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@edkerk edkerk released this 16 Jul 17:50
· 38 commits to main since this release
v0.2.1
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Bugfix release. make_ec_model no longer mutates the GEM it is given.

Fixed

  • make_ec_model leaves the input GEM unchanged. Stages 1–5 (remove_pseudoreaction_gprs, invert_backwards_only_reactions, convert_to_irreversible, expand_model) ran in place on the caller's model, leaving it with _REV / _EXP_ reaction splits, prot_ pseudometabolites, and stripped pseudoreaction GPRs. The pipeline now works on an internal model.copy(), matching MATLAB GECKO's makeEcModel value semantics. (#32)
  • test_loads_sbml_gem on Windows: the test wrote a backslash path into the adapter TOML, which TOML reads as an escape sequence.

Documentation

  • README: disambiguation note stating that this geckopy is a from-scratch port of the MATLAB GECKO Toolbox, unrelated to and sharing no code with the separate PyPI geckopy package described in Carrasco Muriel et al. (2023).

Internal

  • CI: leaner test matrix — full Python range (3.11–3.13) on Linux plus a single Python (3.12) on macOS and Windows, instead of the full 3×3 OS × Python grid. Same OS coverage at roughly half the runner cost. (#31)
  • Removed unused test imports flagged by ruff (F401).

Full changelog: https://github.com/SysBioChalmers/geckopy/blob/main/CHANGELOG.md
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