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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

Fix cFBA implementation #764

Closed stelmo closed 1 year ago

codecov[bot] commented 1 year ago

Codecov Report

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

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

:exclamation: 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 ```diff @@ 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](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore) | Coverage Δ | | |---|---|---| | [src/types/accessors/AbstractMetabolicModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL2FjY2Vzc29ycy9BYnN0cmFjdE1ldGFib2xpY01vZGVsLmps) | `77.61% <ø> (ø)` | | | [src/reconstruction/pipes/community.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL3BpcGVzL2NvbW11bml0eS5qbA==) | `71.42% <71.42%> (ø)` | | | [src/reconstruction/CommunityModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL0NvbW11bml0eU1vZGVsLmps) | `86.66% <86.66%> (ø)` | | | [src/types/wrappers/EqualGrowthCommunityModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL3dyYXBwZXJzL0VxdWFsR3Jvd3RoQ29tbXVuaXR5TW9kZWwuamw=) | `90.62% <90.62%> (ø)` | | | [src/types/misc/CommunityModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21pc2MvQ29tbXVuaXR5TW9kZWwuamw=) | `95.65% <95.65%> (ø)` | | | [src/types/models/CommunityModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3R5cGVzL21vZGVscy9Db21tdW5pdHlNb2RlbC5qbA==) | `98.71% <98.71%> (ø)` | | | [src/analysis/modifications/community.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2FuYWx5c2lzL21vZGlmaWNhdGlvbnMvY29tbXVuaXR5Lmps) | `100.00% <100.00%> (ø)` | | | [src/io/show/CommunityModel.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL2lvL3Nob3cvQ29tbXVuaXR5TW9kZWwuamw=) | `100.00% <100.00%> (ø)` | | | [src/misc/checkkeys.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL21pc2MvY2hlY2trZXlzLmps) | `91.66% <100.00%> (ø)` | | | [src/reconstruction/pipes/generic.jl](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=LCSB-BioCore#diff-c3JjL3JlY29uc3RydWN0aW9uL3BpcGVzL2dlbmVyaWMuamw=) | `44.82% <0.00%> (-6.90%)` | :arrow_down: | | ... and [3 more](https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/pull/764?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 commented 1 year ago

/format

github-actions[bot] commented 1 year ago

:heavy_check_mark: Auto-formatting triggered by this comment succeeded, commited as 264da596af6fceffacb32e27c65e08ef9728196e

stelmo commented 1 year ago

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
stelmo commented 1 year ago

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