Recompute

The package ships precomputed grid CSVs in its data/ directory. That is why explore() and phasemap() work instantly with no kinetic model installed and no ODE solve — they only read and visualize cached steady-state fluxes and metabolite pools.

Regenerating those grids is a separate, heavier operation: it requires the kinetic model and solves the glycolysis + PPP ODE system at every demand cell. This is gated behind a package extension so the model and solver stack are not dependencies of the visualization package.

How to recompute

Install the kinetic model alongside this package:

using Pkg
Pkg.add(url="https://github.com/DenisTitovLab/PentosePhosphatePathway.jl")

Load it. This activates the recompute extension (PentosePhosphatePathwayExt), which pulls in the solver stack and wires up regenerate_grid:
```
using GlycolysisPentosePathwayPhaseMap
using PentosePhosphatePathway
```
Regenerate the grid CSVs:
```
regenerate_grid(; ...)
```

If you call regenerate_grid without the extension loaded, it raises a friendly error telling you to using PentosePhosphatePathway first.

Note

regenerate_grid solves the kinetic ODE model at every demand cell and takes minutes. The first using / solve in a session also pays Julia's compilation cost. This is expected, not a hang.