Merge pull request #1804 from opencobra/develop

Develop

Author: rmtfleming

.artenolis/generateTutorials.m

@@ -15,8 +15,7 @@ function generateTutorials(destinationFolder, varargin)
 
     if strcmp(version('-release'), '2016b')
         openAndConvert = @matlab.internal.richeditor.openAndConvert;
-    end
-    if strcmp(version('-release'), '2017b')
+    else
         openAndConvert = @matlab.internal.liveeditor.openAndConvert;
     end
     [~, ~, ~] = mkdir(destinationFolder);

.gitattributes

@@ -2,6 +2,32 @@
 *.html  linguist-vendored=true
 *.gms   linguist-vendored=true
 
-*.mat -crlf -diff -merge
-*.mlx -crlf -diff -merge
-*.xlsx -crlf -diff -merge
+## https://nl.mathworks.com/help/matlab/matlab_prog/set-up-git-source-control.html#buhx2d6-1_3
+*.fig binary
+*.mat binary
+*.mdl binary
+*.mdlp binary
+*.mexa64 binary
+*.mexw64 binary
+*.mexmaci64 binary
+*.mlapp binary
+*.mldatx binary
+*.mlproj binary
+*.mlx binary
+*.p binary
+*.sfx binary
+*.sldd binary
+*.slreqx binary
+*.slmx binary
+*.sltx binary
+*.slxc binary
+*.slx binary merge=mlAutoMerge
+*.slxp binary
+
+## Other common binary file types
+*.docx binary
+*.exe binary
+*.jpg binary
+*.pdf binary
+*.png binary
+*.xlsx binary

.gitmodules

@@ -49,3 +49,6 @@
 [submodule "external/base/utilities/condalab"]
 	path = external/base/utilities/condalab
 	url = https://github.com/sg-s/condalab
+[submodule "external/analysis/PolytopeSamplerMatlab"]
+	path = external/analysis/PolytopeSamplerMatlab
+	url = https://github.com/ConstrainedSampler/PolytopeSamplerMatlab

binary

@@ -105,7 +105,7 @@
 if ~isfield(options,'textSize')
     options.textSize = ones(max(nNodes,nEdges),1)*12;
     if strcmp(CB_MAP_OUTPUT,'svg')
-        options.textSize = ones(max(nNodes,nEdges),1)*6;
+        options.textSize = ones(max(nNodes,nEdges),1)*10;
     end
 end
 %Font Color
@@ -286,7 +286,7 @@
       if isfield(options, 'rxnTextSize')
         drawText(map.rxnLabelPosition(1,i),map.rxnLabelPosition(2,i),map.connectionAbb{find(map.rxnIndex(i)==map.connection,1)},options.rxnTextSize(i),'italic');
       else
-        drawText(map.rxnLabelPosition(1,i),map.rxnLabelPosition(2,i),map.connectionAbb{find(map.rxnIndex(i)==map.connection,1)},8,'italic');
+        drawText(map.rxnLabelPosition(1,i),map.rxnLabelPosition(2,i),map.connectionAbb{find(map.rxnIndex(i)==map.connection,1)},10,'italic');
       end
     end
 end

deprecated/_maps_old/drawCbMap.m

@@ -51,11 +51,12 @@
 if ~isfield(options,'rxnDirFlag'), rxnDirFlag = false; else rxnDirFlag = options.rxnDirFlag; end
 rxnListZero = model.rxns(abs(flux)<=1e-9);
 absFlag=false;
+origFlux = flux; %need this to set the arrow directions correct if abs is used -mfarshada
 switch lower(options.scaleType)
     case {1, 'linear'}
         options.scaleTypeLabel='Linear;';
     case {2 ,'linear absolute'}
-        flux=abs(flux);
+        flux=abs(flux); 
         absFlag=true;
         options.scaleTypeLabel='Linear absolute;';
     case {3,'log10'}
@@ -109,8 +110,8 @@
 if rxnDirFlag
     options.rxnDir = zeros(length(map.connectionAbb),1);
     for i = 1:length(map.connectionAbb)
-        options.rxnDir(ismember(map.connectionAbb,model.rxns(flux>0))) = 1;
-        options.rxnDir(ismember(map.connectionAbb,model.rxns(flux<0))) = -1;
+        options.rxnDir(ismember(map.connectionAbb,model.rxns(origFlux>0))) = -1; %was 1, inconsistent with drawLine -mfarshada
+        options.rxnDir(ismember(map.connectionAbb,model.rxns(origFlux<0))) = 1; %was -1 
     end
 end
 

deprecated/_maps_old/drawFlux.m

@@ -47,7 +47,35 @@ in /var/tmp/cobratoolbox_doc_timestamp.tar.gz
 You can specify an alternative directory by changing the location of
 the /output mountpoint in the docker run command.
 
+## Building COBRA.tutorials
 
+Clone the cobratoolbox and COBRA.tutorials repository in an empty directory. Then cd to 
+./cobratoolbox/docs directory and create and run the following script:
+
+```
+MATLAB_ROOT=/usr/local/MATLAB
+MATLAB_VERSION=R2020b
+OUTPUT=/var/tmp/COBRA.tutorials_output
+./prepareTutorials.sh  \
+	-p=${OUTPUT} \
+	-t=../../COBRA.tutorials \
+	-c=../../cobratoolbox \
+	-e=${MATLAB_ROOT}/${MATLAB_VERSION}/bin/matlab \
+	-m=html
+
+```
+
+Replace MATLAB_ROOT with the location of the matlab if different to 
+/usr/local, and OUTPUT with the location to which the tutorial HTML files
+are to be written.
+
+Remark: This procedure has been tested with head of cobratoolbox develop branch
+(e8c40f3e74de9f2d671b58dd918305697ffd64b9) and
+head of COBRA.tutorials master branch (0761e66374b0eff81db0f9adde87e118a12e967e)
+on 2021-06-16 running on Ubuntu 18.04 with MATLAB R2020b
+
+Remark: the dependency on matlab for this step makes it difficult to dockerize
+due to the need for matlab licence files.
 
 ## Publishing the HTML to live site
 
@@ -61,6 +89,24 @@ and replace the ./stable or ./latest directory with the build output.
 Tracking code can be added to the template by editing layout.html or footer.html
 in https://github.com/opencobra/sphinx_cobra_theme/tree/develop/sphinx_cobra_theme/
 
+The tracking code is located near the end of the page.
+
+```
+ <!-- Global site tag (gtag.js) - Google Analytics -->
+  <script async src="https://www.googletagmanager.com/gtag/js?id=G-TRCMZL1FKK"></script>
+  <script>
+    window.dataLayer = window.dataLayer || [];
+    function gtag(){dataLayer.push(arguments);}
+    gtag('js', new Date());
+    gtag('config', 'G-TRCMZL1FKK');
+  </script>
+```
+
+## Remarks about sphinx_cobra_theme
+
+The project logo (top-left) is hardcoded in layout.html at approx line 127. A comment in the code indicates this was done
+to expedite configuration issues earlier in the project. Ideally the template should be reuseable (without modification)
+for all the opencobra sub-projects: so need to find a way to externally configure the project logo.
 
 ## Checking for broken links
 

docs/README.md

@@ -1,4 +1,4 @@
-#!/usr/local/bin/bash
+#!/bin/bash
 usage="$(basename $0) -p=pdfPath -t=COBRATutorialsPath -c=COBRAToolBoxPath [-f=folderNameOfATutorial] [-h] [-l] [-m=mode] -- script to create tutorial documentation for the COBRA Toolbox.
 
 where:
@@ -118,7 +118,7 @@ buildHTMLTutorials(){
     do
         createLocalVariables $tutorial
         # create PDF file
-        /usr/local/bin/wkhtmltopdf --page-size A8 --margin-right 2 --margin-bottom 3 --margin-top 3 --margin-left 2 $pdfPath/tutorials/$tutorialFolder/$tutorialName.html $pdfPath/tutorials/$tutorialFolder/$tutorialName.pdf
+        wkhtmltopdf --page-size A8 --margin-right 2 --margin-bottom 3 --margin-top 3 --margin-left 2 $pdfPath/tutorials/$tutorialFolder/$tutorialName.html $pdfPath/tutorials/$tutorialFolder/$tutorialName.pdf
         sed 's#<html><head>#&<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/opencobra/cobratoolbox@ffa0229fc0c01c9236bb7e961f65712443277719/latest/_static/js/iframeResizer.contentWindow.min.js"></script>#g' "$pdfPath/tutorials/$tutorialFolder/$tutorialName.html" > "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
         sed -i.bak 's/white-space:\ pre-wrap/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
         sed -i.bak 's/white-space:\ pre/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
@@ -131,7 +131,7 @@ buildHTMLSpecificTutorial(){
     $matlab -nodesktop -nosplash -r "restoredefaultpath;initCobraToolbox;addpath('.artenolis');generateTutorials('$pdfPath', '$specificTutorial');restoredefaultpath;savepath;exit;"
     createLocalVariables $specificTutorial
     # create PDF file
-    /usr/local/bin/wkhtmltopdf --page-size A8 --margin-right 2 --margin-bottom 3 --margin-top 3 --margin-left 2 $pdfPath/tutorials/$tutorialFolder/$tutorialName.html $pdfPath/tutorials/$tutorialFolder/$tutorialName.pdf
+    wkhtmltopdf --page-size A8 --margin-right 2 --margin-bottom 3 --margin-top 3 --margin-left 2 $pdfPath/tutorials/$tutorialFolder/$tutorialName.html $pdfPath/tutorials/$tutorialFolder/$tutorialName.pdf
     sed 's#<html><head>#&<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/opencobra/cobratoolbox@ffa0229fc0c01c9236bb7e961f65712443277719/latest/_static/js/iframeResizer.contentWindow.min.js"></script>#g' "$pdfPath/tutorials/$tutorialFolder/$tutorialName.html" > "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
     sed -i.bak 's/white-space:\ pre-wrap/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"
     sed -i.bak 's/white-space:\ pre/white-space:\ normal/g' "$pdfPath/tutorials/$tutorialFolder/iframe_$tutorialName.html"