refactor: extract burden-summary renderer from burden_test (PR-5)#183
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burden_test (~780-line CLI orchestrator) inlines its result presentation. Extract the cohesive ASCII summary / top-significant-table renderer into a pure _render_burden_summary(result_df, alpha, phenotype_type) helper — ~100 lines move out of the command body into a named, testable function. Behavior-preserving: output verified byte-identical to the prior inline logic for binary, continuous, and no-significant-results cases. Scope: the other two renderers the plan mentioned (the dry-run plan and the stratified-loop) are left in place — they depend on ~20 command params, so extracting them would be param-soup with little clarity gain; noted as a possible follow-up. flake8 clean; import smoke OK.
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| Category | Results |
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| Documentation | 1 minor |
| Complexity | 2 medium |
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PR-5 (burden_cli) — extract the burden-summary renderer from
burden_testburden_testis a ~780-line CLI orchestrator that inlines its result presentation. This PR extracts the cohesive ASCII summary / top-significant-table renderer into a pure, testable helper:_render_burden_summary(result_df, alpha, phenotype_type)— counts significant gene sets and renders the "BURDEN ANALYSIS SUMMARY" + a top-5 ASCII table, with columns chosen by phenotype type (odds ratio for binary, standard error for continuous). ~100 lines move out of the command body.Scope
The plan also named a dry-run/plan renderer and a stratified-loop helper. Those are left in place: they depend on ~20 of the command's parameters, so extracting them would be param-soup with little real clarity gain. The summary renderer is the cohesive, low-parameter (3 inputs) piece — the clean win. Further decomposition of the param-heavy orchestrator is noted as a possible follow-up.
Verification
_render_burden_summaryoutput verified byte-identical to the prior inline logic across binary, continuous, and no-significant-results cases (capturedclick.echooutput compared against a verbatim copy of the old block).flake8(project selection) clean (no danglingn_significant); my edited region isblack-compliant; diffs scoped to the helper + the command body. Import smoke OK.