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LCSB-BioCore / COBREXA.jl

Constraint-Based Reconstruction and EXascale Analysis
https://lcsb-biocore.github.io/COBREXA.jl/
Apache License 2.0
42 stars 8 forks source link

extensible variable semantics #735

Closed exaexa closed 1 year ago

exaexa commented 1 year ago

Not really working yet, but this should clear the current mess in variables vs. reactions vs. fluxes vs. enzymes vs. mass groups vs. whatnot.

codecov[bot] commented 1 year ago

Codecov Report

Base: 90.33% // Head: 89.38% // Decreases project coverage by -0.96% :warning:

Coverage data is based on head (4e2478a) compared to base (d2d2370). Patch coverage: 67.10% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## next #735 +/- ## ========================================== - Coverage 90.33% 89.38% -0.96% ========================================== Files 81 82 +1 Lines 2008 2053 +45 ========================================== + Hits 1814 1835 +21 - Misses 194 218 +24 ``` | [Impacted Files](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?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/sampling/affine\_hit\_and\_run.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL3NhbXBsaW5nL2FmZmluZV9oaXRfYW5kX3J1bi5qbA==) | `94.11% <ø> (ø)` | | | [src/solver.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3NvbHZlci5qbA==) | `92.85% <ø> (ø)` | | | [src/types/accessors/AbstractMetabolicModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL2FjY2Vzc29ycy9BYnN0cmFjdE1ldGFib2xpY01vZGVsLmps) | `78.33% <ø> (-2.83%)` | :arrow_down: | | [src/types/accessors/bits/missing\_impl.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL2FjY2Vzc29ycy9iaXRzL21pc3NpbmdfaW1wbC5qbA==) | `100.00% <ø> (ø)` | | | [src/types/models/HDF5Model.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9IREY1TW9kZWwuamw=) | `100.00% <ø> (ø)` | | | [src/types/models/JSONModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9KU09OTW9kZWwuamw=) | `98.96% <ø> (ø)` | | | [src/types/models/MATModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9NQVRNb2RlbC5qbA==) | `92.42% <ø> (ø)` | | | [src/types/models/MatrixModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9NYXRyaXhNb2RlbC5qbA==) | `96.66% <ø> (ø)` | | | [src/types/models/ObjectModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9PYmplY3RNb2RlbC5qbA==) | `100.00% <ø> (ø)` | | | [src/types/models/SBMLModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9TQk1MTW9kZWwuamw=) | `93.33% <ø> (+0.57%)` | :arrow_up: | | ... and [8 more](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/735?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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exaexa commented 1 year ago

@stelmo there are some TODOs before I can merge this, but the API for variables is final. I'll do the constraint APIs in a separate PR.