v4.0.0b1

Version realignment: geckopy numbering will be aligned with GECKO (MATLAB),
justifying a jump to 4.x. This is the first release published to PyPI.

• New: kcat_tuning.evotune fits ec.kcat to measured growth rates and
  exchange fluxes with CMA-ES (screen_kcat_leverage, select_tunable_mask,
  cmaes_kcat_tuning, tune_prior_penalty_weight), replacing the earlier
  ABC-SMC approach. EvotuneResult.corrections() reports a tuning run as a
  ranked table of what changed and why, rather than a raw kcat vector. Gated
  behind the new evotune extra.
• New: gather_kcats.review.review_assignment flags kcat-assignment
  problems (repeated values, EC-maximum fallback, implausible magnitude)
  worth curating before a tuning run.
• kcat_sensitivity_analysis renamed to kcat_tuning, with the CMA-ES
  subpackage named evotune rather than bayesian — the shipped method is
  CMA-ES, not Bayesian inference.
• flexibilize_enz_concs: the post-loop refinement now uses MATLAB's soft
  ±0.25% growth band instead of pinning to exp_growth exactly, matching
  flexibilizeEnzConcs.m.
• make_ec_model no longer splits exchange reactions in the irreversibility
  stage, matching makeEcModel.m's nonExchRxns exclusion.
• get_reactions_from_enzyme now matches protein_id case-insensitively,
  matching MATLAB's strcmpi.
• read_dlkcat_output gained an opt-in strict=True fail-fast on
  unrecognized substrates, matching MATLAB, and now reports drop reasons
  separately instead of lumping them together.
• assign_standard_kcat: a NaN-kcat reaction no longer counts toward a
  subsystem's threshold eligibility or gets folded into the subsystem
  median; unset kcats now get filled for NaN too, not just literal zeros.
• parse_okp_output now tags provenance with the OKP- prefix MATLAB
  applies; merge_kcats strips it again before source-priority matching so
  tagged rows still rank correctly.
• set_kcat_for_reactions now accepts a per-isozyme kcat list against an
  un-suffixed base name (assigned positionally, matching MATLAB), and writes
  ec.source = "setKcatForReactions" (MATLAB's actual value) instead of
  "manual".
• ec_fseof: scan floor now anchors to the production target's flux at
  biomass-optimum instead of a fixed fraction of the theoretical maximum,
  and candidates are restricted to gene-associated, non-standard reactions
  before classification — both matching ecFSEOF.m.
• ec_fva's parallel path now uses cobra.util.process_pool.ProcessPool
  instead of a hand-rolled multiprocessing.Pool — fixes a slow Windows
  initializer handoff and gives graceful pool teardown. Public signature
  unchanged.
• raven-toolbox dependency switched from a git+...@develop pin to the
  PyPI >=3.0.0b1 release, which carries the convert_to_irreversible(..., rxns=...) addition make_ec_model needs.
• Packaging: the sdist was bundling the entire local .venv-win
  virtualenv (~60MB, including a compiled scipy wheel) because .gitignore
  listed .venv/ but not .venv-win/, and hatchling's default sdist
  selection only reads the top-level .gitignore.
• release.yml: PyPI publish job enabled (trusted publishing).
• README: disambiguation note simplified and repointed at the specific old
  geckopy release (2.0.2 and earlier), now that this project has taken
  over the PyPI project name itself.

Full changelog: https://github.com/SysBioChalmers/geckopy/blob/main/CHANGELOG.md
Compare: v0.3.0...v4.0.0b1