refactor: land the completed refactor in main (PRs #31–#37) - #38

Merged

nceglia merged 34 commits into

mainfrom

Jul 30, 2026

Commits on Jul 12, 2026

refactor(pr2): delete 14 dead / out-of-scope symbols (Phase 2)

nceglia
and
claude
committed
8e3b4e4
refactor(pr2): audit fixes — drop orphaned import, correct doc counts

nceglia
and
claude
committed
7fc2ece
refactor(pr3): split model/_model.py into scvi-style modules

nceglia
and
claude
committed
5769136
refactor(pr3): add explicit __all__ per module (audit MED fix)

nceglia
and
claude
committed
f543f02
chore(env): pin verified-recent scverse stack; pandas-3.0 compat fix

nceglia
and
claude
committed
792593e
refactor(pr4): model→AnnData streamline (to_anndata, predict; retire manager stash)

nceglia
and
claude
committed
5f380b1
docs(pr4): agenda diary + model knob-test matrix + correctness debt

nceglia
and
claude
committed
19d2426
refactor(pr4): audit fixes — knob-matrix math + test tightening

nceglia
and
claude
committed
7fd7991
refactor(pr5): unified joint_distribution engine (tools/ + _compute/)

nceglia
and
claude
committed
71806d3
docs(pr5): agenda diary + engine invariants; reconcile joint_distribution signature

nceglia
and
claude
committed
3e1f0c0
refactor(pr5): audit fixes — subset guard, local_scale error, gate test

nceglia
and
claude
committed
7c6b6a0
refactor(pr6): migrate 4 metrics + compare_groups onto the engine; flip tl->tools

nceglia
and
claude
committed
2f5be6a
refactor(pr7): plotting split + 4 pl twins; delete old metrics + engines

nceglia
and
claude
committed
5c82e4c
refactor(pr8): diag/ PPCs + relocated plots; fix PR6 audit findings

nceglia
and
claude
committed
5ca5819
refactor(pr9): move model PGM out of package to docs/; drop daft runtime dep

nceglia
and
claude
committed
21067ba
docs(pr6-9): agenda diaries + PR6 audit-log; mark PR6-9 done
nceglia
committed
47a7295
refactor(pr7-9): audit fixes — enforce pl.* contract; faithful reconstruction_ppc

nceglia
and
claude
committed
4aa67a6
docs: PR7-9+plan audit + live R/NR test outcome in the audit log
nceglia
committed
29a7cb6

Commits on Jul 13, 2026

fix(model): train the phenotype classifier + methods-note conformance

nceglia
and
claude
committed
da9a6e2

Commits on Jul 14, 2026

fix(model): apply α (global_scale) to the eq-1 clonotype prior [G]

nceglia
and
claude
committed
fc26dd1

Commits on Jul 27, 2026

Merge pull request #36 from nceglia/model/classifier-fix
nceglia
authored
f24dfa5
feat(contract): formalize Supplementary Note 1 as an enforced model contract

nceglia
and
claude
committed
b1e2243
fix(contract): close 3 escapes found by the adversarial audit

nceglia
and
claude
committed
f233acd

Commits on Jul 28, 2026

perf(stats): O(n_pos) permutation AUROC + bincount joint build

nceglia
and
claude
committed
8be2f19

Commits on Jul 29, 2026

fix(model): guardrails for K, param-store reuse, batch_size, Trainer knobs

nceglia
and
claude
committed
9e609ca
perf(engine): bypass the DataFrame round-trip; chunk the draw materialization

nceglia
and
claude
committed
74a19a3
perf(model): inference batch size, buffer registration, per-step scalar copy

nceglia
and
claude
committed
1a5c47f
fix(model): route lr/weight_decay to Pyro's optimizer; drop the phantom Adam

nceglia
and
claude
committed
83b244f
feat(contract): freeze the metrics as a third enforced contract

nceglia
and
claude
committed
05e51b6
test(knobs): complete the knob-test matrix with a WIRING layer

nceglia
and
claude
committed
9ed2b6a
fix(model): recalibrate reconstruction_loss_scale 1e-3 -> 1e-2 (deviation [E])

nceglia
and
claude
committed
19db68e
refactor: complete the deferred Phase-4 legacy-key removal

nceglia
and
claude
committed
eed1ead
docs(agenda): audit-log entry for the goal run (metrics contract, knob test, [E], legacy keys)

nceglia
and
claude
committed
0917039
Merge pull request #37 from nceglia/model/contract
nceglia
authored
5c2baef