Add LP/MILP/topological gap-filling algorithms#663
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Implement fastGapFill/swiftGapFill (gapFillFastLP via gapFillFastCore and gapFillSwiftCore), the Kumar 2007 growth-floor MILP with directionality reversal (gapFillMILP), and Meneco-style topological pre-screening (gapFillTopological). Wire them into fillGaps via an 'algorithm' name-value option. Subroutine filenames are prefixed gapFill* to avoid COBRA Toolbox collisions. Extend tGapfilling with coverage for all new paths.
Function test results224 tests 198 ✅ 37s ⏱️ Results for commit f61c028. |
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Summary
Adds three new gap-filling strategies alongside the existing reference-model MILP in
fillGaps, plus the supporting subroutines and tests.gapFillFastLP, viagapFillFastCoreandgapFillSwiftCore) — LP-relaxation connectivity gap-filling (Thiele et al. 2014; SWIFTCORE single-LP variant, Tefagh & Boyd 2020). No MILP solver required.gapFillMILP) — Kumar et al. 2007 global growth-floor MILP, with directionality-reversal repair (Big-M coupling) in addition to database-reaction addition.gapFillTopological) — Meneco-inspired BFS metabolite-producibility scope; identifies unreachable metabolites and prunes the candidate reaction set with no solver call.fillGapsgains analgorithmname-value option ('reference'default,'fastLP','swiftLP','gapfillMILP','topological') that dispatches to these while preserving the existing output signature.Naming
New subroutine filenames are prefixed
gapFill*to avoid clashes with COBRA Toolbox function names (fastcore.m,swiftcore.m, etc.).Testing
tGapfillingextended with coverage for every new path. Full suite run on MATLAB R2024b: 21/21 passing (MILP-dependent tests exercised with an available MILP solver; LP/topological paths on GLPK).