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- Status: Open.#321 In rnabioco/leech;
tracking: 2026-09-13 codebase review — 35 specs, tiered
review-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#293 In rnabioco/leech;tests: split the grab-bag module, share the builders, move benches out, and close the coverage gaps found in review
enhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#292 In rnabioco/leech;docs: generate the CLI reference from click, add the v0.25.0 changelog line, retire
--reference-anchoreddocumentationImprovements or additions to documentationImprovements or additions to documentationreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#291 In rnabioco/leech;ty: re-enable the nine blanket-ignored rules with per-file ignores
enhancementNew feature or requestNew feature or requestgood first issueGood for newcomersGood for newcomersreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#290 In rnabioco/leech;merge: stream through the spill instead of holding the merged corpus in RAM
enhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#289 In rnabioco/leech;chunk format: one
CHUNK_FIELDSspec, ASCII text inChunkSpool, one BAM tag parserenhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#288 In rnabioco/leech;models: port the hand-written cross-attention classes to TOML variants (after the tier decision)
enhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#287 In rnabioco/leech;trainer hygiene: duplicated AMP/loss branches, two seeding routines, patience not checkpointed, weights stored twice
enhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#286 In rnabioco/leech;dataset: split
LeechDatasetinto a frozenTensorCorpusand an augmenting dataset; block-only twins; batched cross-layer augmentationenhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#285 In rnabioco/leech;deployment helpers: calibration, bundling, metrics and the BAM writer carry copies of each other
enhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#284 In rnabioco/leech;cli: shared option decorators, one
--device/--num-workers/--seedconvention, lazy startupenhancementNew feature or requestNew feature or requestreview-2026-09Findings from the 2026-09-13 codebase reviewFindings from the 2026-09-13 codebase reviewStatus: Open.#271 In rnabioco/leech;