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geckopy v0.1.0a1 — first public alpha

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@edkerk edkerk released this 29 May 22:28
· 62 commits to main since this release
v0.1.0a1
14a34cb

First public alpha. Every MATLAB GECKO 3.2.5 function used in the standard ecModel build is ported; the yeast-GEM tutorial runs end-to-end. See CHANGELOG.md for the full PR-grouped list of changes.

Install

pip install \
    git+https://github.com/SysBioChalmers/raven-python.git@main \
    git+https://github.com/SysBioChalmers/geckopy.git@v0.1.0a1

geckopy depends on raven-python for shared model-manipulation primitives (expand_model, convert_to_irreversible). Neither is on PyPI yet — both install from GitHub.

Requires Python 3.11 or newer.

What's in this release

  • Build an enzyme-constrained model from a conventional GEM + adapter
  • Source kcats from BRENDA (fuzzy matching), DLKcat, OpenKineticsPredictor, or manual lists; merge across sources
  • Integrate proteomics, fit sigma, flexibilise enzyme concentrations
  • Analyse with parallel ecFVA, ecFSEOF, enzyme bottlenecks, control coefficients (shadow-price), pFBA on enzyme usage
  • Persist via YAML or SBML round-trip with ec_* metadata
  • Reproducible BRENDA snapshot refresh via geckopy brenda-refresh CLI
  • Full full_ecModel tutorial walking through yeast-GEM end-to-end

The build artefacts (sdist + wheel) will be attached by the release workflow shortly.

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