Merge pull request #417 from SysBioChalmers/devel

RAVEN 2.7.0
SysBioChalmers · May 13, 2022 · fbbdba1 · fbbdba1
2 parents 16298dc + 940aca0
commit fbbdba1
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diff --git a/.gitattributes b/.gitattributes
@@ -3,7 +3,8 @@
 # Use MATLAB style diff
 *.m text diff=matlab
 # Mark as binary to prevent EOL changes. Also no need to track 
-mafft-linux*/*  binary
+mafft.bat  binary
+mafft/  binary
 # Files/folders that should not be included when downloading repo as ZIP
 .gitattributes	export-ignore
 .gitignore	export-ignore

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -7,22 +7,24 @@ jobs:
     runs-on: self-hosted
 
     steps:
+      - name: Checkout
+        uses: actions/checkout@v2
 
-    - 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($2, v, "(___+)|(===+)|(---+)"); for (i = 0; ++i <= n;) { print v[i] } }')
+          PARSED_RESULTS="${PARSED_RESULTS//'%'/'%25'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'%0A'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'%0D'}"
+          echo ::set-output name=results::$PARSED_RESULTS
 
-    - 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}}
+      - 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}}
diff --git a/INIT/getINITModel.m b/INIT/getINITModel.m
@@ -109,6 +109,8 @@
 
 if nargin<3
     celltype=[];
+else
+    celltype=char(celltype);
 end
 if nargin<4
     hpaData=[];
@@ -121,6 +123,8 @@
 end
 if nargin<7
     taskFile=[];
+else
+    taskFile=char(taskFile);
 end
 if nargin<8 || isempty(useScoresForTasks)
     useScoresForTasks=true;

diff --git a/INIT/runINIT.m b/INIT/runINIT.m
@@ -67,24 +67,17 @@
 if isempty(rxnScores)
     rxnScores=zeros(numel(model.rxns),1);
 end
-if nargin<3
+if nargin<3 || isempty(presentMets)
     presentMets={};
+else
+    presentMets=convertCharArray(presentMets);
 end
-if isempty(presentMets)
-    presentMets={};
-end
-presentMets=presentMets(:);
-if nargin<4
-    essentialRxns={};
-end
-if isempty(essentialRxns)
+if nargin<4 || isempty(essentialRxns)
     essentialRxns={};
+else
+    essentialRxns=convertCharArray(essentialRxns);
 end
-essentialRxns=essentialRxns(:);
-if nargin<5
-    prodWeight=0.5;
-end
-if isempty(prodWeight)
+if nargin<5 || isempty(prodWeight)
     prodWeight=0.5;
 end
 if nargin<6

diff --git a/core/FSEOF.m b/core/FSEOF.m
@@ -23,6 +23,9 @@
 %
 %   Usage: targets=FSEOF(model,biomassRxn,targetRxn,iterations,coefficient,outputFile)
 
+biomassRxn=char(biomassRxn);
+targetRxn=char(targetRxn);
+
 if nargin<4
     iterations=10;
     coefficient=0.9;
@@ -96,6 +99,7 @@
 %Generating output
 formatSpec='%s\t%s\t%s\t%s\t%s\t%s\t%s\n';
 if output == 1    %Output to a file
+    outputFile=char(outputFile);
     fid=fopen(outputFile,'w');
     fprintf(fid,formatSpec,'Slope','rowID','Enzyme ID','Enzyme Name','Subsystems','Direction','Gr Rule');
 else              %Output to screen

diff --git a/core/addExchangeRxns.m b/core/addExchangeRxns.m
@@ -23,11 +23,14 @@
 
 if nargin<3
     mets=model.mets;
+elseif ~islogical(mets) && ~isnumeric(mets)
+    mets=convertCharArray(mets);
 end
-reactionType=upper(reactionType);
 J=getIndexes(model,mets,'mets',false);
 mets=model.mets(J);
 
+reactionType=char(upper(reactionType));
+
 %Production is positive for OUT and BOTH
 if strcmp(reactionType,'IN')
     I=speye(numel(model.mets));

diff --git a/core/addGenesRaven.m b/core/addGenesRaven.m
@@ -32,11 +32,8 @@
 if ~isfield(genesToAdd,'genes')
     EM='genes is a required field in genesToAdd';
     dispEM(EM);
-end
-
-if ~iscellstr(genesToAdd.genes)
-    EM='genesToAdd.genes must be a cell array of strings';
-    dispEM(EM);
+else
+    genesToAdd.genes=convertCharArray(genesToAdd.genes);
 end
 
 %Number of genes
@@ -68,14 +65,11 @@
 
 %Some more checks and if they pass then add each field to the structure
 if isfield(genesToAdd,'geneShortNames')
+    genesToAdd.geneShortNames=convertCharArray(genesToAdd.geneShortNames);
     if numel(genesToAdd.geneShortNames)~=nGenes
         EM='genesToAdd.geneShortNames must have the same number of elements as genesToAdd.genes';
         dispEM(EM);
     end
-    if ~iscellstr(genesToAdd.geneShortNames)
-        EM='genesToAdd.geneShortNames must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'geneShortNames')
         newModel.geneShortNames=largeFiller;

diff --git a/core/addMets.m b/core/addMets.m
@@ -58,6 +58,8 @@
 end
 if nargin<4
     prefix='m_';
+else
+    prefix=char(prefix);
 end
 
 newModel=model;
@@ -69,35 +71,19 @@
 %Check some stuff regarding the required fields
 if ~isfield(metsToAdd,'mets')
     metsToAdd.mets=generateNewIds(newModel,'mets',prefix,numel(metsToAdd.metNames));
+else
+    metsToAdd.mets=convertCharArray(metsToAdd.mets);
 end
 if ~isfield(metsToAdd,'metNames')
     metsToAdd.metNames=metsToAdd.mets;
+else
+    metsToAdd.metNames=convertCharArray(metsToAdd.metNames);
 end
 if ~isfield(metsToAdd,'compartments')
     EM='compartments is a required field in metsToAdd';
     dispEM(EM);
-end
-if ischar(metsToAdd.mets)
-    metsToAdd.mets={metsToAdd.mets};
-elseif ~iscellstr(metsToAdd.mets)
-    EM='metsToAdd.mets must be a cell array of strings';
-    dispEM(EM);
-end
-if ischar(metsToAdd.metNames)
-    metsToAdd.metNames={metsToAdd.metNames};
-elseif ~iscellstr(metsToAdd.metNames)
-    EM='metsToAdd.metNames must be a cell array of strings';
-    dispEM(EM);
-end
-if ~iscellstr(metsToAdd.compartments)
-    if ischar(metsToAdd.compartments)
-        temp=cell(numel(metsToAdd.mets),1);
-        temp(:)={metsToAdd.compartments};
-        metsToAdd.compartments=temp;
-    else
-        EM='metsToAdd.compartments must be a cell array of strings';
-        dispEM(EM);
-    end
+else
+    metsToAdd.compartments=convertCharArray(metsToAdd.compartments);
 end
 
 %Number of metabolites
@@ -193,14 +179,11 @@
 end
 
 if isfield(metsToAdd,'inchis')
+    metsToAdd.inchis=convertCharArray(metsToAdd.inchis);
     if numel(metsToAdd.inchis)~=nMets
         EM='metsToAdd.inchis must have the same number of elements as metsToAdd.mets';
         dispEM(EM);
     end
-    if ~iscellstr(metsToAdd.inchis)
-        EM='metsToAdd.inchis must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'inchis')
         newModel.inchis=largeFiller;
@@ -214,14 +197,11 @@
 end
 
 if isfield(metsToAdd,'metFormulas')
+    metsToAdd.metFormulas=convertCharArray(metsToAdd.metFormulas);
     if numel(metsToAdd.metFormulas)~=nMets
         EM='metsToAdd.metFormulas must have the same number of elements as metsToAdd.mets';
         dispEM(EM);
     end
-    if ~iscellstr(metsToAdd.metFormulas)
-        EM='metsToAdd.metFormulas must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'metFormulas')
         newModel.metFormulas=largeFiller;
@@ -243,6 +223,9 @@
         EM='metsToAdd.metCharges must be of type "double"';
         dispEM(EM);
     end
+    if ~isfield(newModel,'metCharges')
+        newModel.metCharges=NaN(numel(largeFiller),1);
+    end
     newModel.metCharges=[newModel.metCharges;metsToAdd.metCharges(:)];
 else
     %Add default
@@ -252,19 +235,16 @@
 end
 
 if isfield(metsToAdd,'metNotes')
+    metsToAdd.metNotes=convertCharArray(metsToAdd.metNotes);
     if numel(metsToAdd.metNotes)~=nMets
         EM='metsToAdd.metNotes must have the same number of elements as metsToAdd.mets';
         dispEM(EM);
     end
-    if ~iscellstr(metsToAdd.metNotes)
-        EM='metsToAdd.metNotes must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'metNotes')
         newModel.metNotes=largeFiller;
     end
-    newModel.metNotes=[newModel.inchis;metsToAdd.metNotes(:)];
+    newModel.metNotes=[newModel.metNotes;metsToAdd.metNotes(:)];
 else
     %Add empty strings if structure is in model
     if isfield(newModel,'metNotes')
@@ -326,16 +306,3 @@
     end
 end
 end
-
-%For getting the numerical form of metabolite ids on the form "m1".
-function I=getInteger(s)
-%Checks if a string is on the form "m1" and if so returns the value of the
-%integer
-I=0;
-if strcmpi(s(1),'m')
-    t=str2double(s(2:end));
-    if ~isnan(t) && ~isempty(t)
-        I=t;
-    end
-end
-end