LCSB-BioCore / COBREXA.jl

Constraint-Based Reconstruction and EXascale Analysis
https://lcsb-biocore.github.io/COBREXA.jl/
Apache License 2.0
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Add pipes to all the analysis functions #751

Closed stelmo closed 1 year ago

stelmo commented 1 year ago

I want this to be a reality:

model |> with_changed_bounds(...) |> with_added_reaction(...) |> with_enzyme_constraints(...) |> flux_balance_analysis(...) |> to_dict(:enzymes)
stelmo commented 1 year ago

Related to #747

codecov[bot] commented 1 year ago

Codecov Report

Base: 88.79% // Head: 88.62% // Decreases project coverage by -0.17% :warning:

Coverage data is based on head (773dfda) compared to base (61b2d8c). Patch coverage: 0.00% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## next #751 +/- ## ========================================== - Coverage 88.79% 88.62% -0.17% ========================================== Files 88 88 Lines 2097 2101 +4 ========================================== Hits 1862 1862 - Misses 235 239 +4 ``` | [Impacted Files](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/751?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/751?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL2ZsdXhfYmFsYW5jZV9hbmFseXNpcy5qbA==) | `81.81% <0.00%> (-18.19%)` | :arrow_down: | | [src/analysis/parsimonious\_flux\_balance\_analysis.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/751?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL3BhcnNpbW9uaW91c19mbHV4X2JhbGFuY2VfYW5hbHlzaXMuamw=) | `70.83% <0.00%> (-6.44%)` | :arrow_down: | 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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exaexa commented 1 year ago

This is good. Do we add the Result overloads here?

stelmo commented 1 year ago

Yes! I was thinking that each analysis function returns both the input model and the solved jump model (probably wrapped up into a type)