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[bot]]

:heavy_check_mark: Auto-formatting triggered by this comment succeeded, commited as dba3ae168b8fd55896eea7a97df4e7594b42762a

[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[bot]]

Codecov Report

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

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

:exclamation: 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

```diff @@ 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](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | Coverage Δ | | |---|---|---| | [src/analysis/flux\_balance\_analysis.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL2ZsdXhfYmFsYW5jZV9hbmFseXNpcy5qbA==) | `77.77% <ø> (ø)` | | | [src/analysis/minimize\_metabolic\_adjustment.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21pbmltaXplX21ldGFib2xpY19hZGp1c3RtZW50Lmps) | `100.00% <ø> (ø)` | | | [src/analysis/screening.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL3NjcmVlbmluZy5qbA==) | `98.00% <ø> (ø)` | | | [src/analysis/variability\_analysis.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL3ZhcmlhYmlsaXR5X2FuYWx5c2lzLmps) | `97.29% <ø> (ø)` | | | [src/reconstruction/pipes/enzymes.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL3BpcGVzL2VuenltZXMuamw=) | `100.00% <ø> (ø)` | | | [src/reconstruction/pipes/generic.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL3BpcGVzL2dlbmVyaWMuamw=) | `51.72% <47.61%> (+25.05%)` | :arrow_up: | | [src/reconstruction/ObjectModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL09iamVjdE1vZGVsLmps) | `84.27% <76.77%> (+3.36%)` | :arrow_up: | | [src/analysis/modifications/generic.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21vZGlmaWNhdGlvbnMvZ2VuZXJpYy5qbA==) | `60.00% <100.00%> (ø)` | | | [src/analysis/modifications/optimizer.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21vZGlmaWNhdGlvbnMvb3B0aW1pemVyLmps) | `100.00% <100.00%> (ø)` | | | [src/misc/check\_keys.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL21pc2MvY2hlY2tfa2V5cy5qbA==) | `100.00% <100.00%> (ø)` | | | ... and [3 more](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/762?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore)

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[stelmo]

@exaexa I think this should be ready now

[stelmo]

/format

[github-actions[bot]]

:heavy_check_mark: Auto-formatting triggered by this comment succeeded, commited as fbc5352dcd276216cea9ad8c5d1235969f2ec597

[stelmo]

/format

[github-actions[bot]]

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