pFBA pipe

[stelmo]

Adds a basic pipe-able pFBA variant. Should play nicely with more interesting model types, e.g. enzyme constrained etc.

gm_changed_bound =
    model |>
    with_changed_bound("BIOMASS_Ecoli_core_w_GAM", lower_bound = growth_lb) |>
    with_enzyme_constraints(
        gene_product_mass_group_bound = Dict(
            "uncategorized" => total_gene_product_mass,
        ),
    )

pfba_sol =
  gm_changed_bound |>
  with_parsimonious_solution(:enzyme) |>
  flux_balance_analysis(Clarabel.Optimizer)

@exaexa what do you think?

[codecov]

Codecov Report

Patch coverage: 73.46% and project coverage change: +0.33 🎉

Comparison is base (c3ee550) 88.30% compared to head (a58407a) 88.63%.

Additional details and impacted files

@@            Coverage Diff             @@
##             next     #747      +/-   ##
==========================================
+ Coverage   88.30%   88.63%   +0.33%     
==========================================
  Files          90       89       -1     
  Lines        2248     2262      +14     
==========================================
+ Hits         1985     2005      +20     
+ Misses        263      257       -6     

Impacted Files	Coverage Δ
src/analysis/flux_balance_analysis.jl	100.00% <ø> (+22.22%)	⬆️
src/analysis/minimize_metabolic_adjustment.jl	100.00% <ø> (ø)
src/analysis/modifications/generic.jl	60.00% <ø> (ø)
src/analysis/parsimonious_flux_balance_analysis.jl	80.00% <ø> (ø)
src/wrappers/MatrixCoupling.jl	89.47% <ø> (ø)
src/wrappers/misc/MatrixModel.jl	100.00% <ø> (ø)
src/wrappers/misc/enzyme_constrained.jl	100.00% <ø> (ø)
src/wrappers/misc/mmdf.jl	100.00% <ø> (ø)
src/wrappers/misc/simplified_enzyme_constrained.jl	100.00% <ø> (ø)
src/wrappers/MinimizeDistance.jl	57.69% <57.69%> (ø)
... and 11 more

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[stelmo]

/format

[github-actions]

✔️ Auto-formatting triggered by this comment succeeded, commited as dabbe84

[stelmo]

/format

[github-actions]

✔️ Auto-formatting triggered by this comment succeeded, commited as f916bfb

[stelmo]

NOTE: variables are not the semantic variables!

[stelmo]

this poses problems for MOMA too

[stelmo]

and also for pFBA in general

[exaexa]

ok now we have wrapper architecture nicely split off and there's the "generic" QP objective wrappers. I guess pFBA can be done over these as well, right?

[exaexa]

awright