OpenAPI specs from https://github.com/github/rest-api-description with the 'x-octokit' extension required by the Octokit SDKs
A chemical reaction network simulator.
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Alignment abstraction for gapsmith: blast/diamond/mmseqs2 runners + precomputed TSV ingestion.
Command-line interface for gapsmith.
Core types for gapsmith: Model, Reaction, Metabolite, StoichMatrix, GPR.
Loaders for gapseq's reference data tables (SEED, MNXref, biomass JSON, pathway tables).
Draft model construction for gapsmith (port of src/generate_GSdraft.R + helpers).
FBA / pFBA / gap-filling via good_lp + HiGHS for gapseq
Pathway/reaction finder for gapsmith: selects pathways, orchestrates alignment, classifies hits, scores completeness.
I/O helpers for gapsmith: model (de)serialization (CBOR/JSON), paths, TSV/FASTA utilities.