Commits · dc0571e7f3da97bbfe65572ecb2ac06e7eddae07 · LCSB-BioCore / SBML.jl

This project is mirrored from https://*****@github.com/LCSB-BioCore/SBML.jl.git. Pull mirroring updated Jun 25, 2022.

15 Jul, 2021 2 commits
- Use `Unitful` for units, instead of a custom struct · dc0571e7
  Mosè Giordano authored Jul 08, 2021
  
  dc0571e7
- allow switching off reporting of certain error severities · 54b60a1c
  Miroslav Kratochvil authored Jul 15, 2021
```
fixes terminal flood on many existing models
```
  54b60a1c
13 Jul, 2021 2 commits
- constantize the stoichiometry-adding function · e6681aa3
  Miroslav Kratochvil authored Jul 13, 2021
  
  e6681aa3
- quickfix: do not load invalid information for species with double stoichiometry · f6b416c8
  Miroslav Kratochvil authored Jul 13, 2021
  
  f6b416c8
09 Jul, 2021 1 commit
- Turn some anonymous functions into proper named functions · 977cafad
  Mosè Giordano authored Jul 09, 2021
  
  977cafad
03 Jul, 2021 1 commit
- juliaformatter · b24d1b13
  Miroslav Kratochvil authored Jul 03, 2021
  
  b24d1b13
02 Jul, 2021 1 commit
- Improve reporting of errors in documents · e0b28a52
  Mosè Giordano authored Jul 02, 2021
```
This rationalise the way we report errors from libsbml in a few different
places.
```
  e0b28a52
25 Jun, 2021 1 commit
- fix getInitialConcentrations · 71305c0b
  paulflang authored Jun 25, 2021
  
  71305c0b
22 Jun, 2021 1 commit

Strip whitespaces when reporting error messages from `readSBML` · 3da6281d

Mosè Giordano authored Jun 21, 2021

Also:

* replace `@warn` with `@error`
* actually test the logging message in `readSBML`, instead of showing an extra
  message saying to ignore it.

3da6281d

17 Jun, 2021 1 commit
- clean up documentation and types · 7f1506c8
  Miroslav Kratochvil authored Jun 17, 2021
  
  7f1506c8
15 Jun, 2021 3 commits
- clean up the converters to work nicely with ICs · 42299f85
  Miroslav Kratochvil authored Jun 15, 2021
  
  42299f85
- oops, forgot this line · adf92572
  Miroslav Kratochvil authored Jun 14, 2021
  
  adf92572
- add initial concentration, fix certainty of units · 42bb9e33
  Miroslav Kratochvil authored Jun 14, 2021
  
  42bb9e33
14 Jun, 2021 2 commits
- document the converter usage · c819bf86
  Miroslav Kratochvil authored Jun 14, 2021
  
  c819bf86
- add reversible flag · 7dc26ae5
  paulflang authored Jun 14, 2021 and Miroslav Kratochvil committed Jun 14, 2021
  
  7dc26ae5
07 Jun, 2021 1 commit
- add support for running SBML converters · bfb423cc
  paulflang authored Jun 07, 2021 and Miroslav Kratochvil committed Jun 07, 2021
  
  bfb423cc
29 May, 2021 2 commits
- rm unitpart · e24275c8
  anand jain authored May 28, 2021
  
  e24275c8
- Model -> SBML.Model · 8ce374a2
  anand jain authored May 28, 2021
  
  8ce374a2
13 Apr, 2021 10 commits
- extract boundary condition for species · 3233b323
  Miroslav Kratochvil authored Apr 13, 2021
  
  3233b323
- import more Compartment metadata, mainly the sizes · 6daf9850
  Miroslav Kratochvil authored Apr 13, 2021
  
  6daf9850
- fix previous (also sanitize naming of notes/annotation getters) · b55ca9f8
  Miroslav Kratochvil authored Apr 13, 2021
  
  b55ca9f8
- support parsing out function definitions · 5f1c9ae8
  Miroslav Kratochvil authored Apr 13, 2021
  
  5f1c9ae8
- support parsing of a small subset of MathML · e924dcbe
  Miroslav Kratochvil authored Apr 13, 2021
```
...let's see what can be done with it
```
  e924dcbe
- add space for kineticLaw math rules · aefe4708
  Miroslav Kratochvil authored Apr 13, 2021
  
  aefe4708
- retrieve Species initial amount · 8d14fb90
  Miroslav Kratochvil authored Apr 13, 2021
```
(((
Should we also take initialConcentration?

What is the purpose of hasOnlySubstanceUnits then when there's both
initialAmount and initialConcentration?
)))
```
  8d14fb90
- extract hasOnlySubstanceUnits from Species · 6fd46e64
  Miroslav Kratochvil authored Apr 13, 2021
  
  6fd46e64
- Species.name is optional, don't fail if it's not present · bd12b466
  Miroslav Kratochvil authored Apr 13, 2021
```
Improves upon #35
```
  bd12b466
- make string extraction a bit more error-proof · 21794da5
  Miroslav Kratochvil authored Apr 13, 2021
  
  21794da5
16 Mar, 2021 2 commits
- save the association to reaction struct · 26c13d0a
  Miroslav Kratochvil authored Mar 16, 2021
  
  26c13d0a
- read gene product associations · fbc19f90
  Miroslav Kratochvil authored Mar 16, 2021
  
  fbc19f90
15 Mar, 2021 7 commits
- cleaning: distinguish between missing and empty formula · d1fbeaf6
  Miroslav Kratochvil authored Mar 15, 2021
  
  d1fbeaf6
- document the new functions · da50e144
  Miroslav Kratochvil authored Mar 15, 2021
```
(readModel has certainly grown a bit)
```
  da50e144
- read FBC gene products · 9b8e9af2
  Miroslav Kratochvil authored Mar 15, 2021
```
Co-authored-by: st elmo <stelmozors@gmail.com>
```
  9b8e9af2
- extract freetext annotations · 2da1a154
  Miroslav Kratochvil authored Mar 15, 2021
  
  2da1a154
- read notes from species, reactions and models · f2db233d
  St. Elmo authored Mar 14, 2021 and Miroslav Kratochvil committed Mar 15, 2021
```
Co-authored-by: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
```
  f2db233d
- load FBC charges · 8b58a03a
  Miroslav Kratochvil authored Mar 14, 2021
  
  8b58a03a
- read FBC chemical formulae · 31e63fe7
  Miroslav Kratochvil authored Mar 14, 2021
  
  31e63fe7
14 Mar, 2021 2 commits
- read FBC objectives · e6d30729
  Miroslav Kratochvil authored Mar 14, 2021
  
  e6d30729
- support reading FBC flux bounds · 86df302a
  St. Elmo authored Mar 14, 2021 and Miroslav Kratochvil committed Mar 14, 2021
```
Co-authored-by: Mirek Kratochvil <miroslav.kratochvil@uni.lu>
```
  86df302a
26 Feb, 2021 1 commit
- fix null kinetic law · 8e78100e
  Miroslav Kratochvil authored Feb 23, 2021
  
  8e78100e