Commits · b90df728e88ee028c66167e7ee82c3770746d766 · LCSB-BioCore / COBREXA.jl

This project is mirrored from https://github.com/LCSB-BioCore/COBREXA.jl.git. Pull mirroring updated Jan 24, 2022.

30 Aug, 2021 1 commit
- improve parametrization of objective_envelope · b90df728
  Miroslav Kratochvil authored Aug 30, 2021
  
  b90df728
26 Aug, 2021 2 commits
- Merge pull request #445 from... · 1a9348ef
  Miroslav Kratochvil authored Aug 26, 2021
```
Merge pull request #445 from LCSB-BioCore/compathelper/new_version/2021-08-26-00-10-35-964-1506605829

CompatHelper: bump compat for "SBML" to "0.8"
```
  1a9348ef
- CompatHelper: bump compat for "SBML" to "0.8" · 2854acde
  github-actions[bot] authored Aug 26, 2021
  
  2854acde
23 Aug, 2021 2 commits
- Merge pull request #444 from LCSB-BioCore/mo-project-status · bb82625a
  St. Elmo authored Aug 23, 2021
```
Added repostatus badge
```
  bb82625a
- update readme · f17df816
  St. Elmo authored Aug 23, 2021
  
  f17df816
18 Aug, 2021 3 commits
- Merge pull request #443 from LCSB-BioCore/mk-eff-sparse · cf0f49ef
  Miroslav Kratochvil authored Aug 18, 2021
```
more efficient building of sparse stoichiometries
```
  cf0f49ef
- efficient stoichiometry building from StandardModel · 73774a74
  Miroslav Kratochvil authored Aug 18, 2021
  
  73774a74
- efficient building of JSONModel stoichiometry · 939d677b
  Miroslav Kratochvil authored Aug 18, 2021
  
  939d677b
16 Aug, 2021 12 commits
- Merge pull request #442 from LCSB-BioCore/mk-bump-104 · 6857bbc6
  Miroslav Kratochvil authored Aug 16, 2021
```
bump version 1.0.4
```
  6857bbc6
- Merge pull request #438 from LCSB-BioCore/mo-more-modifications · ecf802e1
  Miroslav Kratochvil authored Aug 16, 2021
```
Update modifications
```
  ecf802e1
- Merge pull request #441 from LCSB-BioCore/mk-envelope-example · 07cb13f7
  Miroslav Kratochvil authored Aug 16, 2021
```
add an example for objective_envelope
```
  07cb13f7
- bump version 1.0.4 · 9c8dd472
  Miroslav Kratochvil authored Aug 16, 2021
  
  9c8dd472
- separate crowding to its own file · 95381a03
  Miroslav Kratochvil authored Aug 16, 2021
  
  95381a03
- Implement crowding constraint, unify change_constraint [BREAKING] · 70beba9f
  St. Elmo authored Aug 13, 2021
```
Also implement `looks_like_internal_reaction` for convenience
```
  70beba9f
- typos · 8a62eb6e
  Taneli Pusa authored Aug 16, 2021
  
  8a62eb6e
- Merge pull request #433 from LCSB-BioCore/mk-remove-stuff · 2ba7b7b8
  Miroslav Kratochvil authored Aug 16, 2021
```
start the grand unification of remove_whatever
```
  2ba7b7b8
- explain `lattice_args` a bit better · 69340c9a
  Miroslav Kratochvil authored Aug 16, 2021
  
  69340c9a
- fix the remove_reaction plurality in notebook · 870f492f
  Miroslav Kratochvil authored Aug 16, 2021
  
  870f492f
- fix the docstring · 8ed7d68d
  Miroslav Kratochvil authored Aug 16, 2021
  
  8ed7d68d
- add an example for objective_envelope · 5bb05b29
  Miroslav Kratochvil authored Aug 16, 2021
  
  5bb05b29
15 Aug, 2021 4 commits
- finish for coupled model, clean up the tests · 6f7d15c0
  Miroslav Kratochvil authored Aug 15, 2021
  
  6f7d15c0
- minor side fixes · 725b426a
  Miroslav Kratochvil authored Aug 15, 2021
  
  725b426a
- finish the remove reactions/metabolites for core+std models · 9463b710
  Miroslav Kratochvil authored Aug 14, 2021
  
  9463b710
- start the grand unification of remove_whatever · 6e713c42
  Miroslav Kratochvil authored Aug 12, 2021
  
  6e713c42
12 Aug, 2021 4 commits
- Merge pull request #425 from LCSB-BioCore/mo-core-add-reactions · f20e41f1
  Miroslav Kratochvil authored Aug 12, 2021
```
Add in place `add_reaction!` and `add_reactions!` 
```
  f20e41f1
- rm DSEs · 2df93981
  St. Elmo authored Aug 12, 2021
  
  2df93981
- Added in place `add_reaction` and tests · f0d48d3a
  St. Elmo authored Aug 09, 2021
  
  f0d48d3a
- Merge pull request #432 from LCSB-BioCore/mo-tiny-fix · 977c5ff8
  St. Elmo authored Aug 12, 2021
```
Small fix in docstring + function kwarg
```
  977c5ff8
11 Aug, 2021 1 commit
- Fix docstrings and simplify function arguments · 63d9a3ca
  St. Elmo authored Aug 11, 2021
  
  63d9a3ca
10 Aug, 2021 4 commits
- Merge pull request #430 from LCSB-BioCore/mk-compat-sbml-070 · 558c8629
  Miroslav Kratochvil authored Aug 10, 2021
```
bump SBML compat to 0.7.x
```
  558c8629
- Merge pull request #429 from LCSB-BioCore/mo-undo-accident · 9b236914
  Miroslav Kratochvil authored Aug 10, 2021
```
Add `back stoichiometry_string`
```
  9b236914
- add back stoichiometry_string · 0c72a4bf
  St. Elmo authored Aug 10, 2021
  
  0c72a4bf
- bump SBML compat to 0.7.x · c7339ee0
  Miroslav Kratochvil authored Aug 10, 2021
```
Also closes #427
```
  c7339ee0
09 Aug, 2021 7 commits
- Merge pull request #426 from LCSB-BioCore/mo-fix-notebook · 60a1abab
  Miroslav Kratochvil authored Aug 09, 2021
```
Fix docs
```
  60a1abab
- remove Gurobi · 7585e9e8
  St. Elmo authored Aug 09, 2021
  
  7585e9e8
- Merge pull request #424 from LCSB-BioCore/mo-fva-details · fe477a48
  St. Elmo authored Aug 09, 2021
```
Add some more explanations for FVA and add `flux_summary` usage to notebook
```
  fe477a48
- added some more explanations · 07b2f494
  St. Elmo authored Aug 09, 2021
  
  07b2f494
- Merge pull request #420 from LCSB-BioCore/mo-tiny-fixes · ff038a24
  St. Elmo authored Aug 09, 2021
```
Mo tiny fixes
```
  ff038a24
- Added fusing + some small modifications to functions · 1cf394f7
  St. Elmo authored Aug 05, 2021
  
  1cf394f7
- Merge pull request #421 from LCSB-BioCore/mk-clarify-set-optmodel-bound · 0ac76bdd
  Miroslav Kratochvil authored Aug 09, 2021
```
simplify & unsurprise `set_optmodel_bound!`
```
  0ac76bdd