Faithful set-variant networks + LinkML output contract + diagram connectivity + determinism - #43

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adamjohnwright merged 17 commits into

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fix/complex-as-single-node

Jul 14, 2026

Commits on May 26, 2026

Add entity→reaction proxy mapping for decomposed species

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claude
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Commits on May 27, 2026

Decompose boundary complexes positionally, per occurrence

adamjohnwright
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claude
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Commits on May 28, 2026

Make dissociation members separate readout sinks, not shared with functional nodes

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claude
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validate-against-mpbiopath: signed propagator + proxy-mapping support

adamjohnwright
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claude
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Commits on May 29, 2026

Variant decomposition for negative regulators

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claude
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Commits on May 30, 2026

Emit substrate-depletion edges for phosphatase reactions

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claude
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Commits on May 31, 2026

Revert ubiquitin-ligase depletion filter (-0.5pp regression)

adamjohnwright
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claude
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Commits on Jun 1, 2026

Topology-based ubiquitin substrate-depletion edges (+1.75pp)

adamjohnwright
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claude
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Commits on Jun 3, 2026

Coerce stoichiometry column to Int64 in the final DataFrame

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claude
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Commits on Jul 10, 2026

Gitignore graphify-out/ (code-graph tool output)

adamjohnwright
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claude
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Commits on Jul 14, 2026