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extensible variable semantics #735

Merged
merged 19 commits into from
Feb 8, 2023
Merged

extensible variable semantics #735

merged 19 commits into from
Feb 8, 2023

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exaexa
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@exaexa exaexa commented Feb 2, 2023

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

@exaexa exaexa requested a review from stelmo February 2, 2023 13:06
@exaexa exaexa marked this pull request as draft February 2, 2023 13:06
@exaexa exaexa changed the title WIP: extensible variable semantics extensible variable semantics Feb 2, 2023
@exaexa exaexa force-pushed the mk-extensible-variables branch from 6e8d79d to c00e228 Compare February 2, 2023 13:11
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lg2m

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codecov bot commented Feb 3, 2023

Codecov Report

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

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
@@            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 Coverage Δ
src/analysis/sampling/affine_hit_and_run.jl 94.11% <ø> (ø)
src/solver.jl 92.85% <ø> (ø)
src/types/accessors/AbstractMetabolicModel.jl 78.33% <ø> (-2.83%) ⬇️
src/types/accessors/bits/missing_impl.jl 100.00% <ø> (ø)
src/types/models/HDF5Model.jl 100.00% <ø> (ø)
src/types/models/JSONModel.jl 98.96% <ø> (ø)
src/types/models/MATModel.jl 92.42% <ø> (ø)
src/types/models/MatrixModel.jl 96.66% <ø> (ø)
src/types/models/ObjectModel.jl 100.00% <ø> (ø)
src/types/models/SBMLModel.jl 93.33% <ø> (+0.57%) ⬆️
... and 8 more

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@exaexa exaexa requested a review from stelmo February 3, 2023 10:55
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exaexa commented Feb 3, 2023

@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.

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Really good work

@exaexa exaexa force-pushed the mk-extensible-variables branch from 1d840d2 to efb6ed8 Compare February 7, 2023 13:03
@exaexa exaexa force-pushed the mk-extensible-variables branch from 164008c to 17958d0 Compare February 7, 2023 20:48
@exaexa exaexa marked this pull request as ready for review February 7, 2023 21:36
@exaexa exaexa force-pushed the mk-extensible-variables branch from 76332a2 to add7fee Compare February 8, 2023 13:41
@exaexa exaexa force-pushed the mk-extensible-variables branch from add7fee to 4e2478a Compare February 8, 2023 14:30
@exaexa exaexa merged commit 5d7f628 into next Feb 8, 2023
@exaexa exaexa deleted the mk-extensible-variables branch February 8, 2023 14:57
@exaexa exaexa added this to the v2.0 milestone Feb 16, 2023
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2 participants