Commit graph

2 commits

Author SHA1 Message Date
kshitijk4poor
66827f8947 chore: prune unused imports and duplicate import redefinitions
Remove unused imports (F401) and duplicate/shadowed import
redefinitions (F811) across the codebase using ruff's safe
autofixes. No behavioral changes -- imports only.

- ~1400 safe autofixes applied across 644 files (net -1072 lines)
- __init__.py re-exports preserved (excluded from F401 removal so
  public re-export surfaces stay intact)
- Re-exports that are imported or monkeypatched by tests but look
  unused in their defining module are kept with explicit # noqa:
  F401 (gateway/run.py load_dotenv; run_agent re-exports from
  agent.message_sanitization, agent.context_compressor,
  agent.retry_utils, agent.prompt_builder, agent.process_bootstrap,
  agent.codex_responses_adapter)
- Unsafe F841 (unused-variable) fixes deliberately skipped -- those
  can change behavior when the RHS has side effects
- ruff lints remain disabled in pyproject.toml (only PLW1514 is
  selected); this is a one-time cleanup, not a config change

Verification:
- python -m compileall: clean
- pytest --collect-only: all 27161 tests collect (zero import errors)
- core entry points import clean (run_agent, model_tools, cli,
  toolsets, hermes_state, batch_runner, gateway)
- static scan: every name any test imports directly from an edited
  module still resolves
2026-05-28 22:26:25 -07:00
oluwadareab12
a91b9bb855 feat(skills): add drug-discovery optional skill — ChEMBL, PubChem, OpenFDA, ADMET analysis
Pharmaceutical research skill covering bioactive compound search (ChEMBL),
drug-likeness screening (Lipinski Ro5 + Veber via PubChem), drug-drug
interaction lookups (OpenFDA), gene-disease associations (OpenTargets
GraphQL), and ADMET reasoning guidance. All free public APIs, zero auth,
stdlib-only Python. Includes helper scripts for batch Ro5 screening and
target-to-compound pipelines.

Moved to optional-skills/research/ (niche domain skill, not built-in).
Fixed: authors→author frontmatter, removed unused jq prerequisite,
bare except→except Exception.

Co-authored-by: bennytimz <oluwadareab12@gmail.com>
Salvaged from PR #8695.
2026-04-13 23:03:08 -07:00