RAVEN 2.6.0

.github/issue_template.md

@@ -1,12 +1,12 @@
 ### Description of the issue:
-*Try to be as clear as possible, e.g.:
+<!-- Try to be as clear as possible, e.g.
 - Is there a functionality missing?
 - Did an existing function fail?
 - What is the exact error message, and other output that you got?
-- What have you tried yourself to fix it?
+- What have you tried yourself to fix it? -->
 
 #### Reproducing this issue:
-*If applicable, please attach the problematic code. PLEASE DELETE THIS LINE.*
+<!-- If applicable, please attach the problematic code. -->
 ```matlab
 INSERT CODE HERE
 ```
@@ -17,8 +17,7 @@ INSERT CODE HERE
 2. Operating system (Windows/Mac/Linux; include version)
 
 **I hereby confirm that I have:**
+<!-- Note: replace [ ] with [X] to check the box -->
 - [ ] Followed the [guidelines](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) to install RAVEN.
 - [ ] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?utf8=%E2%9C%93&q=is%3Aissue)
 - [ ] If suitable, needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/RAVEN) about the issue
-
-*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.github/pull_request_template.md

@@ -1,14 +1,12 @@
 ### Main improvements in this PR:
-*Pointwise mention what changes were made in what function. Examples: 
+<!-- Pointwise mention what changes were made in what function. Examples: 
 - fix bug where `functionName` failed to do function X
-- updated all documentation
-PLEASE DELETE THESE LINES*
+- updated all documentation -->
 
 **I hereby confirm that I have:**
+<!-- Note: replace [ ] with [X] to check the box -->
 
 - [ ] Tested my code on my own machine
 - [ ] Followed the [development guidelines](https://github.com/SysBioChalmers/RAVEN/wiki/DevGuidelines).
 - [ ] Selected `devel` as a target branch
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/RAVEN) about this PR
-
-*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.github/workflows/testing-comment.md

@@ -0,0 +1,7 @@
+This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/RAVEN/actions/runs/{GH_ACTION_RUN}). Here is the output of the tests:
+
+```
+{TEST_RESULTS}
+```
+
+> _Note: In the case of multiple test runs, this post will be edited._

.github/workflows/testing.yml

@@ -0,0 +1,28 @@
+name: Testing
+
+on: [pull_request]
+
+jobs:
+  matlab-tests:
+    runs-on: self-hosted
+
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Run tests
+      id: matlab-test
+      run: |
+        TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); cd('testing/unit_tests'); runtests(struct2table(dir('*.m')).name); exit;")
+        PARSED_RESULTS=$(echo $TEST_RESULTS | awk -F'.com.' '{ n = split($2, v, "__________"); for (i = 0; ++i <= n;) { print v[i] } }')
+        echo ::set-output name=results::$PARSED_RESULTS
+
+    - name: Post comment
+      uses: NejcZdovc/comment-pr@v1
+      with:
+        file: "testing-comment.md"
+      env:
+        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        TEST_RESULTS: ${{steps.matlab-test.outputs.results}}
+        GH_ACTION_RUN: ${{github.run_id}}

core/checkModelStruct.m

@@ -246,6 +246,18 @@ function checkModelStruct(model,throwErrors,trimWarnings)
 EM='The following reactions have bounds contradicting their reversibility:';
 dispEM(EM,throwErrors,model.rxns(model.lb<0 & model.rev==0),trimWarnings);
 
+%Multiple or no objective functions not allowed in SBML L3V1 FBCv2
+if numel(find(model.c))>1
+    EM='Multiple objective functions found. This might be intended, but exportModel will fail due to SBML FBCv2 non-compliance:';
+    dispEM(EM,false,model.rxns(find(model.c)),trimWarnings);
+elseif ~any(model.c)
+    EM='No objective function found. This might be intended, but exportModel will fail due to SBML FBCv2 non-compliance';
+    dispEM(EM,false);
+end
+
+EM='The following reactions have contradicting bounds:';
+dispEM(EM,throwErrors,model.rxns(model.lb>model.ub),trimWarnings);
+
 %Mapping of compartments
 if isfield(model,'compOutside')
     EM='The following compartments are in "compOutside" but not in "comps":';

core/compareModels.m → core/compareRxnsGenesMetsComps.m

@@ -1,5 +1,5 @@
-function compStruct=compareModels(models,printResults)
-% compareModels
+function compStruct=compareRxnsGenesMetsComps(models,printResults)
+% compareRxnsGenesMetsComps
 %   Compares two or more models with respect to overlap in terms of genes,
 %   reactions, metabolites and compartments.
 %
@@ -23,7 +23,7 @@
 %           nElements   vector with the number of elements for each
 %                       comparison
 %
-%   Usage: compStruct=compareModels(models,printResults)
+%   Usage: compStruct=compareRxnsGenesMetsComps(models,printResults)
 
 if nargin<2
     printResults=true;

core/convertToIrrev.m

@@ -14,13 +14,13 @@
 %   Usage: irrevModel=convertToIrrev(model,rxns)
 
 if nargin<2
-    rxns=model.rxns;
+    I=true(numel(model.rxns),1);
+else
+    I=getIndexes(model,rxns,'rxns',true);
 end
 
 irrevModel=model;
 
-I=getIndexes(model,rxns,'rxns',true);
-
 revIndexesBool=model.rev~=0 & I;
 revIndexes=find(revIndexesBool);
 if any(revIndexesBool)

core/dispEM.m

@@ -42,6 +42,8 @@ function dispEM(string,throwErrors,toList,trimWarnings)
     end
 end
 if throwErrors==false
+    %Escape special characters, required for fprintf
+    errorText=regexprep(errorText,'(\\|\%|'')','\\$0');
     fprintf([errorText '\n']);
 else
     throw(MException('',errorText));

core/permuteModel.m

@@ -2,111 +2,155 @@
 % permuteModel
 %   Changes the order of the reactions or metabolites in a model
 %
+%   Input:
 %   model     a model structure
-%   indexes   a vector with the same length as the number of reactions in the
-%             model which gives the new order of reactions
-%   type      'rxns' for reactions and 'mets' for metabolites
+%   indexes   a vector with the same length as the number of items in the
+%             model, which gives the new order of items
+%   type      'rxns' for reactions, 'mets' for metabolites, 'genes' for
+%             genes, 'comps' for compartments
 %
-% 	newModel  an updated model structure
+% 	Output:
+%   newModel  an updated model structure
 %
 % 	Usage: newModel=permuteModel(model, indexes, type)
 
 newModel=model;
 indexes=indexes(:);
 
-if strcmp(type,'rxns')
-    if isfield(newModel,'rxns')
-        newModel.rxns=newModel.rxns(indexes);
-    end
-    if isfield(newModel,'lb')
-        newModel.lb=newModel.lb(indexes);
-    end
-    if isfield(newModel,'ub')
-        newModel.ub=newModel.ub(indexes);
-    end
-    if isfield(newModel,'rev')
-        newModel.rev=newModel.rev(indexes);
-    end
-    if isfield(newModel,'c')
-        newModel.c=newModel.c(indexes);
-    end
-    if isfield(newModel,'S')
-        newModel.S=newModel.S(:,indexes);
-    end
-    if isfield(newModel,'rxnNames')
-        newModel.rxnNames=newModel.rxnNames(indexes);
-    end
-    if isfield(newModel,'rxnGeneMat')
-        newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:);
-    end
-    if isfield(newModel,'grRules')
-        newModel.grRules=newModel.grRules(indexes);
-    end
-    if isfield(newModel,'subSystems')
-        newModel.subSystems=newModel.subSystems(indexes);
-    end
-    if isfield(newModel,'eccodes')
-        newModel.eccodes=newModel.eccodes(indexes);
-    end
-    if isfield(newModel,'equations')
-        newModel.equations=newModel.equations(indexes);
-    end
-    if isfield(newModel,'rxnMiriams')
-        newModel.rxnMiriams=newModel.rxnMiriams(indexes);
-    end
-    if isfield(newModel,'rxnComps')
-        newModel.rxnComps=newModel.rxnComps(indexes);
-    end
-    if isfield(newModel,'rxnFrom')
-        newModel.rxnFrom=newModel.rxnFrom(indexes);
-    end
-    if isfield(newModel,'rxnScores')
-        newModel.rxnScores=newModel.rxnScores(indexes);
-    end
-    if isfield(newModel,'rxnNotes')
-        newModel.rxnNotes=newModel.rxnNotes(indexes);
-    end
-    if isfield(newModel,'rxnReferences')
-        newModel.rxnReferences=newModel.rxnReferences(indexes);
-    end
-    if isfield(newModel,'rxnConfidenceScores')
-        newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes);
-    end
-end
-
-if strcmp(type,'mets')
-    if isfield(newModel,'mets')
-        newModel.mets=newModel.mets(indexes);
-    end
-    if isfield(newModel,'metNames')
-        newModel.metNames=newModel.metNames(indexes);
-    end
-    if isfield(newModel,'b')
-        newModel.b=newModel.b(indexes,:);
-    end
-    if isfield(newModel,'metComps')
-        newModel.metComps=newModel.metComps(indexes);
-    end
-    if isfield(newModel,'S')
-        newModel.S=newModel.S(indexes,:);
-    end
-    if isfield(newModel,'unconstrained')
-        newModel.unconstrained=newModel.unconstrained(indexes);
-    end
-    if isfield(newModel,'metMiriams')
-        newModel.metMiriams=newModel.metMiriams(indexes,:);
-    end
-    if isfield(newModel,'inchis')
-        newModel.inchis=newModel.inchis(indexes);
-    end
-    if isfield(newModel,'metFormulas')
-        newModel.metFormulas=newModel.metFormulas(indexes);
-    end
-    if isfield(newModel,'metFrom')
-        newModel.metFrom=newModel.metFrom(indexes);
-    end
-    if isfield(newModel,'metCharges')
-        newModel.metCharges=newModel.metCharges(indexes);
-    end
+switch type
+    case 'rxns'
+        if isfield(newModel,'rxns')
+            newModel.rxns=newModel.rxns(indexes);
+        end
+        if isfield(newModel,'lb')
+            newModel.lb=newModel.lb(indexes);
+        end
+        if isfield(newModel,'ub')
+            newModel.ub=newModel.ub(indexes);
+        end
+        if isfield(newModel,'rev')
+            newModel.rev=newModel.rev(indexes);
+        end
+        if isfield(newModel,'c')
+            newModel.c=newModel.c(indexes);
+        end
+        if isfield(newModel,'S')
+            newModel.S=newModel.S(:,indexes);
+        end
+        if isfield(newModel,'rxnNames')
+            newModel.rxnNames=newModel.rxnNames(indexes);
+        end
+        if isfield(newModel,'rxnGeneMat')
+            newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:);
+        end
+        if isfield(newModel,'grRules')
+            newModel.grRules=newModel.grRules(indexes);
+        end
+        if isfield(newModel,'subSystems')
+            newModel.subSystems=newModel.subSystems(indexes);
+        end
+        if isfield(newModel,'eccodes')
+            newModel.eccodes=newModel.eccodes(indexes);
+        end
+        if isfield(newModel,'equations')
+            newModel.equations=newModel.equations(indexes);
+        end
+        if isfield(newModel,'rxnMiriams')
+            newModel.rxnMiriams=newModel.rxnMiriams(indexes);
+        end
+        if isfield(newModel,'rxnComps')
+            newModel.rxnComps=newModel.rxnComps(indexes);
+        end
+        if isfield(newModel,'rxnFrom')
+            newModel.rxnFrom=newModel.rxnFrom(indexes);
+        end
+        if isfield(newModel,'rxnScores')
+            newModel.rxnScores=newModel.rxnScores(indexes);
+        end
+        if isfield(newModel,'rxnNotes')
+            newModel.rxnNotes=newModel.rxnNotes(indexes);
+        end
+        if isfield(newModel,'rxnReferences')
+            newModel.rxnReferences=newModel.rxnReferences(indexes);
+        end
+        if isfield(newModel,'rxnConfidenceScores')
+            newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes);
+        end
+    case 'mets'
+        if isfield(newModel,'mets')
+            newModel.mets=newModel.mets(indexes);
+        end
+        if isfield(newModel,'metNames')
+            newModel.metNames=newModel.metNames(indexes);
+        end
+        if isfield(newModel,'b')
+            newModel.b=newModel.b(indexes,:);
+        end
+        if isfield(newModel,'metComps')
+            newModel.metComps=newModel.metComps(indexes);
+        end
+        if isfield(newModel,'S')
+            newModel.S=newModel.S(indexes,:);
+        end
+        if isfield(newModel,'unconstrained')
+            newModel.unconstrained=newModel.unconstrained(indexes);
+        end
+        if isfield(newModel,'metMiriams')
+            newModel.metMiriams=newModel.metMiriams(indexes,:);
+        end
+        if isfield(newModel,'inchis')
+            newModel.inchis=newModel.inchis(indexes);
+        end
+        if isfield(newModel,'metFormulas')
+            newModel.metFormulas=newModel.metFormulas(indexes);
+        end
+        if isfield(newModel,'metFrom')
+            newModel.metFrom=newModel.metFrom(indexes);
+        end
+        if isfield(newModel,'metCharges')
+            newModel.metCharges=newModel.metCharges(indexes);
+        end
+    case 'genes'
+        if isfield(newModel,'genes')
+            newModel.genes=newModel.genes(indexes);
+        end
+        if isfield(newModel,'geneComps')
+            newModel.geneComps=newModel.geneComps(indexes);
+        end
+        if isfield(newModel,'geneMiriams')
+            newModel.geneMiriams=newModel.geneMiriams(indexes);
+        end
+        if isfield(newModel,'geneShortNames')
+            newModel.geneShortNames=newModel.geneShortNames(indexes);
+        end
+        if isfield(newModel,'rxnGeneMat')
+            newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes);
+        end
+    case 'comps'
+        if isfield(newModel,'comps')
+            newModel.comps=newModel.comps(indexes);
+        end
+        if isfield(newModel,'compNames')
+            newModel.compNames=newModel.compNames(indexes);
+        end
+        if isfield(newModel,'compOutside')
+            newModel.compOutside=newModel.compOutside(indexes);
+        end
+        if isfield(newModel,'compMiriams')
+            newModel.compMiriams=newModel.compMiriams(indexes);
+        end
+        [~,J]=sort(indexes); % The *index* of compartment is used in next fields
+        if isfield(newModel,'metComps')
+            [toreplace, bywhat] = ismember(newModel.metComps,1:length(J));
+            newModel.metComps(toreplace) = J(bywhat(toreplace));
+        end
+        if isfield(model,'rxnComps')
+            [toreplace, bywhat] = ismember(model.rxnComps,1:length(J));
+            model.rxnComps(toreplace) = J(bywhat(toreplace));
+        end
+        if isfield(model,'geneComps')
+            [toreplace, bywhat] = ismember(model.geneComps,1:length(J));
+            model.geneComps(toreplace) = J(bywhat(toreplace));
+        end
 end
 end