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Turn MMDF analysis into a wrapper #699

Merged
merged 3 commits into from
Feb 12, 2023
Merged

Turn MMDF analysis into a wrapper #699

merged 3 commits into from
Feb 12, 2023

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stelmo
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@stelmo stelmo commented Nov 10, 2022

Wrappers fit in more with the COBREXA ecosystem. Let's convert all the MMDF analyses into a ThermodynamicModel that is a wrapper.

Closes #614 when complete

@stelmo stelmo changed the base branch from master to next November 10, 2022 12:02
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stelmo commented Nov 13, 2022

#700 needs to be done before this one

@stelmo stelmo added the do not merge When a PR is labelled as such, do not merge label Feb 11, 2023
@stelmo stelmo mentioned this pull request Feb 11, 2023
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stelmo commented Feb 12, 2023

NB: merge only after #742

@stelmo stelmo changed the base branch from next to mo-enzyme-semantics February 12, 2023 12:48
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codecov bot commented Feb 12, 2023 •
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Codecov Report

Base: 88.68% // Head: 88.79% // Increases project coverage by +0.11% 🎉

Coverage data is based on head (0e8c780) compared to base (b1c47d1).
Patch coverage: 93.50% of modified lines in pull request are covered.

Additional details and impacted files 
@@            Coverage Diff             @@
##             next     #699      +/-   ##
==========================================
+ Coverage   88.68%   88.79%   +0.11%     
==========================================
  Files          85       88       +3     
  Lines        2085     2097      +12     
==========================================
+ Hits         1849     1862      +13     
+ Misses        236      235       -1
Impacted Files Coverage Δ
src/reconstruction/pipes/thermodynamic.jl 0.00% <0.00%> (ø)
src/types/accessors/AbstractMetabolicModel.jl 78.33% <ø> (ø)
src/types/wrappers/MaxMinDrivingForceModel.jl 95.77% <95.77%> (ø)
src/reconstruction/thermodynamic.jl 100.00% <100.00%> (ø)
src/types/misc/thermodynamic.jl 100.00% <100.00%> (ø)
src/types/accessors/bits/semantics.jl 65.30% <0.00%> (+4.08%) ⬆️

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stelmo commented Feb 12, 2023

/format

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✔️ Auto-formatting triggered by this comment succeeded, commited as f2ecc34

github-actions bot pushed a commit that referenced this pull request Feb 12, 2023
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triggered by @stelmo on PR #699
@stelmo stelmo removed the do not merge When a PR is labelled as such, do not merge label Feb 12, 2023
@stelmo stelmo requested a review from exaexa February 12, 2023 14:05
Base automatically changed from mo-enzyme-semantics to next February 12, 2023 16:43
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Pretty much OK. I'll need to fix the semantics-generating macro to allow sensible plurals for energys etc., then I'll merge it. There are some notes for code moving/reorganization, that should be easy. These should go to misc/ or so, as with other modules (Analysis AFAIK has the same).

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lovely. Let's not care about the gibbs issue for now.

@stelmo stelmo merged commit 61b2d8c into next Feb 12, 2023
@stelmo stelmo deleted the mo-mmdf-wrapper branch February 12, 2023 18:56
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max_min_driving_force and moment should be a ModelWrapper
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