feat(loveless): Role-2 signature consumable — resolve private signature URLs 6cda24b
Anne Voigt Claude Opus 4.8 commited on
Commit History
feat(loveless): ADR-0006 + agent-side sc serving scaffold 6e9f020
avoigt1121 Claude Opus 4.8 commited on
feat(integration): ComBat per-sample scoring tool decoupler_pool_cohorts (ADR-0001 item 10) 81f5db6
avoigt1121 Claude Opus 4.8 commited on
refactor(loader): centralize authenticated URL->local resolution 04b26ba
avoigt1121 Claude Opus 4.8 commited on
ADR-0001 Phase 2 Mode A: early integration (T7 + T8 + T9) a7a8caa
avoigt1121 Claude Opus 4.8 commited on
feat(concordance): same-cohort normalization concordance routine (decoupler_normalization_concordance) b36d5ce
avoigt1121 Claude Opus 4.8 commited on
fix(loaders): accept http(s)/ftp URLs in bulk dataset loaders e12ae0f
avoigt1121 Claude Opus 4.8 commited on
feat(sanity): ADR-0002 Phase 2 — auto-fire tissue-identity contamination + PROGENy/Hallmark parity a568d6e
avoigt1121 Claude Opus 4.8 commited on
feat(sanity): ADR-0002 Layer-2 result-aware sanity layer (Phase 1 + S1) 7fc62b9
avoigt1121 Claude Opus 4.8 commited on
ADR-0001 Phase 1, step 4: meta-analysis engine (Mode B late integration) bb944d5
avoigt1121 Claude Opus 4.8 commited on
Dedup: extract subset_and_require_group shared by activity_stats + microarray c9ed4f0
avoigt1121 Claude Opus 4.8 commited on
Mark planned survival-stub params as intentionally unused (vulture) 4c5d3f4
avoigt1121 Claude Opus 4.8 commited on
Lint cleanup: remove unused imports, empty f-strings, split import lines 3bfbf14
avoigt1121 Claude Opus 4.8 commited on
HF wheel registry, pinned deps, apt probe, security scan, API-key fallback 18391e3
avoigt1121 commited on
Fix 4 GPL-annotation fallback edge cases + 2 integration test bugs 90366d6
avoigt1121 Claude Sonnet 4.6 commited on
Document residual GPL annotation limitations (Known Gaps #15) 7cf6449
avoigt1121 commited on
Add GEOparse fallback for GPL platforms with no .annot.gz (Tier 2) 089536c
avoigt1121 Claude Sonnet 4.6 commited on
Switch GPL platform annotation to NCBI .annot.gz instead of _family.soft.gz b3ed7f4
avoigt1121 Claude Sonnet 4.6 commited on
Replace rpy2 limma bridge with Rscript subprocess — fixes all conversion errors 95543ce
avoigt1121 Claude Sonnet 4.6 commited on
Fix run_limma: rename R globals from _lm_ to .lm_ (R names can't start with underscore) 20a83dd
avoigt1121 commited on
Rewrite run_limma: build design matrix in R to fix non-conformable arrays cbf6b80
avoigt1121 Claude Sonnet 4.6 commited on
Broaden rpy2 converter fallback to catch TypeError in addition to AttributeError be3cb0a
avoigt1121 commited on
Fix limma: wrap all numpy→R and R→pandas ops in localconverter 2ff8776
avoigt1121 Claude Sonnet 4.6 commited on
Fix limma: replace deprecated rpy2 .activate() API with localconverter 0ead534
avoigt1121 Claude Sonnet 4.6 commited on
Add dataset_validate_manifest_against_data tool and tests ebc2734
avoigt1121 Claude Sonnet 4.6 commited on
Refactor manifest/metadata to separate semantics from runtime counts d2b9c5b
avoigt1121 Claude Sonnet 4.6 (1M context) commited on
Fix decode_geo_numeric_codes to decode all code segments, not just last ee375b1
avoigt1121 Claude Sonnet 4.6 (1M context) commited on
Remove dead code and standardize MCP tool return schemas 93a454a
avoigt1121 Claude Sonnet 4.6 (1M context) commited on
Added seperate files, added tests 33406e8
avoigt1121 commited on
Add PDAC dataset adapter, workflow, semantic, and analysis layers 352e308
avoigt1121 Claude Sonnet 4.6 (1M context) commited on