mcvickerlab / GenVarLoader

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Jeder Punkt umfasst 4 Tage.

Vollständig aufgelöster Abhängigkeitssatz aus dem GitHub-Abhängigkeitsgraphen: 45 direkte und 311 indirekte (transitive) Pakete. Die transitive Hülle ist vollständig, wenn das Repository eine Lockfile eincheckt.

Dieses Repository veröffentlicht kein vom Index auflösbares Paket, daher wurde sein eigener Abhängigkeitsgraph bewertet – 321 Pakete, darunter auch Entwicklungs- und Test-Pins, die nie ausgeliefert werden: 17 tragen bekannte Advisories, davon 4 direkte. 35 konnten nicht bewertet werden – keine aufgelöste Version, ein nicht unterstütztes Ökosystem, oder außerhalb der ausgewiesenen Paketliste.

Ein Advisory bedeutet, dass die im Abhängigkeitsgraphen erfasste Version in den betroffenen Bereich eines Advisories fällt. Erreichbarkeit wird nicht analysiert, und der Graph enthält Entwicklungs- und Test-Pins — ein Fund kann das Werkzeug betreffen und nicht die ausgelieferte Software.

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          "body": "…ation in _token_alphabet_from_lut\n\nThe contiguity check (recovered token ids must form 0..k-1) missed the\nboundary case unknown_token == len(alphabet)-1: it collides with the last\nsymbol's own token id, so the recovered alphabet silently drops that symbol\nwithout raising (e.g. b\"ACGT\" with unknown_\n[…]\nilt LUT is byte-identical, since a\nbyte at that token id behaves the same whether classified as \"in the\nalphabet\" or \"unknown\") while still rejecting genuinely lossy collisions\n(e.g. unknown_token=0).",
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          "body": "…window support\n\nTDD, bite-sized plan for the 2026-07-20 spec. Phase 1 (PR1, buffered,\nin-process): byte accounting, flat window/flank slicing, guard narrowing.\nPhase 2 (PR2, double_buffered): producer-schema VarWindowOpt replay, shm\nkind=4 for _FlatVariantWindows, kind=2 flank_tokens extension, consumer\nreshape. Both configs (variant-windows + variants-with-flank-tokens),\nboth transports, parity vs mode=None.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(plan): implementation plan for buffered/double-buffered variant-…",
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          "oid": "fcf31d83d15fe05634bd7e23dd0df2dddca23114",
          "body": "…-window output\n\nDesign for lifting the variant-windows / variants-with-flank-tokens\nrejection in gvl.Dataset's buffered and double_buffered torch transports.\nCovers both output configs and both transports as a 2-PR stack (buffered\nfirst, in-process; double_buffered adds shm kind=4 + producer-schema\nreplay of VarWindowOpt). Targets main.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(spec): buffered & double-buffered dataloader support for variant…",
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          "body": "style(docstrings): convert NumPy docstrings to Google style and enforce with ruff",
          "is_bot": false,
          "headline": "Merge pull request #294 from mcvickerlab/worktree-google-docstrings",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T23:30:26Z",
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        },
        {
          "oid": "85546fa3fb7d71a444f941061f711d74f65f0199",
          "body": "…rings\n\n# Conflicts:\n#\tpython/genvarloader/_dataset/_impl.py",
          "is_bot": false,
          "headline": "Merge remote-tracking branch 'origin/main' into worktree-google-docst…",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T23:20:30Z",
          "body_truncated": false,
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        },
        {
          "oid": "d3cd84c703987c1842c1fa58e5350ab50fb6452a",
          "body": "…ce with ruff\n\nConvert all NumPy-style docstrings in `python/genvarloader/` to Google style and\nturn on ruff's pydocstyle (`D`) rules with `convention = \"google\"` to keep them\nthat way. The `D1xx` missing-docstring rules stay off (style is enforced on\ndocstrings that exist, not their presence) and `\n[…]\nh a `--check` gate; exposed as the `docstring-style` pixi task.\n- CLAUDE.md: document the Google-style convention and the verification command.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "style(docstrings): convert NumPy docstrings to Google style and enfor…",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T23:09:21Z",
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        {
          "oid": "4a8b496ce1f5a94adf75a4bec0957848de733584",
          "body": "fix(flat-variants): accept str/bytes/NucleotideAlphabet for with_settings(token_alphabet=...)",
          "is_bot": false,
          "headline": "Merge pull request #293 from mcvickerlab/worktree-fix-292-token-alphabet",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T21:54:36Z",
          "body_truncated": false,
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        },
        {
          "oid": "269d9e027bc95420496df9cd801703f0308df816",
          "body": null,
          "is_bot": false,
          "headline": "Merge branch 'main' into worktree-fix-292-token-alphabet",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T21:44:59Z",
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        },
        {
          "oid": "5376bf74c29c9cfa0be9ddbb551fe00f10f7f1d5",
          "body": "…ings(token_alphabet=...)\n\nThe `with_settings(token_alphabet=...)` ride-along flank-tokens path forwarded the\nalphabet straight to `build_token_lut`, which only accepted `bytes` and crashed with\n`IndexError` on a `str` (it iterates the alphabet and indexes `lut[b]`, where a `str`\nyields `str` chars,\n[…]\nering is\npreserved verbatim across all three input types.\n\nCloses #292. Follow-up to #291, which scoped the same normalization to VarWindowOpt.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(flat-variants): accept str/bytes/NucleotideAlphabet for with_sett…",
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        {
          "oid": "ea8f70250fe4156e83e535224bb4cb33be686779",
          "body": null,
          "is_bot": true,
          "headline": "bump: version 0.38.0 → 0.39.0",
          "author_name": "github-actions[bot]",
          "author_login": "github-actions[bot]",
          "committed_at": "2026-07-17T21:28:14Z",
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          "oid": "3a5637b190aee25223b2a47f5d7d557e58bc7c2b",
          "body": "fix(reference): reject in_memory=False with reordered/subset contigs (#285)",
          "is_bot": false,
          "headline": "Merge pull request #290 from mcvickerlab/fix/285-reference-mmap-contigs",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T21:05:09Z",
          "body_truncated": false,
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        },
        {
          "oid": "704091e836cb88262f444ee9fee9af2bc8961d74",
          "body": null,
          "is_bot": false,
          "headline": "Merge branch 'main' into fix/285-reference-mmap-contigs",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:55:16Z",
          "body_truncated": false,
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        },
        {
          "oid": "8d0cf0e501abffb83740f190c18d8eeda11641dd",
          "body": "…abet\n\nfeat(flat-variants): accept str/bytes/NucleotideAlphabet for VarWindowOpt.token_alphabet",
          "is_bot": false,
          "headline": "Merge pull request #291 from mcvickerlab/worktree-var-window-opt-alph…",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:45:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "95913d50e6f97865f752ff33f7bec838eccde00b",
          "body": null,
          "is_bot": false,
          "headline": "Merge branch 'main' into fix/285-reference-mmap-contigs",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:44:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "741dbe59c59eee40392c772f6e08367c5c5f1cc9",
          "body": "…wOpt.token_alphabet\n\nVarWindowOpt.token_alphabet now accepts str, bytes, or seqpro.NucleotideAlphabet\n(e.g. sp.alphabets.DNA) and normalizes to bytes in __post_init__, so downstream\nbuild_token_lut only ever sees bytes. Byte position remains the token id, so\nordering is preserved verbatim.\n\nThis also fixes the documented skill example, which passed sp.DNA.alphabet (a\nstr) and would previously have crashed in build_token_lut.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "feat(flat-variants): accept str/bytes/NucleotideAlphabet for VarWindo…",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:34:19Z",
          "body_truncated": false,
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        },
        {
          "oid": "0abdce46c5f667e948a8417dcbae0311c53cbf4e",
          "body": "…(#285)\n\nReference.from_path only rebuilt offsets into the caller's contig order on\nthe in_memory=True branch. On the in_memory=False (memory-mapped) branch the\ncontigs argument was accepted but offsets stayed in full-FASTA order, so any\ncaller indexing offsets by its own contig index silently read \n[…]\nero impact on current callers (the only contigs-passing caller uses\nin_memory=True; every in_memory=False call passes no contigs).\n\nCloses #285\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(reference): reject in_memory=False with reordered/subset contigs …",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:32:38Z",
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        },
        {
          "oid": "f84682bbd6883813a308b06b25c469a32495174f",
          "body": "…bench\n\nperf(svar2): 2.3–5.5× spliced-variant decode via vectorized build_splice_plan + cohort-scale benchmark",
          "is_bot": false,
          "headline": "Merge pull request #289 from mcvickerlab/perf/svar2-spliced-variants-…",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:10:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "12b2fd6a97d6160de86b2a16b05e7c69b476a286",
          "body": "build_splice_plan looped over n_rows*n_samples pairs in Python to build the splice\npermutation -- 1.28M iterations at 256 transcripts x 5000 samples, 6.4M at 25000\nsamples. pyinstrument attributed 68% of the spliced with_seqs('variants') getitem to\nthis loop (36.5s of 52.7s), dwarfing the Rust decod\n[…]\n4   1011 -> 183  (5.5x)    S5000/T256  15935 -> 5498 (2.9x)\n  S1000/T256  2886 -> 784  (3.7x)    S25000/T64  18625 -> 7032 (2.6x)\n  S5000/T64   3516 -> 1101 (3.2x)    S25000/T256 77391 -> 33042 (2.3x)",
          "is_bot": false,
          "headline": "perf(svar2): vectorize build_splice_plan permutation",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:00:12Z",
          "body_truncated": true,
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        },
        {
          "oid": "1b89303912e3d090e27af32a8683aa4a90f76cd5",
          "body": "…scale\n\nThe existing build_svar_splice.py is pinned to a committed 5-sample PGEN and cannot\nvary cohort size -- the dominant axis for PR #286's SVAR2 spliced with_seqs('variants')\ndecode. Add vcfixture-rs bulk cohorts so n_samples can grow toward AoU scale.\n\n- data/build_svar2_splice_bulk.py: vcfixt\n[…]\n-identical RaggedVariants oracle (--check mode).\n- profiling/profile_svar2_splice_variants.py: pyinstrument driver.\n- test_e2e_svar2_splice_variants.py: pytest-benchmark regression + determinism test.",
          "is_bot": false,
          "headline": "test(svar2): bulk spliced-variant decode benchmark harness at cohort …",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:00:12Z",
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        },
        {
          "oid": "8bbdf9980c52cdb20493117d326ec81e34103182",
          "body": "…mization",
          "is_bot": false,
          "headline": "docs(bench): spec + plan for SVAR2 spliced-variant benchmark and opti…",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T20:00:12Z",
          "body_truncated": false,
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        },
        {
          "oid": "fe969511d6a7b33ee96b44535195c5111185ffac",
          "body": null,
          "is_bot": false,
          "headline": "feat(svar2): support spliced variant records",
          "author_name": "bschilder",
          "author_login": "bschilder",
          "committed_at": "2026-07-17T20:00:12Z",
          "body_truncated": false,
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        },
        {
          "oid": "1f0ad21defbc8a1743b12718db60760e777fd93e",
          "body": "…oord\n\ndocs(claude): coordinate StreamingDataset work via GitHub Project",
          "is_bot": false,
          "headline": "Merge pull request #287 from mcvickerlab/worktree-streaming-project-c…",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T17:51:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9f6d65ef6d3a42fb2720db78b04173dfbcd3bbba",
          "body": "Streaming work now targets a long-lived `streaming` integration branch off\nmain (PRs #274/#280/#282 merged into it), which lands on main as one\nintegrated PR at milestone boundaries — keeps main's queue to a single\nstreaming-facing PR instead of a deep stack.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(claude): route streaming PRs to the long-lived `streaming` branch",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T17:32:12Z",
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          "is_coding_agent": true
        },
        {
          "oid": "be7c77eb1c56e70e97d9f04b6ff0294b6bba8e17",
          "body": "All write-free StreamingDataset work is now tracked on the \"StreamingDataset\"\nGitHub Project. Adds a CLAUDE.md section directing streaming tasks to check the\nboard first, file issues with a `streaming:` prefix + `type:` label on the\nproject, keep PR \"Closes/relates\" refs accurate, and keep the board in sync with\ndocs/roadmaps/streaming-dataset.md.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(claude): coordinate StreamingDataset work via GitHub Project",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T17:32:12Z",
          "body_truncated": false,
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        },
        {
          "oid": "e364f5dfac3a04533cd63cc375be8c0627fe92ac",
          "body": "…profile\n\nperf(svar2): scatter-write spliced haplotypes (#273)",
          "is_bot": false,
          "headline": "Merge pull request #281 from mcvickerlab/worktree-spike+svar2-splice-…",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:25:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "97b5014e68dd64711c6ef76c84a6d22458eb8f47",
          "body": "Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(roadmap): link PR #281 for svar2 spliced scatter-write (#273)",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "74405900725fd25d4405e1bcdf4c0b0eb6f42fab",
          "body": "Sorting out_bounds by start alone (both the parallel carve in\nreconstruct::reconstruct_haplotypes_from_svar2 and the FFI-boundary\ncheck_disjoint_bounds_within overlap sweep) gives an unspecified tie\norder for rows sharing a start. A zero-length row produced by an\nexon-spanning deletion under var_fil\n[…]\n the 10.2 ms\ngap\" note in the rust-migration roadmap (both are independent\nminimums-over-reps on a noisy node, not a single-rep decomposition).\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): deterministic tie-break for scatter-write bounds sort",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": true,
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        },
        {
          "oid": "d06d2defc39f977a41b75c2492fd34f0e441f3f0",
          "body": null,
          "is_bot": false,
          "headline": "docs(roadmap): record svar2 spliced scatter-write results (#273)",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "55e0898e2ce16775f5c228831f991917bf8b74cc",
          "body": "Permutes per-row metadata and lets each contig group's kernel call write\nstraight into the final spliced buffer, deleting the O(bytes) concatenate\nand the RC post-pass. Byte-identical to SVAR1.",
          "is_bot": false,
          "headline": "perf(svar2): scatter-write spliced haplotypes, no Python re-order",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8443435bb22cd4bec2df4aa27fca5e739fea8c3c",
          "body": "reconstruct_haplotypes_from_svar2_readbound_into took out_bounds and\nto_rc straight from Python with no validation, unlike every sibling\nentry (whose bounds are Rust-computed via bounds_from_offsets). An\nout-of-range out_bounds row was a silent OOB write; an overlapping row\nwas aliasing UB under py.\n[…]\nn PyValueError\nbefore py.detach. Also carries over the allocating entry's pure-DEL\nanchor-read NOTE, verified to apply unchanged to this entry.\n\nCo-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): validate out_bounds and to_rc in scatter-write FFI entry",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "93b49f2e82298effb0e30cc241e71b771eebc431",
          "body": "…tions\n\nThe old 2-transcript, 2-contig splice_bed only reordered contig groups\nwithout splitting either into non-contiguous destination blocks, so it\ncould not catch a regression in the Rust carve's gap-tolerance for\nscattered-destination writes. Switch to a 3-transcript bed that\nalternates contigs in splice order (Ta:chr2, Tb:chr1, Tc:chr2), which\ngenuinely splits chr2's group around chr1's block, and make Tc\nminus-strand so the RC pass runs on rows landing in that gapped group.",
          "is_bot": false,
          "headline": "test(svar2): fix multicontig splice fixture to produce gapped destina…",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e39051d36de6ab112ecf7fdd75dc5c7770d5645c",
          "body": "Writes rows at caller-supplied destinations and skips the diffs sizing\npass (sizes come from out_bounds). Unused until the Python path lands.",
          "is_bot": false,
          "headline": "feat(svar2): scatter-write FFI entry for read-bound haplotypes",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2a6be4830a342863a80a271279481055c59ce1de",
          "body": "The chr22 benchmark and existing spliced tests are single-contig, so no\ntest covers a spliced read whose rows scatter across contig groups.",
          "is_bot": false,
          "headline": "test(svar2): multi-contig spliced parity guard",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2ff0b1ab58ab9b2fb39d52773a6173cd38b8b6cc",
          "body": "Adds a bounds-addressed counterpart to rc_flat_rows_inplace for reverse-\ncomplementing scattered rows at non-contiguous destinations. Extends\nndarray imports to include ArrayView2.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "feat(reverse): rc_bounded_rows_inplace for scattered rows",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "db816dec1ef143fd83621f80bec91163a140edb1",
          "body": "Generalizes out_offsets to (n_work, 2) out_bounds so callers can scatter\nrows into non-contiguous destinations; carve in ascending-start order.\nNo behavior change - both FFI callers adapt via bounds_from_offsets.",
          "is_bot": false,
          "headline": "refactor(svar2): per-row destination bounds in the reconstruct core",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
          "body_truncated": false,
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        },
        {
          "oid": "41bf14da350a06ed95a4df97d88d1c5140f9d767",
          "body": "Six tasks; 1-3 are independent (core bounds, RC helper, multi-contig\nparity guard) and dispatch in parallel, then FFI -> Python -> measure.\n\nAmends the spec: the spliced path gets its own _reconstruct_spliced\nrather than parameterizing get_haps_and_shifts by destination bounds.\nThe two paths call different FFI entries and differ on shifts/sizing;\nwhat they share is already factored into _gather_inputs/_ref_for_contig.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(plan): svar2 spliced scatter-write implementation plan (#273)",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-17T03:03:51Z",
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          "oid": "50c46a97ea483804d96c73e45441289231797294",
          "body": "Phase 0 spike attributes the svar2-vs-svar1 spliced gap: the Python\nre-order pass (`_ragged_arange_gather`) is 13.7 ms of a 10.2 ms total\ngap, and at ~9x the memcpy floor for the same bytes it is per-row numpy\ndispatch overhead (6600 rows), not bandwidth.\n\nDesign: scatter-write the svar2 read-bound \n[…]\nr1's \"fused\" spliced entry\npermutes metadata instead of bytes. Drops the gather-reuse lever (3.4 ms,\npartly shared with svar1) as out of scope.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(spec): svar2 spliced scatter-write design (#273)",
          "author_name": "d-laub",
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          "is_bot": true,
          "headline": "bump: version 0.37.0 → 0.38.0",
          "author_name": "github-actions[bot]",
          "author_login": "github-actions[bot]",
          "committed_at": "2026-07-16T21:33:16Z",
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          "oid": "09d5055a8b9c27f229fc9fca4097a56995c8d466",
          "body": "perf(svar2): vectorize spliced haplotype row reorder (8x)",
          "is_bot": false,
          "headline": "Merge pull request #272 from mcvickerlab/perf/svar2-spliced-gather",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-15T18:12:41Z",
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        {
          "oid": "3b62a8e768c8ee89050ddbb8a3f808ff2c34e9eb",
          "body": "Replace the byte-level fancy-index in `_ragged_arange_gather` (which built\n`arange(n_bytes)` plus two `np.repeat` arrays over every output byte) with a\nper-row slice + single `np.concatenate`. The Python-level work now scales with\nthe number of ragged rows (`len(perm)`), not the number of output byt\n[…]\nfe chr22 PGEN. Skips cleanly when the full test reference /\nplink2 are unavailable, mirroring the e2e suite's committed-data skip.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "perf(svar2): vectorize spliced haplotype row reorder",
          "author_name": "d-laub",
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          "body": null,
          "is_bot": false,
          "headline": "feat(svar2): support spliced exonic haplotypes",
          "author_name": "bschilder",
          "author_login": "bschilder",
          "committed_at": "2026-07-15T16:02:25Z",
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          "is_bot": true,
          "headline": "bump: version 0.36.0 → 0.37.0",
          "author_name": "github-actions[bot]",
          "author_login": "github-actions[bot]",
          "committed_at": "2026-07-15T08:03:36Z",
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          "headline": "chore: revert version",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-15T08:02:24Z",
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          "oid": "4d85fe1e641e4b711a8acffe7decaed4d107e527",
          "body": "…-bump\n\nfix(deps): bump genoray to Windows-compatible rev (fixes release pipeline)",
          "is_bot": false,
          "headline": "Merge pull request #268 from mcvickerlab/worktree-fix-windows-genoray…",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-15T07:57:32Z",
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        },
        {
          "oid": "bfa3c025c24f2016850899e88558bde68e2cf95e",
          "body": "Bumps the pinned genoray rev (both svar2-codec and genoray_core) from\n4ec0216 to 66ba734, which replaces the Unix-only File::read_exact_at in\nthe svar2 LongAlleleReader with a cross-platform pread_exact helper.\n\nThe old rev broke all Windows wheel builds in the release pipeline\n(publish / windows ar\n[…]\nied GVL now cross-compiles to\nx86_64-pc-windows-gnu (previously failed) and still builds natively.\n\nDepends on d-laub/genoray#112.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(deps): bump genoray to Windows-compatible rev",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-15T07:48:39Z",
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        },
        {
          "oid": "4d2b6e7d9309ab4ccb810cabfa5c1830e1ca3fff",
          "body": "…progress\n\nRevert \"feat(write): add structured progress reporting\"",
          "is_bot": false,
          "headline": "Merge pull request #270 from mcvickerlab/revert-269-codex/structured-…",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-15T07:48:06Z",
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          "oid": "3a428a87e0b4fbd133e3ea85c9bceebbea8c8708",
          "body": null,
          "is_bot": false,
          "headline": "Revert \"feat(write): add structured progress reporting\"",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-15T07:34:25Z",
          "body_truncated": false,
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        },
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          "oid": "e82b204565ee96cd111217aa5c409aaea41e5ca9",
          "body": "feat(write): add structured progress reporting",
          "is_bot": false,
          "headline": "Merge pull request #269 from bschilder/codex/structured-progress",
          "author_name": "Brian M. Schilder",
          "author_login": "bschilder",
          "committed_at": "2026-07-15T05:52:00Z",
          "body_truncated": false,
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        },
        {
          "oid": "826d528c6e5eb56ce8972e9b2fa54222e5d2ca3d",
          "body": "for more information, see https://pre-commit.ci",
          "is_bot": true,
          "headline": "chore(pre-commit): auto fixes from pre-commit.com hooks",
          "author_name": "pre-commit-ci[bot]",
          "author_login": "pre-commit-ci[bot]",
          "committed_at": "2026-07-15T05:41:59Z",
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        },
        {
          "oid": "502f0ba66bcf5e1e28768f285a51f44abd555758",
          "body": null,
          "is_bot": false,
          "headline": "fix(write): harden structured progress publication",
          "author_name": "bschilder",
          "author_login": "bschilder",
          "committed_at": "2026-07-15T05:40:54Z",
          "body_truncated": false,
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        {
          "oid": "2c2bfb44dc1901ee2aaddf6572728ab742fa34c9",
          "body": null,
          "is_bot": false,
          "headline": "feat(write): add structured progress reporting",
          "author_name": "bschilder",
          "author_login": "bschilder",
          "committed_at": "2026-07-15T03:50:47Z",
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        },
        {
          "oid": "905ed3c49a73bdd2ef02ab0ac1a896db4093db8e",
          "body": null,
          "is_bot": true,
          "headline": "bump: version 0.36.0 → 0.37.0",
          "author_name": "github-actions[bot]",
          "author_login": "github-actions[bot]",
          "committed_at": "2026-07-14T22:04:30Z",
          "body_truncated": false,
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        },
        {
          "oid": "c3f01d2c866152feb1f38a338cf7ff4d3c4e0f63",
          "body": "feat: SVAR2 read-bound dataset wiring (draft — blocked on genoray svar-2 release)",
          "is_bot": false,
          "headline": "Merge pull request #266 from mcvickerlab/svar2-m6b-kernel",
          "author_name": "David Laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-14T22:01:44Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "da6e27cd0022e5c7d89715933ea5fa714b634ddd",
          "body": "Python: drop the dev-wiring local wheel path and pin genoray>=3.0.0,<4\nfrom PyPI (first release with the INFO/FORMAT field-read API). Re-lock also\naligns seqpro to 0.21.1 in py311-313 (matching py310's pin; the old lock was\nstale there).\n\nRust: bump the genoray git-dep rev to the field_finalize no-c\n[…]\n16). At the prior rev genoray_core failed to compile with\ndefault-features=false (E0433: field_finalize gated behind conversion), which\nbroke gvl's extension build; verified importable at the new rev.",
          "is_bot": false,
          "headline": "build(deps): move onto released genoray 3.0.0",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-14T21:43:06Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "16868c0388619a71ee20c604058f0a9e019cd3b3",
          "body": "Replace the local-path deps on svar2-codec and genoray_core with git\ndeps pinned at genoray main (82668a6). genoray publishes no crates to\ncrates.io; pulling straight from GitHub avoids needing a release. Cargo\nresolves both packages by name from a single clone of the repo.",
          "is_bot": false,
          "headline": "build(deps): source genoray crates from GitHub git dep",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-14T16:11:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "649689d1fff4abf8aba6bb9f700ebf5756522104",
          "body": "The read-bound SVAR2 track kernel is called once per contig group, so its\n`k / ploidy` query index is contig-LOCAL. The FlankSample fill hash\n`hash4(base_seed, query, hap, out_idx+i)` needs the GLOBAL batch row to match\nthe single fused SVAR1 call, which diverged whenever a contig appeared at more\nt\n[…]\nocs/skill/roadmap updated.\n\n(Incidental: `pixi lock` refreshed a stale narwhals transitive pin via the\npixi-lock pre-commit hook.)\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): global fill-seed for multi-contig FlankSample tracks (#267)",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T22:36:27Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "9e1f296c8983e0666dec67a4d4a134a4ab62e432",
          "body": "Task 8: the multi-contig FlankSample track-fill divergence was recorded only in\na code comment behind a NotImplementedError guard. Reference the tracking issue\nso the guard can be lifted once the fill-seed index is made global.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(svar2): reference issue #267 in the FlankSample fill-seed guard",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T22:09:46Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "3ccadd9d2d272543e4cd5833e521d2593d5c559a",
          "body": "A bare `assert` is stripped under `python -O`, so a pathological >~2Mb deletion\nfootprint could silently corrupt the packed composite key. Raise ValueError so\nit fails fast regardless of optimization level. (Final whole-branch review nit.)\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): raise (not assert) on max_ends packing-width overflow",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T21:10:46Z",
          "body_truncated": false,
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        },
        {
          "oid": "853ad617a84dbd2bc8d77e8bfb25eb5051537006",
          "body": "Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(svar2): backfill PR #266 link into Phase 6a roadmap entry",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T21:03:06Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "72d4a0ec69cb0aa517947b966c90e023bfa11181",
          "body": "The tmp/svar2_mvp benchmark/profiling drivers are machine-specific (hardcoded\n/carter paths + real chr21 stores absent in CI) and their perf conclusions\nalready live in docs/roadmaps/rust-migration.md, so they are dropped from git\nrather than relocated into tests/ (adding un-runnable scratch there w\n[…]\nremain on\ndisk (ignored) for local reuse; relocating+parameterizing specific ones into\ntests/benchmarks/ is a follow-up if wanted.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "chore(svar2): untrack tmp/svar2_mvp scratch and blanket-ignore tmp/",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T21:02:16Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "18b624c17ff1581f7aecb048a9d30df21e608935",
          "body": "The write.md build snippet (and a pre-existing SKILL.md twin) used\ndense2sparse(VCF(...), path) — but dense2sparse takes dense numpy arrays and\nreturns a Ragged, and SparseVar2.from_vcf requires reference= or\nno_reference=. Use the verified public API: SparseVar.from_vcf(out, VCF(src),\nmax_mem=...) for .svar and SparseVar2.from_vcf(out, src, reference=...) for\n.svar2.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(svar2): fix genoray build snippets to the real from_vcf API",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T20:49:14Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "727d2ee4ca2717543323f278b1f16a2da4e8bcea",
          "body": "Roadmap Phase 6a: move unphased_union/variant-windows to supported, add the\nextend_to_length + field-routing guard/task lines, drop the stale\nvariant-windows-parity footnote, correct the parity count to the current\n.svar2 suite (55), add a 2026-07-13 notes-log entry, and add a ⛔ release-gate\nsubsect\n[…]\ndex.md source list, format.md .svar2 guard matrix + changelog\npin (0.37.0), write.md build snippet, dataset.md var_fields section.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "docs(svar2): sync roadmap/skill/prose docs + add release-gate checklist",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T20:40:26Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "8f525da7ecb09738e83e6fe3cde2de747f5195ad",
          "body": "The identical LSB-first presence-bit closure in the reconstruct and tracks\nper-hap merge_hap calls is now a documented svar2::present_bit free function;\nboth call sites reduce to a one-line closure over it. Byte-identical: svar2\nparity 36 pass, cargo build clean.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "refactor(svar2): hoist shared present_bit to svar2::present_bit",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T20:12:40Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "3bd5a186c061ff593f75f845032e6965691abb59",
          "body": "annot_v_idxs/annot_ref_pos were None at both call sites of the SVAR2 kernel\nreconstruct_haplotypes_from_svar2 (annotated .svar2 haps are\nNotImplementedError-guarded), so the annotation chunk-carve, 3 of 4 parallel\nmatch arms, and the serial raw-pointer annot views were all unreachable. Drop\nthe two \n[…]\nype_core keeps its\nannot params (the SVAR1 path uses them). Byte-identical: svar2 parity 40 pass,\nreconstruct cargo tests 19 pass.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "refactor(svar2): drop dead annot_* capability from readbound haps kernel",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T20:03:22Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "04931653b01b708aa1f8ee67f53df47d78365fd9",
          "body": "SparseVar2Source and build_readbound_* have no importers under python/ — they\nare the parity oracle + FFI-input builders used only by tests. Move them to\ntests/_oracles/ (renaming _svar2_store_py.py -> svar2_readbound_inputs.py,\nsince it holds no store class), convert their relative imports to absol\n[…]\nnvarloader, genvarloader._dataset.\n_rag_variants), and repoint the 7 test files' imports + the Svar2Haps\ndocstring back-reference.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "refactor(svar2): move test-only oracles out of the shipped package",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T19:51:37Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "f70a22d77412502ad4575b4e7adffea5b634b66e",
          "body": "region_starts was written, memmapped into _Svar2Cache, and never fed to the\nFFI (its own docstring said \"parity/debug only\" — the read path recomputes\nper-query starts post-jitter from the regions array). Remove it from the write\npath, the svar2_meta.json schema, the Svar2Haps loader (deriving R fro\n[…]\nd), and the cache-contents test. The genoray\n_find_ranges \"region_starts\" output key and the fresh read-time array are\nunaffected.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "refactor(svar2): drop unused region_starts from the ranges cache",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T19:45:19Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "c7073e71d939c98c7926644a71d885df404f2cde",
          "body": "The composite key packed the absolute end (~pos-sized) into 21 low bits, so any\nvariant past ~2Mb into a contig would assert-fail the write (or, with -O,\nsilently corrupt the per-region ordering). Real chromosomes are hundreds of Mb;\nthe 40bp test fixture masked it. Pack the bounded ext = 1 - min(il\n[…]\nunpack end = (key>>SHIFT) + (key&mask). Add a large-\nposition regression test (stub decode at 3-5Mb) that crashed the old packing.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): pack bounded tie-break in max_ends key (fix >2Mb overflow)",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T19:39:52Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "3c0f17d0e72f42a0e4fec8057d3517bcf8e1e18f",
          "body": "Replace the O(regions x samples x ploidy) write-time Python triple-loop with a\nper-region scatter-max over a (pos<<21)|end composite key that preserves the\npos-then-end tie-break. A single haplotype never carries two variants at the\nsame position, so a global per-region max over the selected samples\n[…]\n a new\nequivalence test carrying the old loop as its oracle (asserted non-vacuous:\nthe DEL at POS 11 extends overlapping regions).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "perf(svar2): vectorize _svar2_region_max_ends (byte-identical)",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T19:33:05Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "0e1e5d61572e511d37a58bbfcc012466b48770de",
          "body": "_write_from_svar2 accepted the flag and ignored it, silently extending\nchromEnd regardless. Raise NotImplementedError (Phase-1 guard-matrix policy)\ninstead of producing a dataset that differs from what was requested.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): reject extend_to_length=False for .svar2 sources",
          "author_name": "d-laub",
          "author_login": "d-laub",
          "committed_at": "2026-07-13T19:29:34Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "ae0cd7958e2b8f4d9bfc6c61a4e578d153ad1198",
          "body": "The Task-4 FFI-boundary guard rejected region_bounds[q,1] > contig_ref_len,\nbut gvl regions legitimately extend past a contig end (jitter/max_jitter\npadding, right-padded with pad_char), so that guard broke valid boundary reads\nand SVAR1 parity on the live read path. The anchor OOB is only reachable\n[…]\nant pos >= contig_len); guard that with a debug_assert at\nthe read site instead. The ref_/tracks contiguity guards are unaffected.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "fix(svar2): drop over-strict anchor region guard; assert at read site",
          "author_name": "d-laub",
          "author_login": "d-laub",
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          "headline": "fix(svar2): guard serial unsafe carve path with monotonicity debug_as…",
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          "headline": "test(svar2): oracle test for INFO/FORMAT field routing (var_key+dense…",
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                "key": "fuzzing",
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                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is not run on all commits -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "14 existing vulnerabilities detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "moderate",
            "name": "Dependency advisories",
            "note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories. Remaining weights renormalized. Matched 321 resolved dependencies against OSV; 35 could not be assessed (no resolved version, an unsupported ecosystem, or beyond the reported package list). This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories"
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                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 321
                }
              },
              {
                "code": "advisories_unassessed",
                "params": {
                  "count": 35
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 53,
            "inputs": {
              "source": "osv",
              "advisories": 59,
              "affected_packages": 17,
              "assessed_packages": 321,
              "unassessed_packages": 35,
              "affected_by_severity": "critical 1, high 6, moderate 4, low 2, unknown 4",
              "direct_affected_packages": 4
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "4 affected: pyarrow 15.0.2 (high 7.0), filelock 3.13.4 (moderate 6.3), tqdm 4.66.2 (low 3.9), +1 more",
                "points": 11.6,
                "status": "partial",
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                    "code": "advisories_affected",
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                  },
                  {
                    "code": "advisories_affected_more",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "3 advisory-carrying package(s) unaddressed past 90 days; oldest published 808 days ago",
                "points": 28,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_stale",
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                      "count": 3,
                      "oldest": 808
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                  }
                ],
                "max_points": 40
              }
            ]
          },
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            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "source": "osv",
              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 321,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
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            "components": [
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                "key": "no_dependency_reported_as_a_malicious_package",
                "name": "No dependency reported as a malicious package",
                "detail": "no dependency is reported as a malicious package",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "no_malicious_dependencies",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
              ],
              "review_only_matches": 0,
              "assessed_self_published_locations": 6
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "good",
        "name": "AI Readiness",
        "value": 76,
        "weight": 0,
        "metrics": [
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            "key": "ai_agent_context",
            "band": "excellent",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
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                "detail": "CLAUDE.md",
                "points": 45,
                "status": "met",
                "details": [
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                    "code": "file_list",
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                "max_points": 45
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                "key": "machine_readable_docs_llms_txt",
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                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
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                "key": "legible_commit_history",
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                "detail": "89 of 94 human commits state their intent (structured subject or explanatory body)",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "legible_history",
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                      "sampled": 94
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                "max_points": 40
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          },
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            "key": "ai_verify_loop",
            "band": "good",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 82,
            "inputs": {
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              "has_tests": true,
              "lockfiles": [
                "Cargo.lock"
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              "has_dockerfile": false,
              "typed_language": false,
              "bootstrap_files": [
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              "has_devcontainer": false,
              "has_linter_config": true,
              "typecheck_configs": [
                "python/genvarloader/py.typed"
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              "agent_commit_share": 0.4,
              "toolchain_manifests": [
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              "dependency_bot_commit_share": 0
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            "components": [
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                "name": "One-command bootstrap",
                "detail": "docs/Makefile",
                "points": 18,
                "status": "met",
                "details": [
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                    "code": "file_list",
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                      "files": "docs/Makefile"
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                "max_points": 18
              },
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                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 22,
                "status": "met",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 11,
                "status": "met",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": "python/genvarloader/py.typed",
                "points": 11,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "python/genvarloader/py.typed"
                    }
                  }
                ],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": "lockfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "lockfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "40 of the last 100 commits agent-authored or agent-credited",
                "points": 10,
                "status": "met",
                "details": [
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                      "sampled": 100
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                  }
                ],
                "max_points": 10
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                "key": "automated_maintenance",
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                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
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                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
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            "key": "ai_code_legibility",
            "band": "good",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 81,
            "inputs": {
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              "largest_source_bytes": 114095,
              "source_files_sampled": 283,
              "oversized_source_files": 5
            },
            "components": [
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                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Python with type-check config (python/genvarloader/py.typed)",
                "points": 27,
                "status": "partial",
                "details": [
                  {
                    "code": "typecheck_config_language",
                    "params": {
                      "files": "python/genvarloader/py.typed",
                      "language": "Python"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "5/283 source files over 60KB",
                "points": 54,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
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                      "kb": 60,
                      "sampled": 283,
                      "oversized": 5
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                  }
                ],
                "max_points": 55
              }
            ]
          },
          {
            "key": "ai_interfaces",
            "band": "at_risk",
            "name": "Machine-readable interfaces",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
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              "has_mcp_signal": false,
              "api_schema_files": []
            },
            "components": [
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                "key": "api_schema_openapi_graphql_proto",
                "name": "API schema (OpenAPI/GraphQL/proto)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 40
              },
              {
                "key": "mcp_server",
                "name": "MCP server",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
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                "key": "runnable_examples",
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                "points": 40,
                "status": "met",
                "details": [
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        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
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    ],
    "metrics_version": "1.13.0"
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  "warnings": [
    "Could not fetch crates package 'genvarloader' from its registry",
    "deps.dev does not index pypi:genvarloader@0.40.0; advisories assessed against the repository dependency graph instead"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-21T16:41:34.731871Z",
  "schema_version": "0.23.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/m/mcvickerlab/GenVarLoader.svg",
  "full_name": "mcvickerlab/GenVarLoader",
  "license_state": "standard",
  "license_spdx": "MIT"
}