Merge pull request #2435 from opencobra/develop

Develop

.github/workflows/cobratoolboxCI_step1.yml

@@ -1,9 +1,12 @@
 name: cobratoolboxCI (merge, test, and upload)
 on:
   pull_request:
+    branches:
+      - develop
+      - master
     types: [opened, synchronize, reopened]
   workflow_dispatch:
-
+    
 permissions:
   contents: read
 

docs/modules/analysis/FBA/index.html

@@ -69,8 +69,8 @@
         <link rel="search" title="Search" href="../../../search.html"/>
     <link rel="top" title="The COBRA Toolbox" href="../../../index.html"/>
         <link rel="up" title="Analysis" href="../index.html"/>
-        <link rel="next" title="Wholebody" href="../wholeBody/index.html"/>
-        <link rel="prev" title="Rumba" href="../rumba/index.html"/> 
+        <link rel="next" title="Percentilecalc" href="../percentileCalc/index.html"/>
+        <link rel="prev" title="Transport" href="../transport/index.html"/> 
 
 
   <script src="../../../_static/js/modernizr.min.js"></script>
@@ -157,41 +157,41 @@ <h1>The COBRA Toolbox</h1>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="../../index.html">Functions</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="../index.html">Analysis</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="../ROOM/index.html">Room</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../MOMA/index.html">Moma</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../deletion/index.html">Deletion</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../fastForest/index.html">Fastforest</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../QFCA/index.html">Qfca</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../sparseFBA/index.html">Sparsefba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../relaxedFBA/index.html">Relaxedfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../KLdistance/index.html">Kldistance</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../rFBA/index.html">Rfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../exploration/index.html">Exploration</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../topology/index.html">Topology</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../gMCS/index.html">Gmcs</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../rMTA/index.html">Rmta</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../multiSpecies/index.html">Multispecies</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../KLdistance/index.html">Kldistance</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../findMIIS/index.html">Findmiis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../exploration/index.html">Exploration</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../percentileCalc/index.html">Percentilecalc</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../igemRNA/index.html">Igemrna</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../robustnessAnalysis/index.html">Robustnessanalysis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../coupling/index.html">Coupling</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../nutritionAlgorithm/index.html">Nutritionalgorithm</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../MOMA/index.html">Moma</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../wholeBody/index.html">Wholebody</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../gMCS/index.html">Gmcs</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../geometricFBA/index.html">Geometricfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../subspaces/index.html">Subspaces</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../rumba/index.html">Rumba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../nutritionAlgorithm/index.html">Nutritionalgorithm</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../parsimoniousFBA/index.html">Parsimoniousfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../ROOM/index.html">Room</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../transport/index.html">Transport</a></li>
 <li class="toctree-l3 current"><a class="current reference internal" href="#">Fba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../wholeBody/index.html">Wholebody</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../percentileCalc/index.html">Percentilecalc</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../FVA/index.html">Fva</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../QFCA/index.html">Qfca</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../subspaces/index.html">Subspaces</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../relaxedFBA/index.html">Relaxedfba</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../uFBA/index.html">Ufba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../parsimoniousFBA/index.html">Parsimoniousfba</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../dynamicFBA/index.html">Dynamicfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../rumba/index.html">Rumba</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../sampling/index.html">Sampling</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../FVA/index.html">Fva</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../ICONGEMs/index.html">Icongems</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../fluxEnrichmentAnalysis/index.html">Fluxenrichmentanalysis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../transport/index.html">Transport</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../thermo/index.html">Thermo</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../multiSpecies/index.html">Multispecies</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../fastForest/index.html">Fastforest</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../igemRNA/index.html">Igemrna</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../ICONGEMs/index.html">Icongems</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../sparseFBA/index.html">Sparsefba</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../mdFBA/index.html">Mdfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../rFBA/index.html">Rfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../rMTA/index.html">Rmta</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../robustnessAnalysis/index.html">Robustnessanalysis</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../fluxEnrichmentAnalysis/index.html">Fluxenrichmentanalysis</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../coupling/index.html">Coupling</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../../base/index.html">Base</a></li>
@@ -519,10 +519,10 @@ <h1>The COBRA Toolbox</h1>
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="../wholeBody/index.html" class="btn btn-default float-right" title="Wholebody" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="../percentileCalc/index.html" class="btn btn-default float-right" title="Percentilecalc" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
-        <a href="../rumba/index.html" class="btn btn-default" title="Rumba" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="../transport/index.html" class="btn btn-default" title="Transport" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

docs/modules/analysis/FVA/fastFVA/index.html

@@ -157,34 +157,22 @@ <h1>The COBRA Toolbox</h1>
 <li class="toctree-l1"><a class="reference internal" href="../../../../installation.html">Installation</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="../../../index.html">Functions</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="../../index.html">Analysis</a><ul class="current">
-<li class="toctree-l3"><a class="reference internal" href="../../ROOM/index.html">Room</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../MOMA/index.html">Moma</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../deletion/index.html">Deletion</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../fastForest/index.html">Fastforest</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../QFCA/index.html">Qfca</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../sparseFBA/index.html">Sparsefba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../relaxedFBA/index.html">Relaxedfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../KLdistance/index.html">Kldistance</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../rFBA/index.html">Rfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../exploration/index.html">Exploration</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../topology/index.html">Topology</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../gMCS/index.html">Gmcs</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../rMTA/index.html">Rmta</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../multiSpecies/index.html">Multispecies</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../KLdistance/index.html">Kldistance</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../findMIIS/index.html">Findmiis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../exploration/index.html">Exploration</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../percentileCalc/index.html">Percentilecalc</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../igemRNA/index.html">Igemrna</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../robustnessAnalysis/index.html">Robustnessanalysis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../coupling/index.html">Coupling</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../nutritionAlgorithm/index.html">Nutritionalgorithm</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../geometricFBA/index.html">Geometricfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../subspaces/index.html">Subspaces</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../rumba/index.html">Rumba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../FBA/index.html">Fba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../MOMA/index.html">Moma</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../wholeBody/index.html">Wholebody</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../uFBA/index.html">Ufba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../gMCS/index.html">Gmcs</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../geometricFBA/index.html">Geometricfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../nutritionAlgorithm/index.html">Nutritionalgorithm</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../parsimoniousFBA/index.html">Parsimoniousfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../dynamicFBA/index.html">Dynamicfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../sampling/index.html">Sampling</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../ROOM/index.html">Room</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../transport/index.html">Transport</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../FBA/index.html">Fba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../percentileCalc/index.html">Percentilecalc</a></li>
 <li class="toctree-l3 current"><a class="reference internal" href="../index.html">Fva</a><ul class="current">
 <li class="toctree-l4 current"><a class="current reference internal" href="#">Fastfva</a><ul>
 <li class="toctree-l5"><a class="reference internal" href="mex/index.html">Mex</a></li>
@@ -193,12 +181,24 @@ <h1>The COBRA Toolbox</h1>
 </li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="../../ICONGEMs/index.html">Icongems</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../fluxEnrichmentAnalysis/index.html">Fluxenrichmentanalysis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../transport/index.html">Transport</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../QFCA/index.html">Qfca</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../subspaces/index.html">Subspaces</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../relaxedFBA/index.html">Relaxedfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../uFBA/index.html">Ufba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../dynamicFBA/index.html">Dynamicfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../rumba/index.html">Rumba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../sampling/index.html">Sampling</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../thermo/index.html">Thermo</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../multiSpecies/index.html">Multispecies</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../fastForest/index.html">Fastforest</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../igemRNA/index.html">Igemrna</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../ICONGEMs/index.html">Icongems</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../sparseFBA/index.html">Sparsefba</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../../mdFBA/index.html">Mdfba</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../../rFBA/index.html">Rfba</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../rMTA/index.html">Rmta</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../robustnessAnalysis/index.html">Robustnessanalysis</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../fluxEnrichmentAnalysis/index.html">Fluxenrichmentanalysis</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../../coupling/index.html">Coupling</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../../../base/index.html">Base</a></li>