Fix and extend reconstruction functions and pipes for objectmodel

[stelmo]

adds non-inplace change_objective as well as pipe
fixes change_bound to copy all fields
adds change_gene_product_bound in-place, non-inplace, as well as pipes
Also change modifications to have the prefix modify_ instead of change. This was to prevent name space issues.

Reconstruction functions have add_, remove_ and change_ prefixes now.

[stelmo]

No idea why this is failing...

[stelmo]

This turned into a big housekeeping session

[stelmo]

/format

[github-actions]

✔️ Auto-formatting triggered by this comment succeeded, commited as dba3ae1

[stelmo]

@exaexa the formatter causes this PR to break because it tries to split lines incorrectly.
Before formatting:

@io_log @warn "Automatically converting $(typeof(model)) to JSONModel for saving, information may be lost."

After formatting (error):

@io_log
@warn "Automatically converting $(typeof(model)) to JSONModel for saving, information may be lost."

[codecov]

Codecov Report

Base: 88.31% // Head: 88.37% // Increases project coverage by +0.06% 🎉

Coverage data is based on head (56c73c8) compared to base (a6e7357).
Patch coverage: 75.77% of modified lines in pull request are covered.

❗ Current head 56c73c8 differs from pull request most recent head fbc5352. Consider uploading reports for the commit fbc5352 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             next     #762      +/-   ##
==========================================
+ Coverage   88.31%   88.37%   +0.06%     
==========================================
  Files          89       90       +1     
  Lines        2113     2236     +123     
==========================================
+ Hits         1866     1976     +110     
- Misses        247      260      +13     

Impacted Files	Coverage Δ
src/analysis/flux_balance_analysis.jl	77.77% <ø> (ø)
src/analysis/minimize_metabolic_adjustment.jl	100.00% <ø> (ø)
src/analysis/screening.jl	98.00% <ø> (ø)
src/analysis/variability_analysis.jl	97.29% <ø> (ø)
src/reconstruction/pipes/enzymes.jl	100.00% <ø> (ø)
src/reconstruction/pipes/generic.jl	51.72% <47.61%> (+25.05%)	⬆️
src/reconstruction/ObjectModel.jl	84.27% <76.77%> (+3.36%)	⬆️
src/analysis/modifications/generic.jl	60.00% <100.00%> (ø)
src/analysis/modifications/optimizer.jl	100.00% <100.00%> (ø)
src/misc/check_keys.jl	100.00% <100.00%> (ø)
... and 3 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

[stelmo]

@exaexa I think this should be ready now

[exaexa]

Mostly okay, small tech changes needed

[stelmo]

/format

[github-actions]

✔️ Auto-formatting triggered by this comment succeeded, commited as fbc5352

[stelmo]

/format

[github-actions]

☀️ Auto-formatting triggered by this comment succeeded, but the code was already formatted correctly.