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Open work

What's still on the books. See raven_migration.md for the function-by- function port status (most of it is done); see IMPROVEMENTS.md for the catalogue of raven-python improvements that should also be back-ported into MATLAB RAVEN.

Major

Visualization (plotting/)

Not started. RAVEN has limited plotting (drawMap etc., MATLAB-bound). For raven-python the most useful targets are:

  • Pathway maps / Escher integration for context-specific models.
  • Omics overlay (gene-score / expression heatmaps on the reaction set).
  • Flux distribution overlays.

cobrapy + Escher already covers a lot here — likely a thin integration layer rather than a port.

Metabolomics-based scoring in ftINIT

The metabolomics-detected metabolite production-reward block in init.ftinit currently raises NotImplementedError if a non-empty metabolomics argument is passed. The linear merge eliminates degree-2 detected metabolites, so it needs producer-group-mapping + negative-producer force-flux constraints — the most intricate MILP piece, for the least-used input. Worth doing only when a real user request lands.

Infrastructure

  • Binary ZIP releases for BLAST/DIAMOND (Phase 3a). The runtime resolver in binaries.py is ready; the registry is empty until ZIPs are published as GitHub release assets.
  • KEGG data artefact releases. See maintaining_kegg_data.md.

Smaller items

  • known_issues.md — backlog of low-priority edge cases / robustness gaps / dead code from the full-codebase review. None affects correctness on well-formed inputs.
  • IMPROVEMENTS.md — items marked 💡 proposed are candidates to implement (and back-port).

Upstream blockers (not raven-python work, but worth tracking)

  • optlang.hybrid_interface.Configuration.clone() bug — blocks HiGHS at any scale (CI catches it in tests/test_init_solvers.py).
  • GLPK's MIP solve ignores configuration.timeout at genome scale — blocks GLPK on large MILPs.
  • Both documented in init_solver_benchmark.md with concrete fix suggestions.