Fix cFBA implementation

[stelmo]

No description provided.

[codecov]

Codecov Report

Base: 88.30% // Head: 88.07% // Decreases project coverage by -0.23% ⚠️

Coverage data is based on head (7bf7029) compared to base (c3ee550).
Patch coverage: 94.63% of modified lines in pull request are covered.

❗ Current head 7bf7029 differs from pull request most recent head c86a6ee. Consider uploading reports for the commit c86a6ee to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             next     #764      +/-   ##
==========================================
- Coverage   88.30%   88.07%   -0.23%     
==========================================
  Files          90       93       +3     
  Lines        2248     2373     +125     
==========================================
+ Hits         1985     2090     +105     
- Misses        263      283      +20     

Impacted Files	Coverage Δ
src/types/accessors/AbstractMetabolicModel.jl	77.61% <ø> (ø)
src/reconstruction/pipes/community.jl	71.42% <71.42%> (ø)
src/reconstruction/CommunityModel.jl	86.66% <86.66%> (ø)
src/types/wrappers/EqualGrowthCommunityModel.jl	90.62% <90.62%> (ø)
src/types/misc/CommunityModel.jl	95.65% <95.65%> (ø)
src/types/models/CommunityModel.jl	98.71% <98.71%> (ø)
src/analysis/modifications/community.jl	100.00% <100.00%> (ø)
src/io/show/CommunityModel.jl	100.00% <100.00%> (ø)
src/misc/checkkeys.jl	91.66% <100.00%> (ø)
src/reconstruction/pipes/generic.jl	44.82% <0.00%> (-6.90%)	⬇️
... and 3 more

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[stelmo]

/format

[github-actions]

✔️ Auto-formatting triggered by this comment succeeded, commited as 264da59

[stelmo]

this PR allows this kind of functionality:

cm = CommunityModel(
    members = [cm1, cm2],
    abundances = [a1, a2],
    environmental_links = [
        EnvironmentalLink(rid, mid, lb, ub) for
        (rid, mid, lb, ub) in zip(ex_rxns, ex_mids, ex_lbs, ex_ubs)
    ],
)

cm |> 
    with_changed_environmental_bound(...) |> 
    with_changed_abundances(...)
    with_equal_growth_objective() |>
    flux_balance_analysis(...; modifications =[modify_abundances(...)]) |>
    values_dict(:environmental_reaction)

and some other convenience functions

[exaexa]

The structure is okay, there are a few minor things in the comments but generally this should go in.

[exaexa]

minor technical stuff, otherwise good to go

[exaexa]

btw FFTM when the type annotations are fixed

[stelmo]

Fixed the types issues and renamed the cryptic methods. Did not fix the delimiter issue, will need tlc in #765