Refactor: modernize CLI routing, optimize MPA pipeline and taxonomic sorting - #18

Merged

ilypopv merged 9 commits into

mainfrom

May 31, 2026

Commits on May 22, 2026

build: exclude __main__ guard lines from coverage reporting
ilypopv
committed
bf0f182

Commits on May 31, 2026

refactor(docs): update CLI usage to use --step flag
ilypopv
committed
3cedb39
refactor: modernize CLI routing and implement --step interface
ilypopv
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00a381f
feat: add --viruses flag to full pipeline
ilypopv
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bea9762
refactor(mpa): implement hierarchical sorting for combined MPA tables
ilypopv
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e15d1ef
refactor(mpa): overhaul kreport parsing logic for robust hierarchy tracking
ilypopv
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e48266e
test: update unit tests for _parse_line return type changes
ilypopv
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06eedbb
refactor: improve CLI startup output visibility
ilypopv
committed
54bf8e7
docs: update results directory structure in README
ilypopv
committed
766ce52