fishkabio / seqio

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      "description": "Sequencing file parsers and writers for bioinformatics data",
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          "oid": "051d5621fbcf991f5185852e29a140e78b1ad11e",
          "body": "….10.0\n\nresolveGenbankLocation() turns a parsed location AST into 0-based half-open\nsegments in reading order, handling complement (which reverses order and flips\nstrand), join/order, between-boundaries, fuzzy positions, origin-spanning ranges\non circular molecules, and out-of-bounds clamping; unknown operators and remote\nreferences resolve to nothing rather than to untrustworthy geometry.\n\nThe bump also carries the ABIF UTF-8 string decoding from the previous commit.",
          "is_bot": false,
          "headline": "genbank: resolve location expressions to concrete coordinates; bump 0…",
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          "oid": "cbbf8382e319cd37e434d675dd5d426b44c0f549",
          "body": "ABIF fixes no encoding for char/pString/cString, and instruments write their\nlocale: the Nanofor-05 stores cyrillic run metadata as UTF-8, which the previous\nbyte-per-character reading turned into mojibake. decodeAbifText() tries strict\nUTF-8 first and falls back to the old Latin-1 reading, so existing files are\nunaffected; encodeAbifText() is its counterpart for writers. Trailing NULs are\nnow trimmed off the payload before decoding rather than off the decoded string.",
          "is_bot": false,
          "headline": "abif: read string tags as UTF-8 when the bytes are valid UTF-8",
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          "body": "…ns, references); bump 0.8.4\n\nAdd parseGenbankDocument with a full flat-file model (LOCUS, DEFINITION,\nACCESSION/VERSION, DBLINK, SOURCE/ORGANISM, REFERENCE, FEATURES with an\nINSDC location parser, ORIGIN, BASE COUNT) plus recoverable diagnostics.\n\nFix two bugs found while reviewing the implementati\n[…]\nT,\n  PRIMARY, ...); reference subfields are distinguished by indentation.\n- missing-record-terminator diagnostics anchor to the unterminated record\n  so per-record filtering attributes them correctly.",
          "is_bot": false,
          "headline": "genbank: parse GenBank/GenPept documents (metadata, features, locatio…",
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          "committed_at": "2026-07-11T03:29:35Z",
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          "oid": "a53745ad0a9e303fa3f28872b1edb9aad49d5845",
          "body": "…0.8.3\n\n- hasPdbSignal: window scan for a definitive PDB record (ATOM/HETATM with an x/y/z coordinate\n  triplet, SEQRES with optional blank chain, or CRYST1 unit-cell), firing only when the first line\n  is unclassifiable — catches bare-MODEL and I-TASSER 'HEADER protein' coordinate files\n- hasGffFas\n[…]\nected as gff\n- signatures use [ \\t] (not \\s) inter-field so they stay within one line; codex-reviewed\n- sweep of ~10500 UGENE fixtures: pdb 37->41 detected/39 parsed, gff 51->53/16, no false positives",
          "is_bot": false,
          "headline": "detect: recognize coordinate/SEQRES-led PDB and headerless GFF; bump …",
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          "committed_at": "2026-07-10T19:00:38Z",
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          "oid": "8c173e1cfc9bac8906591bcb7736ac828f6da6e1",
          "body": "- MEGA (.meg): #mega header, !directives, #Name residue rows (interleaved), \"...\" comments stripped\n- PDB (.pdb): SEQRES chains, with an ATOM/HETATM first-model fallback for coordinate-only files\n  (HETATM gated to a polymer/modified-residue whitelist: MSE etc., excluding ligands/ions/solvent)\n- ACE\n[…]\n Staden chromatograms (v2 AoS / v3 SoA layouts)\n- detect: coordinate-led PDB, #mega, AS-header ACE signatures\n- validated against UGENE _common_data fixtures (20/20 scf, 35/39 pdb detected, 28/31 ace)",
          "is_bot": false,
          "headline": "Add MEGA, PDB, ACE and SCF sequence readers; bump 0.8.2",
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          "body": "…tion\n\nparseMsf: drop the numeric position-ruler / coordinate lines GCG & GeneDoc\ninterleave between blocks (they carried digits, so were turning into bogus\n\"1\"/\"50\" records). A row is kept iff its residue field is digit-free — lenient\n(genuine rows survive even if Name: labels were truncated) and n\n[…]\nMUSCLE/… banner. Verified on UGENE's 17-file _common_data MSF corpus (lipid8,\nPileUp, GeneDoc-preamble, header-mangled all parse clean; garbage/negative file\nstays unknown). +7 unit tests (203 total).",
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          "headline": "msf: read GeneDoc/PileUp variants; skip position rulers; robust detec…",
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          "headline": "Bump @fishka/seqio to 0.8.0 (sam/bam/gfa readers)",
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          "oid": "9f4a8172c734730aaa9b9865fdffbac4373a3002",
          "body": "parseBam reads inflated BAM bytes (caller peels BGZF/gzip; DecompressionStream decodes\nBGZF's concatenated members). Parses the header ref table (fully bounds-checked against\nmalformed/huge headers) then alignment records: decodes the 4-bit-packed SEQ, maps\nrefID→RNAME, and applies the same rules as\n[…]\nnient: bounded loops + try/catch return partial results, never throw/hang.\nSAM reader refactored onto the shared common.ts. Reviewed with codex (offsets, 4-bit\ndecode, and the header-parse DoS guard).",
          "is_bot": false,
          "headline": "bam: binary BAM reader (parseBam), sharing SAM record semantics",
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          "body": "parseSam: read sequence (SAM field 10) per alignment; skip '@' headers, SEQ='*', and\nsecondary(0x100)/supplementary(0x800) alignments so it yields one sequence per read;\nid = QNAME (+ /1,/2 for paired mates); description = 'RNAME:POS (+/-)' or 'unmapped';\nreverse-strand SEQ stored verbatim (referenc\n[…]\nGFA2 (S sid len seq); skip '*'.\ndetectFormat: +sam/+bam/+gfa — BAM 'BAM\\1' magic (post-inflate), SAM header/headerless\n(11-field CIGAR heuristic), GFA H-version/headerless S-line. Reviewed with codex.",
          "is_bot": false,
          "headline": "sam, gfa: sequence readers + content detection",
          "author_name": "fishka.bio",
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          "headline": "Bump version to 0.7",
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          "body": "Add read-only sequence extractors, all lenient (never throw) and multi-record,\nreturning a uniform SeqRecord {id, description?, sequence}:\n\n- FASTA/FASTQ parsers (parseFasta/parseFastq); fastx split into src/fastx/ with\n  the codec in fastx-format.ts and record types in types.ts\n- GenBank/GenPept (p\n[…]\nextension\n\nShared helpers in src/text.ts and the SeqRecord model in src/seq-record.ts.\n181 Jest tests with real-world fixtures. AGENTS.md: leniency, multi-record, and\ndetection conventions documented.",
          "is_bot": false,
          "headline": "feat: sequence readers for text formats + content-based format detection",
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          "committed_at": "2026-07-10T03:54:24Z",
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          "body": "upsertEntry appended new tags with entries.push(), leaving the directory\nunsorted after a basecaller adds PBAS2/PCON2/PLOC2/DATA9..12. The ABIF\nspec prescribes a directory sorted by (tagName, tagNumber), and readers\nthat binary-search it — notably Chromas — silently miss a tag placed out\nof order: a\n[…]\n;\nensureRawDataChannels() uses it directly to copy DATA1..4 -> DATA9..12\nwith their payload/shape intact (upsertEntry's count*size check would\nreject a tolerated desynced source). Bump 0.6.0 -> 0.6.1.",
          "is_bot": false,
          "headline": "fix(abif): insert new directory entries sorted by (tagName, tagNumber)",
          "author_name": "fishka.bio",
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          "headline": "Release v0.6.0",
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          "committed_at": "2026-07-07T03:53:08Z",
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          "oid": "4813d3d98812744db33f81a01303dd65c40ac6dc",
          "body": "start/end is a half-open sample range in the processed (DATA9..12)\ndomain -- the only domain PLOC maps into. DATA9..12 are sliced\nexactly by that range (rejecting a range past the shortest channel's\nlength, rather than silently clamping it into an inconsistent state).\nDATA1..4/5..8 have no honest co\n[…]\nequenceForVersion/getConfidencesForVersion/getPositionsForVersion\nto the view layer (the existing preferred-version getters now delegate\nto them) so per-version basecall data has a single decode path.",
          "is_bot": false,
          "headline": "Add cropAbif: crop an ABIF file to a DATA9..12 sample range",
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          "headline": "Release v0.5.0",
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          "body": "Rename raw.ts to abif-format.ts and document the raw/domain layered\ndesign as a convention for future formats (AGENTS.md).\n\nwriteAbif now reproduces the original file byte-for-byte when nothing\nwas changed, and keeps every untouched entry at its exact original\noffset when something else is mutated -\n[…]\no longer\ncombine new fields with a stale on-disk shape, and the anchor now\naccounts for the directory's physical size even when a file's declared\ntdir.dataSize is desynced from its actual entry count.",
          "is_bot": false,
          "headline": "Make writeAbif byte-exact on an unmodified round-trip",
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          "headline": "Refresh README API overview",
          "author_name": "fishka.bio",
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          "committed_at": "2026-07-03T22:49:49Z",
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          "headline": "Add Ko-fi funding link",
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          "headline": "Link README to fishka.bio",
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          "headline": "Use GitHub repository URL",
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          "oid": "a25536a59087bb6131b817b9b4e2caeb405a4dce",
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          "headline": "Update repository URL",
          "author_name": "fishka.bio",
          "author_login": "fishkabio",
          "committed_at": "2026-07-03T21:50:38Z",
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          "headline": "Update package description",
          "author_name": "fishka.bio",
          "author_login": "fishkabio",
          "committed_at": "2026-07-03T21:31:25Z",
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          "body": "Turn readAbif into a faithful 1:1 reader and keep parseAbif as the\ninterpreting convenience layer. Breaking public API (0.x → minor bump).\n\nRaw structure (readAbif):\n- every basecall version exposed via baseCallVariants (called/edited by\n  tag number, sequence case preserved); no \"preferred = ground\n[…]\n90 tests incl. exact per-fixture\nlocks (tdir, DATA ranges, PBAS/PCON/PLOC, FWO, RevC, gaps).\n\nContract: meaning-lossless + robust read now; byte-exact layout-preserving\nwriter remains a future opt-in.",
          "is_bot": false,
          "headline": "ABIF: expose full raw file structure, facts not verdicts (0.4.0)",
          "author_name": "fishka.bio",
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          "committed_at": "2026-07-03T02:51:24Z",
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          "oid": "45511ec9504a5d4e74c27ca30da03ec9dd53bb9f",
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          "headline": "Add FASTA support",
          "author_name": "fishka.bio",
          "author_login": "fishkabio",
          "committed_at": "2026-06-29T17:41:08Z",
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          "oid": "f099a0a2c345cd7a83ca5d0ea78ebcdf50cb394a",
          "body": "The old names were misleading. Per the ABIF spec:\n\n  - DATA1..4  are POST-PROCESSED traces (mobility-corrected, baseline-\n                subtracted, color-separated) on modern KB-basecaller-aware\n                instruments. On older instruments DATA1..4 IS the raw signal.\n  - DATA9..12 are RAW flu\n[…]\n longer\npretends to know which block the caller wants. hasProcessedTraces()\nremains as the helper for detecting modern (both-blocks-present) files.\n\nBreaking change → minor bump (we are still on 0.x).",
          "is_bot": false,
          "headline": "Rename basecalled/raw to data1To4/data9To12 (0.2.0)",
          "author_name": "fishka.bio",
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          "committed_at": "2026-05-29T15:25:26Z",
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          "oid": "ac7016f0c0c049197571a0d8186d8c11cb20d55a",
          "body": "The published package now contains only minified output:\n\n  dist/index.{mjs,js}        ESM + CJS, minified, ~12K each\n  dist/abif/index.{mjs,js}   subpath entry, minified\n  dist/*.d.{ts,mts}          generated type declarations\n\nWhat changed\n- Replaced dual-tsc setup (tsconfig.esm.json + tsconfig.cj\n[…]\nnode\"]` because TS 6 + bundler resolution\n  no longer auto-discovers @types/*.\n\nVerification: typecheck clean, 22/22 tests pass, lint clean,\nbuild produces minified .mjs/.js and matching .d.ts/.d.mts.",
          "is_bot": false,
          "headline": "Switch to tsup for minified ESM/CJS + .d.ts build",
          "author_name": "fishka.bio",
          "author_login": "fishkabio",
          "committed_at": "2026-05-29T14:36:29Z",
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          "body": "Copy AGENTS.md / CLAUDE.md and the .agents/.claude/.factory directories\nfrom the mitoseq repo, rewriting the prose to describe this library\n(scope, layered design, dev commands, browser-compat constraint).\n\neslint.config.js is a slim variant of mitoseq's: drops the workspace-\nspecific no-restricted-\n[…]\nd abif-spec.json overrides that\ndon't apply here. prettier-plugin-organize-imports added.\n\nCI sanity:\n- npm run lint  → clean\n- npm test      → 22/22 pass\n- npm run build → ESM + CJS dist/ regenerated",
          "is_bot": false,
          "headline": "Add agent configs, linter and formatter",
          "author_name": "fishka.bio",
          "author_login": "fishkabio",
          "committed_at": "2026-05-29T14:14:24Z",
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          "oid": "2703137ce18d89d1d321f52a6f84b33b2c73685e",
          "body": "Bring up a new sequencing-I/O library to consolidate the four diverged ABIF\nparsers (abifviewer, mitoseq/formats, hiv/common/bio, basecaller-universal)\ninto a single browser- and Node-compatible package.\n\nLayout\n- src/abif/raw.ts    low-level read/write, lossless round-trip\n- src/abif/view.ts   type\n[…]\ne support\n\nTests (22) cover round-trip preservation, BioPython A_forward fixture\nedge case, raw-trace (no PBAS) handling, setter round-trip, and\nhigh-level parseAbif consistency on both fixture types.",
          "is_bot": false,
          "headline": "Initial @fishka/seqio with ABIF parser",
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            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
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            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
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            "reason": "no pull request found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
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            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
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            "reason": "no workflows found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
          },
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            "reason": "no update tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
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          {
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            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
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            "reason": "license file detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
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            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
          },
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            "reason": "no dependencies found",
            "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"
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          {
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            "reason": "security policy file not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
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          {
            "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",
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            "reason": "No tokens found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
          },
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            "name": "Vulnerabilities",
            "score": 5,
            "reason": "5 existing vulnerabilities detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
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      "ci_last_run_at": null,
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      "key": "overall",
      "band": "at_risk",
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      "note": null,
      "notes": [],
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      "inputs": {
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      "components": []
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    "categories": [
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        "key": "vitality",
        "band": "critical",
        "name": "Vitality",
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        "weight": 0.22,
        "metrics": [
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            "note": null,
            "notes": [],
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              "commits_last_year": 28,
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              "days_since_last_push": 8,
              "active_weeks_last_year": 5
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              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 8 days ago",
                "points": 28.8,
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              {
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                "name": "Commit cadence",
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                "points": 3.5,
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                "name": "OpenSSF Scorecard: Maintained",
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                "points": 0,
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                "details": [],
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            "notes": [
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        "weight": 0.18,
        "metrics": [
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            "note": null,
            "notes": [],
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              "growth_state": "unverified",
              "growth_factor_pct": 100,
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            "components": [
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                "points": 0,
                "status": "missed",
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                ],
                "max_points": 60
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              {
                "key": "forks",
                "name": "Forks",
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                "points": 0,
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                "max_points": 25
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              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "0 watchers",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "watchers",
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                  }
                ],
                "max_points": 15
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            ]
          },
          {
            "key": "community_health",
            "band": "moderate",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 50,
            "inputs": {
              "has_readme": true,
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              "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",
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                "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"
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                "max_points": 22.5
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              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 0,
                "status": "missed",
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              },
              {
                "key": "code_of_conduct",
                "name": "Code of conduct",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
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              },
              {
                "key": "issue_template",
                "name": "Issue template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.2
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              {
                "key": "pr_template",
                "name": "PR template",
                "detail": null,
                "points": 0,
                "status": "missed",
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                "max_points": 6.3
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          },
          {
            "key": "ecosystem_adoption",
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            "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": [
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                }
              },
              {
                "code": "weights_renormalized",
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            ],
            "value": 66,
            "inputs": {
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              "dependents": null,
              "ecosystems": "npm",
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              "monthly_downloads": 9601
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            "components": [
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                "key": "monthly_downloads",
                "name": "Monthly downloads",
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                "points": 53.1,
                "status": "partial",
                "details": [
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                    "code": "downloads_monthly",
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                      "count": 9601,
                      "ecosystems": "npm"
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                  }
                ],
                "max_points": 80
              },
              {
                "key": "registry_dependents",
                "name": "Registry dependents",
                "detail": "not reported by this ecosystem",
                "points": 0,
                "status": "excluded",
                "details": [
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                    "code": "not_reported_by_this_ecosystem",
                    "params": {}
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                ],
                "max_points": 20
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            ]
          }
        ],
        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
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      {
        "key": "governance",
        "band": "critical",
        "name": "Sustainability & Governance",
        "value": 28,
        "weight": 0.24,
        "metrics": [
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            "note": null,
            "notes": [],
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            "inputs": {
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              "contributors_sampled": 1,
              "top_contributor_share": 1
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            "components": [
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                "key": "bus_factor",
                "name": "Bus factor",
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                "status": "partial",
                "details": [
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                ],
                "max_points": 54
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              {
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                "detail": "top contributor authored 100% of commits",
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                "status": "missed",
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                    "code": "top_contributor_share",
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                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "1 contributors",
                "points": 1.4,
                "status": "partial",
                "details": [
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                    "code": "contributors_sampled",
                    "params": {
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                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 0 contributing companies or organizations -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
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            ]
          },
          {
            "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": [
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                }
              },
              {
                "code": "weights_renormalized",
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            ],
            "value": 1,
            "inputs": {
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              "issue_closed_ratio": null,
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            "components": [
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                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "no issues or no data",
                "points": 0,
                "status": "excluded",
                "details": [
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                    "code": "no_issues_or_data",
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                ],
                "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",
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                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 0/28 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
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            ]
          },
          {
            "key": "stewardship",
            "band": "critical",
            "name": "Ownership & stewardship",
            "note": "Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
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              },
              {
                "code": "weights_renormalized",
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            "value": 21,
            "inputs": {
              "followers": 0,
              "owner_type": "User",
              "is_verified": null,
              "owner_login": "fishkabio",
              "public_repos": 7,
              "account_age_days": 29
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "personal (user) account",
                "points": 10,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_personal",
                    "params": {}
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                ],
                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": "not applicable to user accounts",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "not_applicable_to_user_accounts",
                    "params": {}
                  }
                ],
                "max_points": 20
              },
              {
                "key": "owner_reach",
                "name": "Owner reach",
                "detail": "0 followers of fishkabio",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 0,
                      "login": "fishkabio"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "7 public repos, account ~0 yr old",
                "points": 6.7,
                "status": "partial",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 7
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                  },
                  {
                    "code": "account_age_years",
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                      "years": 0
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                  }
                ],
                "max_points": 25
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            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "packages": [
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              "ecosystems": "npm",
              "any_deprecated": false,
              "min_days_since_publish": 8
            },
            "components": [
              {
                "key": "published_resolvable",
                "name": "Published & resolvable",
                "detail": "1 package(s) on npm",
                "points": 25,
                "status": "met",
                "details": [
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                      "count": 1,
                      "ecosystems": "npm"
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                ],
                "max_points": 25
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              {
                "key": "publish_recency",
                "name": "Publish recency",
                "detail": "latest publish 8 days ago",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "publish_recency",
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                      "days": 8
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                ],
                "max_points": 35
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              {
                "key": "version_history",
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                "detail": "15 published versions",
                "points": 20,
                "status": "met",
                "details": [
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                    "code": "published_versions",
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                "max_points": 20
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              {
                "key": "not_deprecated",
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                "detail": "active, not deprecated or yanked",
                "points": 20,
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                "max_points": 20
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            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "moderate",
        "name": "Engineering Quality",
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        "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",
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                "points": 24,
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              {
                "key": "linter_config",
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                "points": 16,
                "status": "met",
                "details": [
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                "key": "pre_commit_hooks",
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                "status": "missed",
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              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
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                "max_points": 20
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            ]
          },
          {
            "key": "documentation",
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            "name": "Documentation",
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            "notes": [],
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            "inputs": {
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              "homepage": "https://fishka.bio",
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            "components": [
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                "key": "readme",
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                "key": "documentation_directory",
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              {
                "key": "documentation_homepage_site",
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                "detail": "https://fishka.bio",
                "points": 15,
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                "detail": null,
                "points": 10,
                "status": "met",
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                "max_points": 10
              },
              {
                "key": "topics",
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                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
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                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "critical",
        "name": "Security",
        "value": 20,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
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            "note": "Excluded from scoring (no data or not applicable): CI-Tests, Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.",
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                "code": "excluded_no_data",
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                "key": "binary_artifacts",
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                "key": "branch_protection",
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                "points": 0,
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                "key": "code_review",
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                "key": "dangerous_workflow",
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                "key": "fuzzing",
                "name": "Fuzzing",
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                "key": "maintained",
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                "points": 0,
                "status": "missed",
                "details": [],
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                "key": "packaging",
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                "max_points": 5
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                "key": "pinned_dependencies",
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                ],
                "max_points": 5
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              {
                "key": "sast",
                "name": "SAST",
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                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
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                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
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              {
                "key": "signed_releases",
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                "points": 0,
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                "details": [
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                    "code": "no_data",
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                  }
                ],
                "max_points": 7.5
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                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "No tokens found",
                "points": 0,
                "status": "excluded",
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                    "code": "no_data",
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                  }
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                "max_points": 7.5
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                "points": 3.8,
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            "key": "high_risk_jurisdiction_exposure",
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            "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.",
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                "code": "jurisdiction_evidence_limits",
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            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
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              "review_only_matches": 0,
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                "key": "policy_exposure_multiplier",
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                "points": 100,
                "status": "met",
                "details": [
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                    "code": "jurisdiction_no_match",
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                "max_points": 100
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        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
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            "inputs": {
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                "key": "machine_readable_docs_llms_txt",
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                "status": "missed",
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            "notes": [
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                "code": "excluded_no_data",
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}