Merge pull request SysBioChalmers#524 from SysBioChalmers/develop

RAVEN 2.8.7

.github/issue_template.md

@@ -14,9 +14,9 @@ INSERT CODE HERE
 #### System information
 <!-- Please report the complete output from checkInstallation, for instance:
  > Installing from location             C:\Work\GitHub\RAVEN
- > Checking RAVEN release               2.7.12
+ > Checking RAVEN release               2.8.6
    > You are running the latest RAVEN release
- > Checking MATLAB release              2022a
+ > Checking MATLAB release              2023b
  > Checking system architecture         win64
  > Set RAVEN in MATLAB path             Pass
  > Save MATLAB path                     Pass
@@ -26,4 +26,4 @@ etc. etc.
 
 **I hereby confirm that I have:**
 <!-- Note: replace [ ] with [X] to check the box -->
-- [ ] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?utf8=%E2%9C%93&q=is%3Aissue)
+- [ ] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?q=is%3Aissue) or is already [discussed](https://github.com/SysBioChalmers/RAVEN/discussions).

.github/pull_request_template.md

@@ -1,8 +1,14 @@
 ### Main improvements in this PR:
 <!-- Pointwise mention what changes were made in what function. Examples: 
-- fix bug where `functionName` failed to do function X
-- updated all documentation -->
+- Fixes:
+  - `functionName` failed to do action X
+- Documentation:
+  - Updated all documentation 
+- Features:
+  - Introduced option to do function Y (issue #12345) -->
 
-**I hereby confirm that I have:**
-<!-- Note: replace [ ] with [X] to check the box -->
-- [ ] Selected `develop` as a target branch
+#### Instructions on merging this PR:
+<!-- Chose ONE of the following two options
+and replace [ ] with [X] to check the box.-->
+- [ ] This PR has `develop` as target branch, and will be resolved with a *squash-merge*.
+- [ ] This PR has `main` as target branch, and will be resolved with a *merge commit*.

.gitignore

@@ -40,6 +40,8 @@ Temporary Items
 #external/kegg/keggRxns.mat
 external/kegg/keggModel.mat
 #software
+software/scip/
+!.keep
 #doc
 
 # IDE stuff #

INIT/ftINIT.m

@@ -58,7 +58,7 @@
 %                       is for the fitTasks step. For the INIT algorithm,
 %                       see params (opt, default [])
 %   verbose             if true, the MILP progression will be shown. 
-%                       (opt, default true)
+%                       (opt, default false)
 %
 %   model                   the resulting model structure
 %   metProduction           array that indicates which of the
@@ -114,7 +114,7 @@
 end
 
 if nargin < 11
-    verbose = true;
+    verbose = false;
 end
 %Handle detected mets:
 %Previously, this was handled by giving a bonus for secreting those metabolites,
@@ -351,9 +351,9 @@
     %in the current formulation. Therefore, such reactions will have to be
     %assigned a small negative score instead.
     exchRxns = getExchangeRxns(prepData.refModel);
-    refModelNoExc = removeReactions(prepData.refModelWithBM,exchRxns,true,true);
+    refModelNoExc = removeReactions(prepData.refModelWithBM,exchRxns,false,true);
     exchRxns = getExchangeRxns(initModel);
-    initModelNoExc = removeReactions(closeModel(initModel),exchRxns,true,true);
+    initModelNoExc = removeReactions(closeModel(initModel),exchRxns,false,true);
 
     if useScoresForTasks == true
         %map the rxn scores to the model without exchange rxns

INIT/scoreComplexModel.m

@@ -218,10 +218,10 @@
 % each genes from its fold change between the tissue/celltype(s) in question
 % and all other celltypes, or the threshold if supplied. This is a lower 
 % quality data than protein abundance, since gene abundance is an indirect 
-% estimate of protiein level. These scores are therefore only used for genes
+% estimate of protein level. These scores are therefore only used for genes
 % for which there is no HPA data available. The fold changes are transformed
 % as min(5*log(x),10) for x > 1 and max(5*log(x),-5) for x < 1 in order to 
-% have negative scores for lower expressed genes and to scale the scrores
+% have negative scores for lower expressed genes and to scale the scores
 % to have somewhat lower weights than the HPA scores
 tempArrayLevels = arrayData.levels;
 tempArrayLevels(isnan(tempArrayLevels)) = 0;

core/standardizeGrRules.m

@@ -130,10 +130,7 @@
 
 if ~isempty(indexes2check)
 
-    if embedded
-        EM = 'Potentially problematic ") AND (" in the grRules for reaction(s): ';
-        dispEM(EM,false,model.rxns(indexes2check),true)
-    else
+    if ~embedded
         STR = 'Potentially problematic ") AND (", ") AND" or "AND ("relat';
         STR = [STR,'ionships found in\n\n'];
         for i=1:length(indexes2check)

doc/INIT/ftINIT.html

@@ -86,7 +86,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
                        is for the fitTasks step. For the INIT algorithm,
                        see params (opt, default [])
    verbose             if true, the MILP progression will be shown. 
-                       (opt, default true)
+                       (opt, default false)
 
    model                   the resulting model structure
    metProduction           array that indicates which of the
@@ -195,7 +195,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0058 <span class="comment">%                       is for the fitTasks step. For the INIT algorithm,</span>
 0059 <span class="comment">%                       see params (opt, default [])</span>
 0060 <span class="comment">%   verbose             if true, the MILP progression will be shown.</span>
-0061 <span class="comment">%                       (opt, default true)</span>
+0061 <span class="comment">%                       (opt, default false)</span>
 0062 <span class="comment">%</span>
 0063 <span class="comment">%   model                   the resulting model structure</span>
 0064 <span class="comment">%   metProduction           array that indicates which of the</span>
@@ -251,7 +251,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0114 <span class="keyword">end</span>
 0115 
 0116 <span class="keyword">if</span> nargin &lt; 11
-0117     verbose = true;
+0117     verbose = false;
 0118 <span class="keyword">end</span>
 0119 <span class="comment">%Handle detected mets:</span>
 0120 <span class="comment">%Previously, this was handled by giving a bonus for secreting those metabolites,</span>
@@ -488,9 +488,9 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0351     <span class="comment">%in the current formulation. Therefore, such reactions will have to be</span>
 0352     <span class="comment">%assigned a small negative score instead.</span>
 0353     exchRxns = getExchangeRxns(prepData.refModel);
-0354     refModelNoExc = removeReactions(prepData.refModelWithBM,exchRxns,true,true);
+0354     refModelNoExc = removeReactions(prepData.refModelWithBM,exchRxns,false,true);
 0355     exchRxns = getExchangeRxns(initModel);
-0356     initModelNoExc = removeReactions(closeModel(initModel),exchRxns,true,true);
+0356     initModelNoExc = removeReactions(closeModel(initModel),exchRxns,false,true);
 0357     
 0358     <span class="keyword">if</span> useScoresForTasks == true
 0359         <span class="comment">%map the rxn scores to the model without exchange rxns</span>

doc/INIT/scoreComplexModel.html

@@ -325,10 +325,10 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0218 <span class="comment">% each genes from its fold change between the tissue/celltype(s) in question</span>
 0219 <span class="comment">% and all other celltypes, or the threshold if supplied. This is a lower</span>
 0220 <span class="comment">% quality data than protein abundance, since gene abundance is an indirect</span>
-0221 <span class="comment">% estimate of protiein level. These scores are therefore only used for genes</span>
+0221 <span class="comment">% estimate of protein level. These scores are therefore only used for genes</span>
 0222 <span class="comment">% for which there is no HPA data available. The fold changes are transformed</span>
 0223 <span class="comment">% as min(5*log(x),10) for x &gt; 1 and max(5*log(x),-5) for x &lt; 1 in order to</span>
-0224 <span class="comment">% have negative scores for lower expressed genes and to scale the scrores</span>
+0224 <span class="comment">% have negative scores for lower expressed genes and to scale the scores</span>
 0225 <span class="comment">% to have somewhat lower weights than the HPA scores</span>
 0226 tempArrayLevels = arrayData.levels;
 0227 tempArrayLevels(isnan(tempArrayLevels)) = 0;

doc/core/standardizeGrRules.html

@@ -53,7 +53,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
 <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
 This function calls:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>	dispEM</li></ul>
+</ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
 <li><a href="addRxns.html" class="code" title="function newModel=addRxns(model,rxnsToAdd,eqnType,compartment,allowNewMets,allowNewGenes)">addRxns</a>	addRxns</li><li><a href="changeGrRules.html" class="code" title="function model = changeGrRules(model,rxns,grRules,replace)">changeGrRules</a>	changeGrRules</li><li><a href="contractModel.html" class="code" title="function [reducedModel, removedRxns, indexedDuplicateRxns]=contractModel(model,distReverse,mets)">contractModel</a>	contractModel</li><li><a href="expandModel.html" class="code" title="function [newModel, rxnToCheck]=expandModel(model)">expandModel</a>	expandModel</li><li><a href="getModelFromHomology.html" class="code" title="function [draftModel, hitGenes]=getModelFromHomology(models,blastStructure,getModelFor,preferredOrder,strictness,onlyGenesInModels,maxE,minLen,minIde,mapNewGenesToOld)">getModelFromHomology</a>	getModelFromHomology</li><li><a href="mergeModels.html" class="code" title="function model=mergeModels(models,metParam,supressWarnings)">mergeModels</a>	mergeModels</li><li><a href="predictLocalization.html" class="code" title="function [outModel, geneLocalization, transportStruct, scores,removedRxns] = predictLocalization(model, GSS,defaultCompartment, transportCost, maxTime, plotResults)">predictLocalization</a>	predictLocalization</li><li><a href="removeGenes.html" class="code" title="function reducedModel = removeGenes(model,genesToRemove,removeUnusedMets,removeBlockedRxns,standardizeRules)">removeGenes</a>	removeGenes</li></ul>
@@ -196,44 +196,41 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0130 
 0131 <span class="keyword">if</span> ~isempty(indexes2check)
 0132     
-0133     <span class="keyword">if</span> embedded
-0134         EM = <span class="string">'Potentially problematic &quot;) AND (&quot; in the grRules for reaction(s): '</span>;
-0135         <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,model.rxns(indexes2check),true)
-0136     <span class="keyword">else</span>
-0137         STR = <span class="string">'Potentially problematic &quot;) AND (&quot;, &quot;) AND&quot; or &quot;AND (&quot;relat'</span>;
-0138         STR = [STR,<span class="string">'ionships found in\n\n'</span>];
-0139         <span class="keyword">for</span> i=1:length(indexes2check)
-0140             index = indexes2check(i);
-0141             STR = [STR <span class="string">'  - grRule #'</span> model.rxns{index} <span class="string">': '</span> grRules{index} <span class="string">'\n'</span>];
-0142         <span class="keyword">end</span>
-0143         STR = [STR,<span class="string">'\n This kind of relationships should only be present '</span>];
-0144         STR = [STR,<span class="string">'in  reactions catalysed by complexes of isoenzymes e'</span>];
-0145         STR = [STR,<span class="string">'.g.\n\n  - (G1 or G2) and (G3 or G4)\n\n For these c'</span>];
-0146         STR = [STR,<span class="string">'ases modify the grRules manually, writing all the po'</span>];
-0147         STR = [STR,<span class="string">'ssible combinations e.g.\n\n  - (G1 and G3) or (G1 a'</span>];
-0148         STR = [STR,<span class="string">'nd G4) or (G2 and G3) or (G2 and G4)\n\n For other c'</span>];
-0149         STR = [STR,<span class="string">'ases modify the correspondent grRules avoiding:\n\n '</span>];
-0150         STR = [STR,<span class="string">' 1) Overall container brackets, e.g.\n        &quot;(G1 a'</span>];
-0151         STR = [STR,<span class="string">'nd G2)&quot; should be &quot;G1 and G2&quot;\n\n  2) Single unit en'</span>];
-0152         STR = [STR,<span class="string">'zymes enclosed into brackets, e.g.\n        &quot;(G1)&quot; s'</span>];
-0153         STR = [STR,<span class="string">'hould be &quot;G1&quot;\n\n  3) The use of uppercases for logi'</span>];
-0154         STR = [STR,<span class="string">'cal operators, e.g.\n        &quot;G1 OR G2&quot; should be &quot;G'</span>];
-0155         STR = [STR,<span class="string">'1 or G2&quot;\n\n  4) Unbalanced brackets, e.g.\n        '</span>];
-0156         STR = [STR,<span class="string">'&quot;((G1 and G2) or G3&quot; should be &quot;(G1 and G2) or G3&quot;\n'</span>];
-0157         warning(sprintf(STR))
-0158     <span class="keyword">end</span>
-0159 <span class="keyword">end</span>
-0160 <span class="keyword">end</span>
-0161 
-0162 <a name="_sub4" href="#_subfunctions" class="code">function grRules = grRulesPreparation(grRules)</a>
-0163 <span class="comment">%Remove unnecessary blanks</span>
-0164 grRules=strrep(grRules,<span class="string">'  '</span>,<span class="string">' '</span>);
-0165 grRules=strrep(grRules,<span class="string">'( '</span>,<span class="string">'('</span>);
-0166 grRules=strrep(grRules,<span class="string">' )'</span>,<span class="string">')'</span>);
-0167 <span class="comment">% Make sure that AND and OR strings are in lowercase</span>
-0168 grRules=strrep(grRules,<span class="string">' AND '</span>,<span class="string">' and '</span>);
-0169 grRules=strrep(grRules,<span class="string">' OR '</span>,<span class="string">' or '</span>);
-0170 <span class="keyword">end</span></pre></div>
+0133     <span class="keyword">if</span> ~embedded
+0134         STR = <span class="string">'Potentially problematic &quot;) AND (&quot;, &quot;) AND&quot; or &quot;AND (&quot;relat'</span>;
+0135         STR = [STR,<span class="string">'ionships found in\n\n'</span>];
+0136         <span class="keyword">for</span> i=1:length(indexes2check)
+0137             index = indexes2check(i);
+0138             STR = [STR <span class="string">'  - grRule #'</span> model.rxns{index} <span class="string">': '</span> grRules{index} <span class="string">'\n'</span>];
+0139         <span class="keyword">end</span>
+0140         STR = [STR,<span class="string">'\n This kind of relationships should only be present '</span>];
+0141         STR = [STR,<span class="string">'in  reactions catalysed by complexes of isoenzymes e'</span>];
+0142         STR = [STR,<span class="string">'.g.\n\n  - (G1 or G2) and (G3 or G4)\n\n For these c'</span>];
+0143         STR = [STR,<span class="string">'ases modify the grRules manually, writing all the po'</span>];
+0144         STR = [STR,<span class="string">'ssible combinations e.g.\n\n  - (G1 and G3) or (G1 a'</span>];
+0145         STR = [STR,<span class="string">'nd G4) or (G2 and G3) or (G2 and G4)\n\n For other c'</span>];
+0146         STR = [STR,<span class="string">'ases modify the correspondent grRules avoiding:\n\n '</span>];
+0147         STR = [STR,<span class="string">' 1) Overall container brackets, e.g.\n        &quot;(G1 a'</span>];
+0148         STR = [STR,<span class="string">'nd G2)&quot; should be &quot;G1 and G2&quot;\n\n  2) Single unit en'</span>];
+0149         STR = [STR,<span class="string">'zymes enclosed into brackets, e.g.\n        &quot;(G1)&quot; s'</span>];
+0150         STR = [STR,<span class="string">'hould be &quot;G1&quot;\n\n  3) The use of uppercases for logi'</span>];
+0151         STR = [STR,<span class="string">'cal operators, e.g.\n        &quot;G1 OR G2&quot; should be &quot;G'</span>];
+0152         STR = [STR,<span class="string">'1 or G2&quot;\n\n  4) Unbalanced brackets, e.g.\n        '</span>];
+0153         STR = [STR,<span class="string">'&quot;((G1 and G2) or G3&quot; should be &quot;(G1 and G2) or G3&quot;\n'</span>];
+0154         warning(sprintf(STR))
+0155     <span class="keyword">end</span>
+0156 <span class="keyword">end</span>
+0157 <span class="keyword">end</span>
+0158 
+0159 <a name="_sub4" href="#_subfunctions" class="code">function grRules = grRulesPreparation(grRules)</a>
+0160 <span class="comment">%Remove unnecessary blanks</span>
+0161 grRules=strrep(grRules,<span class="string">'  '</span>,<span class="string">' '</span>);
+0162 grRules=strrep(grRules,<span class="string">'( '</span>,<span class="string">'('</span>);
+0163 grRules=strrep(grRules,<span class="string">' )'</span>,<span class="string">')'</span>);
+0164 <span class="comment">% Make sure that AND and OR strings are in lowercase</span>
+0165 grRules=strrep(grRules,<span class="string">' AND '</span>,<span class="string">' and '</span>);
+0166 grRules=strrep(grRules,<span class="string">' OR '</span>,<span class="string">' or '</span>);
+0167 <span class="keyword">end</span></pre></div>
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