fix: reduce dependency

README.md

@@ -50,20 +50,19 @@ You can obtained the model by any of the following methods:
 
 If you want to use the model for your own model simulations, you can use **any software** that accepts SBML L3V1 FBCv3 formatted model files. This includes any of the following:
 * MATLAB-based
-  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.6.1 or later (recommended)  
+  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.7.0 or later (recommended)  
   * [COBRA Toolbox](https://github.com/opencobra/cobratoolbox)
 
 * Python-based
   * [cobrapy](https://github.com/opencobra/cobrapy)  
 
-Please see the installation instructions for each software package. You may need to install [libSBML](https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/stable/MATLAB%20interface/) and an LP-solver (e.g. [Gurobi](https://www.gurobi.com/downloads/gurobi-optimizer-eula/)).
+Please see the installation instructions for each software package.
 
 ### Developer
 
 * MATLAB-based  
   If you want to contribute to the development of yeast-GEM, or otherwise want to run any of the [provided](https://github.com/SysBioChalmers/yeast-GEM/tree/main/code) MATLAB functions, then the following software is required:
-  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.6.1 or later
-  * [git wrapper](https://github.com/manur/MATLAB-git)  
+  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.7.0 or later
 
 * Python-based  
   Contribution via python (cobrapy) is not yet functional. In essence, if you can retain the same format of the model files, you can still contribute to the development of yeast-GEM. However, you cannot use the MATLAB functions.

code/increaseVersion.m

@@ -14,7 +14,7 @@ function increaseVersion(bumpType)
 %
 
 %Check if in main:
-currentBranch = git('rev-parse --abbrev-ref HEAD');
+[~,currentBranch] = system('git rev-parse --abbrev-ref HEAD');
 if ~strcmp(currentBranch,'main')
     error('ERROR: not in main')
 end
@@ -72,7 +72,7 @@ function increaseVersion(bumpType)
 saveYeastModel(model,true,true,true)   %only save if model can grow
 
 %Check if any file changed (except for history.md and 1 line in yeast-GEM.xml):
-diff   = git('diff --numstat');
+[~,diff]   = system('git diff --numstat');
 diff   = strsplit(diff,'\n');
 change = false;
 for i = 1:length(diff)

code/missingFields/mapIDsViaMNXref.m

@@ -59,18 +59,18 @@
     disp([toolbox ' toolbox cannot be found'])
 end
 %Check if this branch is feat/add_MetaNetX
-currentBranch = git('rev-parse --abbrev-ref HEAD');
+[~,currentBranch] = system('git rev-parse --abbrev-ref HEAD');
 if ~strcmp(currentBranch,'feat/add_MetaNetX')
-    git checkout feat/add_MetaNetX
-    currentBranch = git('rev-parse --abbrev-ref HEAD');
+    system('git checkout feat/add_MetaNetX');
+    [~,currentBranch] = system('git rev-parse --abbrev-ref HEAD');
     if ~strcmp(currentBranch,'feat/add_MetaNetX')
         error(['ERROR: branch:add_MetaNetX not exists. Check-out the RAVEN toolbox:https://github.com/SysBioChalmers/RAVEN'])
     end
 end
 cd external/MetaNetX/
 load('MNXref.mat');
 % swich back to the main branch of RAVEN
-git checkout main
+system('git checkout main');
 cd(currentPath);
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

code/modelCuration/minimal_Y6.m

@@ -8,7 +8,7 @@
 % start with a clean slate: set all exchange reactions to upper bound = 1000
 % and lower bound = 0 (ie, unconstrained excretion, no uptake)
 
-exchangeRxns = findExcRxns(model);
+[~,exchangeRxns] = getExchangeRxns(model,'out');
 model.lb(exchangeRxns) = 0;
 model.ub(exchangeRxns) = 1000;
 
@@ -34,9 +34,9 @@
 
 glucoseExchange = {'r_1714'};     % D-glucose exchange
 
-uptakeRxnIndexes     = findRxnIDs(model,desiredExchanges);
-glucoseExchangeIndex = findRxnIDs(model,glucoseExchange);
-BlockedRxnIndex      = findRxnIDs(model,blockedExchanges);
+uptakeRxnIndexes     = getIndexes(model,desiredExchanges,'rxns');
+glucoseExchangeIndex = getIndexes(model,glucoseExchange,'rxns');
+BlockedRxnIndex      = getIndexes(model,blockedExchanges,'rxns');
 
 if length(find(uptakeRxnIndexes~= 0)) ~= 15
     warning('Not all exchange reactions were found.')

model/dependencies.txt

@@ -1,4 +1,4 @@
 MATLAB	9.10.0.1602886 (R2021a)
 libSBML	5.19.0
-RAVEN_toolbox	commit a49a911
-COBRA_toolbox	commit 28acb94
+RAVEN_toolbox	2.7.0
+COBRA_toolbox	unknown