fix: dataset_load Path P now returns the h5ad; re-pin biodata-registry 0.1.16

feat(de): surface the results-CSV schema; prompt bans schema-sniff re-reads

feat(datasets): dataset_load — execute the loading plan by dataset_id in one call

feat(de): nested-batch guard now recommends the de-confounded alternative

feat(de): default low-count gene filter pre-DESeq2 + stat-ranking prompt rule

feat(upload): assemble raw counts/TPM/metadata into an h5ad inside the gate

feat(de): sample-level library-size pre-flight in decoupler_differential_expression

fix(enrichment): drop non-finite DE stat genes before ulm; report n_dropped_nonfinite

fix(de): apply subset_query on the DESeq2 branch too

feat(mouse): thin mouse-intake path — staging script, ENSMUSG→MGI map, nested-batch guard

fix(tools): select the contrast row positionally so top_table cannot fail the tool

fix(tools): keep top_table inside the executor's 4000-char output cap

merge: dev's n_post_analysis_reads instrumentation into the top_table fix

perf(tools): return the reporting table inline from every chain-terminating tool

Revert "perf(agent): pin results artifacts across the memory window"

feat(metrics): instrument n_post_analysis_reads to test the 808b91d claim

perf(agent): pin results artifacts across the memory window

fix(reporting): return the top table inline so the report needs no re-read

Merge branch 'lane/modest-hellman-160126'

fix(schema): port the survival-only group_columns exemption from biodata-registry

fix(planner): dataset_plan_analysis must say how to LOAD the dataset

fix(agent,ui,prompt): cut the measured step waste, and stop mislabelling timeouts

fix(loaders): authenticate the h5ad fetch in decoupler_load_url_counts

fix(scoring): resolve gene symbols from var; never let a sample filter no-op

fix(sc,ui): filter lowly-expressed genes after pseudobulk; sweep every output dir

feat(sc): add decoupler_pseudobulk_aggregate — the missing Path P step

fix(scoring): close the six PROGENy per-sample gaps from the GSE205154 eval

merge: security-review-prep (README orientation + _resolve_env_vars docstring)

fix(uploads): scan before parse; drop ungated URL/HF originals (ADR-0011)

fix(uploads): make the deployed malware-scan posture explicit and honest

feat(auth): OAuth + allow-list gate on the specialist UI (ADR-0012) (#1)

refactor: move writable-dir constants to core.paths, fix workflow->tools layer violation

docs(security): clarify _resolve_env_vars is read-only env substitution

refactor: tighten invariant-length zips to strict=True (B905)

style: apply ruff lint --fix + ruff format across the tree

Merge remote-tracking branch 'origin/main' into feat/sandbox-executor

style(exec): move nosec B310 rationale to a comment (ADR-0014 bandit hygiene)

feat(integrity): ADR-0010 on-load verify for GEO series-matrix loads

feat(uploads): local content scan + manifest drafting (ADR-0011)

feat(auth): ADR-0012 identity seam + identity into audit trace (Now slice)

feat(logging): ADR-0013 audit-trace redaction (secret/credential/PII scrubbing)

feat(exec): ADR-0007 Phase 2 local hardening for ContainerLauncher

feat(exec): real MCP handshake + container-launch fixes (ADR-0007 Phase 1 validation)

feat(exec): sandboxed per-session exec-kernel executor (ADR-0007 Phase 1)

feat(exec): extract Executor seam + EXECUTOR config switch (ADR-0007 Phase 0)

feat(integrity): wire ADR-0010 on-load verify + re-pin 0.1.9 (deploy slice)

feat(uploads): validate flat-matrix (csv/tsv) uploads, not just h5ad

refactor(integrity): unify ADR-0010/0011 into one src/core/integrity.py

feat(uploads): ADR-0011 manual-upload safety gate ("Now" slice)

Merge feat/configurable-log-sink: always-on audit log sink (ADR-0008 + ADR-0009)