ]
          },
          {
            "key": "abandonment",
            "band": "excellent",
            "name": "Abandonment",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "cap": null,
              "state": "unverified",
              "guards": [],
              "signals": [],
              "red_flag": false,
              "multiplier_pct": 100,
              "declared_reason": null,
              "unverified_reason": "repository_too_young",
              "unanswered_open_prs": null,
              "unanswered_open_issues": null,
              "days_since_last_merged_pr": null,
              "days_since_last_human_commit": null,
              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "maintenance record not established from the collected data",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_unverified",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "at_risk",
        "name": "Community & Adoption",
        "value": 32,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "critical",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 1,
            "inputs": {
              "forks": 0,
              "stars": 0,
              "watchers": 0,
              "growth_state": "unverified",
              "growth_factor_pct": 100,
              "growth_unverified_reason": "no_history"
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "0 stars",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 0
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "0 forks",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 0
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "0 watchers",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 0
                    }
                  }
                ],
                "max_points": 15
              }
            ]
          },
          {
            "key": "community_health",
            "band": "moderate",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 50,
            "inputs": {
              "has_readme": true,
              "has_license": true,
              "has_contributing": false,
              "has_issue_template": false,
              "has_code_of_conduct": false,
              "has_pull_request_template": false
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 22.5,
                "status": "met",
                "details": [],
                "max_points": 22.5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "recognized license (Apache-2.0)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "Apache-2.0"
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 18
              },
              {
                "key": "code_of_conduct",
                "name": "Code of conduct",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 13.5
              },
              {
                "key": "issue_template",
                "name": "Issue template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.2
              },
              {
                "key": "pr_template",
                "name": "PR template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.3
              }
            ]
          },
          {
            "key": "ecosystem_adoption",
            "band": "moderate",
            "name": "Ecosystem adoption (downloads)",
            "note": "Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "registry_dependents"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 58,
            "inputs": {
              "packages": [
                "rsomics-common"
              ],
              "dependents": null,
              "ecosystems": "crates",
              "total_downloads": 8865,
              "monthly_downloads": 2955
            },
            "components": [
              {
                "key": "monthly_downloads",
                "name": "Monthly downloads",
                "detail": "2,955 downloads/month across crates",
                "points": 46.3,
                "status": "partial",
                "details": [
                  {
                    "code": "downloads_monthly",
                    "params": {
                      "count": 2955,
                      "ecosystems": "crates"
                    }
                  }
                ],
                "max_points": 80
              },
              {
                "key": "registry_dependents",
                "name": "Registry dependents",
                "detail": "not reported by this ecosystem",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "not_reported_by_this_ecosystem",
                    "params": {}
                  }
                ],
                "max_points": 20
              }
            ]
          }
        ],
        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
      },
      {
        "key": "governance",
        "band": "at_risk",
        "name": "Sustainability & Governance",
        "value": 38,
        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
            "band": "critical",
            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 20,
            "inputs": {
              "bus_factor": 1,
              "contributors_sampled": 1,
              "top_contributor_share": 1
            },
            "components": [
              {
                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "1 contributor(s) cover half of all commits",
                "points": 9,
                "status": "partial",
                "details": [
                  {
                    "code": "bus_factor",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 54
              },
              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 100% of commits",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "1 contributors",
                "points": 1.4,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 5 contributing companies or organizations",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "critical",
            "name": "Issue & PR responsiveness",
            "note": "Excluded from scoring (no data or not applicable): Issue resolution, PR acceptance. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "issue_resolution",
                    "pr_acceptance"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 1,
            "inputs": {
              "merged_prs": 0,
              "open_issues": 0,
              "closed_issues": 0,
              "issue_closed_ratio": null,
              "closed_unmerged_prs": 0
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "no issues or no data",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_issues_or_data",
                    "params": {}
                  }
                ],
                "max_points": 46.75
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "no decided pull requests or no data",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_decided_prs_or_data",
                    "params": {}
                  }
                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 0/30 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              }
            ]
          },
          {
            "key": "stewardship",
            "band": "at_risk",
            "name": "Ownership & stewardship",
            "note": null,
            "notes": [],
            "value": 47,
            "inputs": {
              "followers": 10,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "omics-rust",
              "public_repos": 17,
              "account_age_days": 71
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "organization-owned",
                "points": 30,
                "status": "met",
                "details": [
                  {
                    "code": "owner_organization",
                    "params": {}
                  }
                ],
                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "owner_reach",
                "name": "Owner reach",
                "detail": "10 followers of omics-rust",
                "points": 7.5,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 10,
                      "login": "omics-rust"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "17 public repos, account ~0 yr old",
                "points": 9.5,
                "status": "partial",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 17
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 0
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "packages": [
                "rsomics-common"
              ],
              "ecosystems": "crates",
              "any_deprecated": false,
              "min_days_since_publish": 0
            },
            "components": [
              {
                "key": "published_resolvable",
                "name": "Published & resolvable",
                "detail": "1 package(s) on crates",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "packages_published",
                    "params": {
                      "count": 1,
                      "ecosystems": "crates"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "publish_recency",
                "name": "Publish recency",
                "detail": "latest publish 0 days ago",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "publish_recency",
                    "params": {
                      "days": 0
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "version_history",
                "name": "Version history",
                "detail": "9 published versions",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "published_versions",
                    "params": {
                      "count": 9
                    }
                  }
                ],
                "max_points": 20
              },
              {
                "key": "not_deprecated",
                "name": "Not deprecated",
                "detail": "active, not deprecated or yanked",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "package_not_deprecated",
                    "params": {}
                  }
                ],
                "max_points": 20
              }
            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "moderate",
        "name": "Engineering Quality",
        "value": 56,
        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
            "band": "moderate",
            "name": "Engineering practices",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: CI-Tests. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "openssf_scorecard_ci_tests"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 60,
            "inputs": {
              "has_ci": true,
              "has_tests": true,
              "has_editorconfig": false,
              "has_linter_config": false,
              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "1 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 24,
                "status": "met",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
                "name": "Linter config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 16
              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 9.6
              },
              {
                "key": "editorconfig",
                "name": ".editorconfig",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.4
              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
                "detail": "no pull request found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "moderate",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 50,
            "inputs": {
              "topics": [],
              "has_wiki": true,
              "homepage": null,
              "has_readme": true,
              "has_docs_dir": false,
              "has_description": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 30,
                "status": "met",
                "details": [],
                "max_points": 30
              },
              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "repository_description",
                "name": "Repository description",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "at_risk",
        "name": "Security",
        "value": 32,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): CI-Tests, Packaging, Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "ci_tests",
                    "packaging",
                    "signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 32,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 15,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 3,
              "scorecard_aggregate": 3.2
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "no binaries found in the repo",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "branch_protection",
                "name": "Branch-Protection",
                "detail": "branch protection not enabled on development/release branches",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "no pull request found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 0/30 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 5 contributing companies or organizations",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no dangerous workflow patterns detected",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "no update tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "project was created within the last 90 days. Please review its contents carefully",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow not detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "no SAST tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "2 existing vulnerabilities detected",
                "points": 6,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
              ],
              "review_only_matches": 0,
              "assessed_self_published_locations": 1
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "moderate",
        "name": "AI Readiness",
        "value": 58,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "at_risk",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 1,
              "agent_instruction_files": [],
              "agent_instruction_max_bytes": null
            },
            "components": [
              {
                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "no CLAUDE.md / AGENTS.md / editor rules",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_instructions",
                    "params": {}
                  }
                ],
                "max_points": 45
              },
              {
                "key": "machine_readable_docs_llms_txt",
                "name": "Machine-readable docs (llms.txt)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "legible_commit_history",
                "name": "Legible commit history",
                "detail": "52 of 52 human commits state their intent (structured subject or explanatory body)",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 52,
                      "sampled": 52
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "moderate",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 56,
            "inputs": {
              "has_nix": false,
              "has_tests": true,
              "lockfiles": [
                "Cargo.lock"
              ],
              "has_dockerfile": false,
              "typed_language": true,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [],
              "agent_commit_share": 0,
              "toolchain_manifests": [
                "Cargo.toml"
              ],
              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": "Cargo.toml (toolchain convention, no task runner)",
                "points": 12.6,
                "status": "partial",
                "details": [
                  {
                    "code": "toolchain_convention",
                    "params": {
                      "files": "Cargo.toml"
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 22,
                "status": "met",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": "Rust (statically typed)",
                "points": 11,
                "status": "met",
                "details": [
                  {
                    "code": "statically_typed_language",
                    "params": {
                      "language": "Rust"
                    }
                  }
                ],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": "lockfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "lockfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "no agent-authored commits among the last 52",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_authored_commits",
                    "params": {
                      "sampled": 52
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "excellent",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "primary_language": "Rust",
              "largest_source_bytes": 9472,
              "source_files_sampled": 14,
              "oversized_source_files": 0
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Rust (statically typed)",
                "points": 45,
                "status": "met",
                "details": [
                  {
                    "code": "statically_typed_language",
                    "params": {
                      "language": "Rust"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "0/14 source files over 60KB",
                "points": 55,
                "status": "met",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 14,
                      "oversized": 0
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [
    "GitHub dependency-graph SBOM unavailable (404); the dependency graph may be disabled for this repository",
    "deps.dev does not index crates:rsomics-common@0.6.3; advisories assessed against the repository dependency graph instead"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-30T15:42:37.443761Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/o/omics-rust/rsomics-common.svg",
  "full_name": "omics-rust/rsomics-common",
  "license_state": "standard",
  "license_spdx": "Apache-2.0"
}