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Release 3.0.0b2 - #194

Merged

edkerk merged 114 commits into

mainfrom

develop

Nov 1, 2026

Merged

Release 3.0.0b2#194
edkerk merged 114 commits into
mainfrom
develop

Commits on Sep 8, 2026
Commits on Sep 9, 2026
- Fold omics.hpa into init as init.hpa (#158)
  edkerk
  authored
  61da432
Commits on Sep 11, 2026
- Cut three redundant costs in ftinit/taskfill (#159)
  edkerk
  authored
  7a41303
Commits on Sep 20, 2026
- Expose ftINIT's Gurobi tolerances and presolve level as parameters (#160)
  edkerk
  authored
  98d02a8
Commits on Sep 23, 2026
- GNU GPL-v3
  edkerk
  authored
  ea95181
Commits on Sep 24, 2026
- Keep the template's solver in merged models and warn on GLPK ftINIT solves (#161)
  edkerk
  authored
  d7bd984
Commits on Sep 29, 2026
Commits on Oct 5, 2026
- feat: keep gene-free reactions and template notes in get_model_from_homology, drop duplicate genes (#166)
  edkerk
  authored
  d0707de
- feat: set_model_metadata / get_model_metadata, and version and date in export_for_git (#167)
  edkerk
  authored
  3a0d442
Commits on Oct 7, 2026
- fix: write RAVEN-format .mat and RAVEN-readable SBML (#168)
  edkerk
  authored
  7effd68
- fix: keep raven-toolbox bookkeeping out of the SBML notes (#169)
  edkerk
  authored
  ee0f886
Commits on Oct 17, 2026
Commits on Oct 19, 2026
- Follow-ups from the RAVEN 3 Guide review (#176)
  edkerk
  authored
  4128e2a
Commits on Oct 21, 2026
Commits on Oct 22, 2026
Commits on Oct 23, 2026
Commits on Oct 24, 2026
Commits on Oct 27, 2026
- ftinit: per-reaction big-M from each scored reaction's flux capacity, capped at big_m (default 1000)
  edkerk
  committed
  e48e445
Commits on Oct 28, 2026
Commits on Oct 30, 2026
- read_yaml_model reads empty enzymes maps and quotes inside values; fseof follows ecFSEOF (#185)
  edkerk
  authored
  a98e2a1
- fix: align raven-toolbox with RAVEN (parity review, round 3) (#186)
  edkerk
  authored
  94f3940
Commits on Oct 31, 2026
Commits on Nov 1, 2026

Commits

Commits on Sep 8, 2026

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Commits on Sep 11, 2026

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Commits on Sep 29, 2026

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Commits on Oct 23, 2026

Commits on Oct 24, 2026

Commits on Oct 27, 2026

Commits on Oct 28, 2026

Commits on Oct 30, 2026

Commits on Oct 31, 2026

Commits on Nov 1, 2026