Commits · 3ae6fbff12e40b7f24cb7e740dde4436f29b8085 · LCSB-BioCore / COBREXA.jl

This project is mirrored from https://github.com/LCSB-BioCore/COBREXA.jl.git. Pull mirroring updated Aug 11, 2022.

15 Oct, 2021 1 commit
- fix API of screen() to avoid unbounded type parameters · 3ae6fbff
  Miroslav Kratochvil authored Oct 14, 2021 and Miroslav Kratochvil committed Oct 15, 2021
  
  3ae6fbff
09 Sep, 2021 1 commit
- improve the ability of screening functions to use precompiled code · 05ca5133
  Miroslav Kratochvil authored Sep 09, 2021
```
Among other, this fixes a ~5-20% performance regression for FVA.
```
  05ca5133
07 Sep, 2021 1 commit
- correctly forward the workers parameter · d08bff84
  Miroslav Kratochvil authored Sep 07, 2021
  
  d08bff84
31 Aug, 2021 1 commit

slightly improve the objective value handling at FVA · bc4bd821

Miroslav Kratochvil authored Aug 31, 2021

...and finally allow the whole FBA part to be successfully and easily separated
into its own efficient single-threaded step.

bc4bd821

30 Aug, 2021 1 commit
- improve parametrization of objective_envelope · b90df728
  Miroslav Kratochvil authored Aug 30, 2021
  
  b90df728
16 Aug, 2021 6 commits
- 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
- explain `lattice_args` a bit better · 69340c9a
  Miroslav Kratochvil authored Aug 16, 2021
  
  69340c9a
- 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
09 Aug, 2021 1 commit
- Added fusing + some small modifications to functions · 1cf394f7
  St. Elmo authored Aug 05, 2021
  
  1cf394f7
04 Aug, 2021 7 commits
- improve optmodel screening to be able to easily subsume FVA · 0f0ffc05
  Miroslav Kratochvil authored Aug 04, 2021
  
  0f0ffc05
- implement the solver silencer · 7c2660e3
  Miroslav Kratochvil authored Aug 04, 2021
```
this allows sneakiness in linear optimization

Closes #391
```
  7c2660e3
- unify the style of the modifications · cddaea86
  Miroslav Kratochvil authored Aug 04, 2021
  
  cddaea86
- split off the solver-only analysis mods from the model-dependent generic ones · 3b319c0b
  Miroslav Kratochvil authored Aug 04, 2021
  
  3b319c0b
- clean up `change_objective` · 7617de71
  Miroslav Kratochvil authored Aug 04, 2021
```
closes #405
```
  7617de71
- remove prefix · 8c4d50c4
  St. Elmo authored Aug 04, 2021
  
  8c4d50c4
- remove unnecessary COBREXA and JuMP scope where possible · e7054358
  Miroslav Kratochvil authored Aug 04, 2021
  
  e7054358
03 Aug, 2021 3 commits
- better explain the difference to screen · 7dd04d4c
  Miroslav Kratochvil authored Aug 03, 2021
  
  7dd04d4c
- document the new stuff · 874b5e04
  Miroslav Kratochvil authored Aug 03, 2021
  
  874b5e04
- implement objective envelopes (aka production envelopes) · 57be2637
  Miroslav Kratochvil authored Aug 02, 2021
  
  57be2637
02 Aug, 2021 2 commits
- remove all prefixes · 5cae6c88
  St. Elmo authored Aug 02, 2021
  
  5cae6c88
- removed COBREXA.JuMP. · 9314bed6
  St. Elmo authored Aug 02, 2021
  
  9314bed6
28 Jul, 2021 1 commit
- simplify code by removing unnecessary unicode · 5c37fe4f
  Miroslav Kratochvil authored Jul 28, 2021
  
  5c37fe4f
18 Jun, 2021 1 commit
- documentation fixes and formatting, ... · b1e98f28
  Miroslav Kratochvil authored Jun 18, 2021
```
References in tutorial 4 are left out for Mo, to avoid conflicts
```
  b1e98f28
17 Jun, 2021 1 commit
- format 341 + add a tiny simplification · 21a2d7c2
  Miroslav Kratochvil authored Jun 17, 2021
  
  21a2d7c2
16 Jun, 2021 1 commit
- better errors for optimizer mods · 73e1d547
  Taneli Pusa authored Jun 16, 2021
```
typo
```
  73e1d547
11 Jun, 2021 2 commits
- added another example · 989315a4
  St. Elmo authored Jun 11, 2021
  
  989315a4
- clean up analysis documentation and examples · b7f00cf7
  Miroslav Kratochvil authored Jun 11, 2021
```
Closes #318
```
  b7f00cf7
10 Jun, 2021 2 commits
- add a tutorial on screening the variants, also add variants · a486eee5
  Miroslav Kratochvil authored Jun 09, 2021 and Miroslav Kratochvil committed Jun 10, 2021
```
I needed to clean up some extra code. Notably, set_bound functions didn't have
the warning ! attached. That got me reeeeeeeaally confused.
```
  a486eee5
- fix screen docs · 7be37824
  Miroslav Kratochvil authored Jun 09, 2021 and Miroslav Kratochvil committed Jun 10, 2021
  
  7be37824
27 May, 2021 8 commits
- automatic formatting changes · f179860d
  cylon-x authored May 27, 2021
  
  f179860d
- document the sampler · 2ca4bb63
  Miroslav Kratochvil authored May 27, 2021
  
  2ca4bb63
- rename sampling source files to better represent the reality · 4e5ef108
  Miroslav Kratochvil authored May 27, 2021
  
  4e5ef108
- sampling seems to work OK now · a43ad19a
  Miroslav Kratochvil authored May 27, 2021
  
  a43ad19a
- FVA warmup · 0012e659
  Miroslav Kratochvil authored May 26, 2021
  
  0012e659
- WIP · 1685f21b
  Miroslav Kratochvil authored May 26, 2021
  
  1685f21b
- simplify model uploading · 35c07086
  Miroslav Kratochvil authored May 26, 2021
  
  35c07086
- automatic formatting changes · 88babb43
  cylon-x authored May 21, 2021 and St. Elmo committed May 27, 2021
  
  88babb43