v26 usability: fix P0 (invalid track) + 4 P1s (CLI noise, bare exceptions, MCP debug)

[lucapinello]

Summary

Picks up the actionable items from v26 usability audit. One code-correctness bug, four UX polish fixes.

P0 #9 — invalid track ID silently returned predictions for track 0

Both chorus/oracles/enformer.py:346 and chorus/oracles/borzoi.py:300 logged a warning and appended index 0 as a fallback when get_track_by_identifier() returned None. So:

oracle.predict(('chr1', 0, 100_000), ['ENCFF999BADID'])
# → warning "Identifier 'ENCFF999BADID' not found in metadata"
# → silently returns predictions for track 0 (an arbitrary other track)

User output corrupted with no recovery path.

Fix: raise InvalidAssayError naming the missing ID and pointing at oracle.get_track_info(). Also upgraded the env-runner subprocess templates (enformer_source/templates/predict_template.py, borzoi_source/…/predict_template.py) from bare raise Exception to a descriptive ValueError (v26 P1 #12 also).

Regression test: tests/test_prediction_methods.py::test_unknown_track_id_gives_actionable_error. Covers both the ENCFF-ID and description-search branches with a stubbed metadata object.

P1 #4 — leading INFO noise on every CLI invocation

Before:

$ chorus list
2026-04-23 20:21:55,540 - chorus.core.environment.manager - INFO - Found mamba via MAMBA_EXE: /Users/…/miniforge3/bin/mamba
2026-04-23 20:21:55,540 - chorus.core.platform - INFO - Detected platform: Darwin arm64 (key=macos_arm64, cuda=False)
Available oracle environments:

After:

$ chorus list
Available oracle environments:

Demoted both to logger.debug in core/environment/manager.py (3 lines) and core/platform.py (1 line). Diagnostic, not user-facing.

P1 #1 — chorus setup --oracle fakeoracle lists valid names

Before: Environment file not found: environments/chorus-fakeoracle.yml. No hint of valid names.

After: No environment file for oracle 'fakeoracle'. Expected …. Valid oracle names: ['alphagenome','borzoi','chrombpnet','enformer','legnet','sei'].

P1 #13 — bare raise Exception('') in interval.py

CIGAR parser fallback raised an empty Exception. Replaced with IntervalException naming the bad symbol and valid set ('=MIDX').

P1 #18 — MCP _safe_tool hides traceback

The decorator returns {"error", "error_type", "tool"} dicts on failure — MCP clients can't see which line raised.

Fix: opt-in CHORUS_MCP_DEBUG=1 env var includes "traceback" in the error payload. Default behaviour unchanged.

Not addressed here (separate PRs)

• P1 fixes: audit 2026-04-16 follow-up (remove 2 examples + normalizer/report hardening) #10 (TF/absl startup noise): needs TF_CPP_MIN_LOG_LEVEL=3 in env activation scripts — invasive.
• P1 fix: AlphaGenome JAX Metal guard + macOS fresh-install audit v4 #11 (silent env-setup swallow): needs a new EnvironmentNotReadyError exception + flag-on-later-use.
• P2 items: polish pass after these land.

Test plan

• pytest tests/ --ignore=tests/test_smoke_predict.py -q → 340 passed / 1 skipped (+1 new test)
• chorus --help + chorus list → no leading INFO noise
• chorus setup --oracle fakeoracle → lists valid oracle names
• Manual: oracle.predict(..., ['ENCFF999BADID']) → InvalidAssayError with get_track_info() pointer (both use_environment=True/False paths)
• CHORUS_MCP_DEBUG=1 chorus-mcp preserves existing behaviour; unset behaves identically to main

🤖 Generated with Claude Code

[lucapinello]

Superseded by 96fc28d which landed 4 of my 9 files (the track-ID guards + INFO→DEBUG demotion). Opening a follow-up PR with just the 5 files that didn't land: template fixes (P1 #12), interval.py bare Exception (P1 #13), MCP CHORUS_MCP_DEBUG opt-in (P1 #18), and the regression test for the P0.