omics-rust / rsomics-common

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      "description": "Shared primitives for every rsomics-* crate (errors, CLI scaffold, runner, progress, exit codes).",
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          "headline": "chore(common): correct package repository",
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          "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.",
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          "headline": "chore: bump rsomics-common to 0.6.0 (adds Tool trait)",
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          "headline": "chore: strict comment sweep — foundation + formats (bcmr bar)",
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          "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).",
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          "headline": "refactor(workspace): aggressive comment-density cleanup to bcmr standard",
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          "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.",
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          "headline": "feat(rsomics-stats): scaffold Layer A 0.1.0",
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          "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.",
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          "headline": "docs: workspace comment-density sweep — bcmr style",
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          "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",
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          "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",
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          "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 + …",
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          "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",
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          "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…",
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          "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.",
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          "headline": "fix(rsomics-fastq-trim): drop short `-t`/`-T` aliases (collide with -…",
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          "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…",
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          "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",
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          "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",
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          "committed_at": "2026-05-14T17:12:41Z",
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        {
          "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",
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          "committed_at": "2026-05-14T16:53:51Z",
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          "headline": "docs(rsomics-common): flatten-placement rule on CommonFlags",
          "author_name": "Bengerthelorf",
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          "committed_at": "2026-05-14T16:41:45Z",
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          "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",
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        {
          "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",
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          "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,
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        },
        {
          "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",
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        },
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          "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",
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          "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",
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          "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",
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          "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",
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          "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",
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        },
        {
          "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",
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          "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",
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          "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",
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          "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",
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          "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",
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          "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",
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          "body": null,
          "is_bot": false,
          "headline": "feat(rsomics-common): quiet-aware stderr writer",
          "author_name": "Bengerthelorf",
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          "headline": "feat(rsomics-common): CommonFlags clap-derive scaffold",
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          "headline": "feat(rsomics-common): ExitCode enum mapping RsomicsError to process exit",
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          "headline": "feat(rsomics-common): RsomicsError type + Result alias",
          "author_name": "Bengerthelorf",
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          "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",
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          "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",
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          "is_bot": false,
          "headline": "feat(rsomics-common): seed Layer A foundation crate",
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            "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"
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  "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
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                  }
                ],
                "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
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                  }
                ],
                "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
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                  }
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                "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
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            ]
          },
          {
            "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",
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                  "components": [
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              },
              {
                "code": "weights_renormalized",
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            ],
            "value": 1,
            "inputs": {
              "releases_count": 0
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            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "no releases published",
                "points": 0,
                "status": "missed",
                "details": [
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                    "code": "no_releases_published",
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                ],
                "max_points": 27
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              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "no releases",
                "points": 0,
                "status": "missed",
                "details": [
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                    "code": "no_releases",
                    "params": {}
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                ],
                "max_points": 36
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              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "no releases",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_releases",
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                ],
                "max_points": 27
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              {
                "key": "openssf_scorecard_signed_releases",
                "name": "OpenSSF Scorecard: Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
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                    "code": "no_data",
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                ],
                "max_points": 10
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            ]
          },
          {
            "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
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            "components": [
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                "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
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            ]
          }
        ],
        "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"
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            "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": [
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              ],
              "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
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            "components": [
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                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "1 contributor(s) cover half of all commits",
                "points": 9,
                "status": "partial",
                "details": [
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                    "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": [
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                    "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
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                ],
                "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"
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                }
              },
              {
                "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": [
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                    "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"
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                  }
                ],
                "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
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                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 0
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                  }
                ],
                "max_points": 25
              }
            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "packages": [
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              ],
              "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"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "publish_recency",
                "name": "Publish recency",
                "detail": "latest publish 0 days ago",
                "points": 35,
                "status": "met",
                "details": [
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                ],
                "max_points": 35
              },
              {
                "key": "version_history",
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                "detail": "9 published versions",
                "points": 20,
                "status": "met",
                "details": [
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                    "code": "published_versions",
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                ],
                "max_points": 20
              },
              {
                "key": "not_deprecated",
                "name": "Not deprecated",
                "detail": "active, not deprecated or yanked",
                "points": 20,
                "status": "met",
                "details": [
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                ],
                "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": [
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            "key": "engineering_practices",
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            "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": {
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                }
              },
              {
                "code": "weights_renormalized",
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            ],
            "value": 60,
            "inputs": {
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              "has_editorconfig": false,
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            "components": [
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                "key": "ci_workflows",
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                "detail": "1 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
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                    "code": "ci_workflows",
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                ],
                "max_points": 24
              },
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                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 24,
                "status": "met",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
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}