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SysBioChalmers / raven-python Public

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tINIT and ftINIT pipelines with Human-GEM validation#7

Merged

edkerk merged 18 commits into

developSysBioChalmers/raven-python:developfrom

feature/initSysBioChalmers/raven-python:feature/initCopy head branch name to clipboard

May 30, 2026

Conversation Commits18 (18)Checks Files changed

Merged

tINIT and ftINIT pipelines with Human-GEM validation#7
edkerk merged 18 commits into
developfrom
feature/init

Commits

Commits on May 29, 2026

Project scaffold: pyproject + package skeleton + README + LICENSE
edkerk
committed
Add GitHub Actions CI and the maintainer-scripts README
edkerk
committed
Add the foundation utilities: GPR, balance, parse, sort, validate
edkerk
committed
Add the model-manipulation layer (add, remove, transport, merge, etc.)
edkerk
committed
Add binary + data resolvers for external tools and published artefacts
edkerk
committed
Add YAML and SIF model I/O
edkerk
committed
Add Excel export and the Standard-GEM git-layout export
edkerk
committed
Add BLAST and DIAMOND wrappers for protein-homology searches
edkerk
committed
Add the homology-based draft model builder (getModelFromHomology port)
edkerk
committed
Add KEGG download, dump parser and taxonomy parser
edkerk
committed
Add KEGG HMM-library build and HMM-based KO assignment
edkerk
committed
Add KEGG species-model assembly (per-organism reconstruction)
edkerk
committed
Add KEGG artefact-build scripts and HMM-cutoff calibration docs
edkerk
committed
Add metabolic-task parsing and the check_tasks validator
edkerk
committed
Add connectivity gap-filling (MILP) against template models
edkerk
committed
Add the tINIT (INIT) MILP and its supporting machinery
edkerk
committed
Add the ftINIT pipeline and task-aware gap-filling
edkerk
committed
Add Human-GEM validation, parameter studies and cross-solver tests
edkerk
committed

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