Commits · 577b1af4639d5a4b65e4b17315042efbfe8fc2dd · LCSB-BioCore / COBREXA.jl

This project is mirrored from https://github.com/LCSB-BioCore/COBREXA.jl.git. Pull mirroring updated Feb 07, 2023.

08 Apr, 2022 24 commits
- fixup gecko · 577b1af4
  St. Elmo authored Apr 08, 2022
  
  577b1af4
- fix has reaction edge case · dd8f9901
  St. Elmo authored Apr 05, 2022
  
  dd8f9901
- more kwargs · d5163911
  St. Elmo authored Apr 04, 2022
  
  d5163911
- fix kwargs in tests · 7e405eb6
  St. Elmo authored Apr 04, 2022
  
  7e405eb6
- fix another kwarg · 123d6d0a
  St. Elmo authored Apr 04, 2022
  
  123d6d0a
- update kwarg · 4bfa2bcc
  St. Elmo authored Apr 04, 2022
  
  4bfa2bcc
- format and fix · bb31baf0
  St. Elmo authored Apr 04, 2022
  
  bb31baf0
- add isozyme funct · c1379a0f
  St. Elmo authored Apr 04, 2022
  
  c1379a0f
- obliterate traling whitespace · 3998673e
  Miroslav Kratochvil authored Apr 03, 2022 and St. Elmo committed Apr 08, 2022
  
  3998673e
- added data source · 8dd3d1bc
  St. Elmo authored Apr 03, 2022
  
  8dd3d1bc
- format · 885d96b4
  St. Elmo authored Apr 03, 2022
  
  885d96b4
- fixed enzyme constrained problems · cf829449
  St. Elmo authored Apr 03, 2022
  
  cf829449
- gecko streamlined · 9f8aa921
  St. Elmo authored Apr 02, 2022
  
  9f8aa921
- reduce bound, unnecessarily high · 784ecf58
  St. Elmo authored Feb 25, 2022
  
  784ecf58
- fix test · bacdf065
  St. Elmo authored Feb 25, 2022
  
  bacdf065
- make explicit model change · 8ced80f6
  St. Elmo authored Feb 25, 2022
  
  8ced80f6
- update method signatures · 5a07fb50
  St. Elmo authored Feb 25, 2022
  
  5a07fb50
- format · a876a1a8
  St. Elmo authored Feb 25, 2022
  
  a876a1a8
- added smoment and small fixes to gecko · 0068237f
  St. Elmo authored Feb 25, 2022
  
  0068237f
- added gecko and test · f32716bf
  St. Elmo authored Feb 24, 2022
  
  f32716bf
- Merge pull request #602 from LCSB-BioCore/mo-mat-import · 0869d36b
  St. Elmo authored Apr 08, 2022
```
Add some accessors for MATModel
```
  0869d36b
- format · c5ccab9d
  St. Elmo authored Apr 08, 2022
  
  c5ccab9d
- add gets and update accessors · 536e6796
  St. Elmo authored Apr 08, 2022
  
  536e6796
- update accessors · 31a4490b
  St. Elmo authored Apr 08, 2022
  
  31a4490b
06 Apr, 2022 1 commit
- Merge pull request #598 from LCSB-BioCore/mk-extensible-stoichiometries · 46ffc365
  Miroslav Kratochvil authored Apr 06, 2022
```
make stoichiometries easily extensible to encompass more complicated analyses
```
  46ffc365
05 Apr, 2022 6 commits
- flux_variability_analysis now works on fluxes instead of bare reactions · d336a7d6
  Miroslav Kratochvil authored Apr 05, 2022
```
...the way is backwards compatible, and there's completely backwards-compatible
reaction_variability_analysis.
```
  d336a7d6
- adjust flux sampling to new fluxes() vs reactions() · ed460e45
  Miroslav Kratochvil authored Apr 05, 2022
  
  ed460e45
- fix gene enumeration in CoreModel · ff4d4715
  Miroslav Kratochvil authored Apr 05, 2022
  
  ff4d4715
- fix ModelWrapper gene accessors · 1fc46d24
  Miroslav Kratochvil authored Apr 05, 2022
  
  1fc46d24
- fix type of `genes(::CoreModel)` · a14df5be
  Miroslav Kratochvil authored Apr 05, 2022
  
  a14df5be
- clean up MetabolicModel · 0d940de2
  Miroslav Kratochvil authored Apr 05, 2022
  
  0d940de2
04 Apr, 2022 5 commits
- materialize the reactions-to-flux mapping in accessors · 52a9c527
  Miroslav Kratochvil authored Apr 04, 2022
  
  52a9c527
- fix a blatant inconsistency in logo coloring · aa82aa54
  Miroslav Kratochvil authored Apr 04, 2022
```
Preposterous!
```
  aa82aa54
- generalize some of the CMC modifications to CoreCoupling · cf7e80cf
  Miroslav Kratochvil authored Apr 04, 2022
  
  cf7e80cf
- redo CoreModelCoupled as a more generic CoreCoupling · e1059ac2
  Miroslav Kratochvil authored Apr 04, 2022
```
This is in fact applicable to any model to just add "some extra conditions".
```
  e1059ac2
- side-commit: remove a bit of a freshly discovered trailing whitespace · 0e61a714
  Miroslav Kratochvil authored Apr 04, 2022
  
  0e61a714
03 Apr, 2022 4 commits
- fixup: flux_vec and flux_dict use solution_flux · 93978d3b
  Miroslav Kratochvil authored Apr 03, 2022
  
  93978d3b
- abstract out a function for converting optimizer solutions to fluxes · 536ae244
  Miroslav Kratochvil authored Apr 03, 2022
  
  536ae244
- Merge pull request #597 from LCSB-BioCore/mk-systematic-wrappers · 69516a6e
  Miroslav Kratochvil authored Apr 03, 2022
```
Systematic model wrappers
```
  69516a6e
- make the deprecation warning more specific · 73fff04e
  Miroslav Kratochvil authored Apr 03, 2022
  
  73fff04e