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Add soulcap-lookup, soulcap-tokens, type checking, and CI improvements - #15
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…vements - soulcap-lookup: new CLI to search CL terms via EBI OLS4 REST API - soulcap-tokens: new CLI to extract distinct marker tokens from the Marker Combinations CSV (M1 prerequisite) - extract_markers() / extract_markers_from_csv() added to marker_syntax - Fix __version__ duplication: read from importlib.metadata at runtime - Add mypy + pandas-stubs to dev deps; mypy clean across all 7 modules - Fix 4 type bugs surfaced by mypy (None narrowing, Hashable index, ExcelFile stubs, mixed params dict) - CI: split into lint + test jobs; add ruff format --check; add uv sync --frozen; add mypy type-check step - Add Dependabot config for Actions and pip deps - Add pre-commit config (ruff check + format) - Create marker_mappings/ directory for tracked mapping artifacts - Resolve merge conflicts from upstream (pyproject.toml, marker_syntax, marker_validation report) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This was referenced Sep 27, 2026
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Summary
soulcap-lookup/soulcap-tokensandols4_lookup.py(OLS4-backed term resolution)marker_syntax.pyvalidation/token extractionreports/marker_validation.mdfrom the current sheet syncVerified in isolation via a separate worktree (not just as part of the full branch):
pytest: 165 passed, 94.68% coverage (gate is 80%)ruff check .: all checks passedMore pieces will follow once this is reviewed/merged — next up is the
soulcap-matchCLI +soulcap-hgnccommits.Test plan
uv run pytestpasses in isolation (165 passed, 94.68% coverage)uv run ruff check .passes in isolation