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This release introduces support for the open source SCIP solver.

It is now possible to select a solver using --solver. Only cplex and gurobi are available at the moment.

Solves issue with spontaneous/diffusion reactions getting excluded from the models.

New in CarveMe 1.5:

• Updated internal database to BiGG 1.6
• Rebuild and curated universal model (increased from 2383 to 2861 metabolites and from 4343 to 5532 reactions)
• Improved all element annotations (MEMOTE score increased from ~30% to ~80%)

Current benchmark scores:

• Biolog MCC = 0.255
• Essentiality MCC = 0.483

Solves a few problems, including installation issues and two bugs introduced in gapfill and merge_community in the last release.

New in this release:

• New benchmark feature to test each release using biolog and gene essentiality data.
• Updated RefSeq database to release 201.
• Dropped support for GenBank.

Current benchmark scores:

• Biolog MCC = 0.262
• Essentiality MCC = 0.428

• Dropped support for Python 2
• Switched to ReFramed
• Using entry points in setup.py (easier windows installation)

This release introduces Python 3 compatibility.

For the moment, both Python 2 and Python 3 will be supported (we may drop support for Python 2 at some point in the future).

New features in this release:

• Debug mode with --debug (outputs all intermediate computations to flat files for debug purposes)
• Support for experimental constraints (with --soft and --hard)

Plus some minor bug fixes.

Multiple changes:

• new biomass templates (gram positive, gram negative)
• allow external biomass library
• auto-normalize biomass weight to 1 gram
• further manual curation of universal model
• generation of microbial community models
• detailed online documentation