release: 2.4.0 — KEGG (opt-in, stdio-only) + Reactome MIE signed-regulation route - #185

Merged

arkinjo merged 13 commits into

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Jul 31, 2026

Commits on Jul 31, 2026

feat(kegg): parse KGML into a signed directed pathway graph

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66ff166
feat(kegg): add the KEGG sub-server, mounted on stdio only

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66c2150
feat(kegg): expose signed path enumeration and feedback-loop detection

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1916cba
fix(guide): serve the KEGG section only where the KEGG tools exist

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db3314c
fix(kegg): stop kegg_pathway_cycles overselling; signed paths are the primitive

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a600a47
docs(kegg): correct a false claim — Reactome DOES have signed regulation

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4cc3c9c
docs(kegg): correct the prokaryote claim — Reactome has them, just not as pathways

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3ebb3e5
feat(mie): give Reactome a verified signed-regulation route and organism-coverage scoping

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26146d8
docs(readme): surface the KEGG licence note where the decision is actually made

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444a55f
feat(kegg): make KEGG opt-in via TOGOMCP_ENABLE_KEGG so non-academic users can run local

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08fd91b
fix(kegg): compress run_sparql mentions to one tool to stop crowding tool-search

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d314d8f
fix(kegg): finish the de-collision — kegg_conv too

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8f92b4a
release: 2.4.0

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40c1b41