Merge pull request #475 from SysBioChalmers/develop

RAVEN 2.8.0

.github/issue_template.md

@@ -12,12 +12,18 @@ INSERT CODE HERE
 ```
 
 #### System information
-* Please report:
-1. RAVEN version (stabile [release](https://github.com/SysBioChalmers/RAVEN/releases), `devel` branch?)
-2. Operating system (Windows/Mac/Linux; include version)
+<!-- Please report the complete output from checkInstallation, for instance:
+ > Installing from location             C:\Work\GitHub\RAVEN
+ > Checking RAVEN release               2.7.12
+   > You are running the latest RAVEN release
+ > Checking MATLAB release              2022a
+ > Checking system architecture         win64
+ > Set RAVEN in MATLAB path             Pass
+ > Save MATLAB path                     Pass
+
+etc. etc.
+ -->
 
 **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

.github/workflows/testing-comment.md → .github/workflows/commentsFromTests.md

@@ -1,7 +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:
 
-```
+<pre>
 {TEST_RESULTS}
-```
+</pre>
 
-> _Note: In the case of multiple test runs, this post will be edited._
+> _Note: In the case of multiple test runs, this post will be edited._

.github/workflows/tests.yml

@@ -0,0 +1,29 @@
+name: Tests
+
+on: [pull_request]
+
+jobs:
+  matlab-tests:
+    runs-on: self-hosted
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Run tests
+        id: matlab-test
+        run: |
+          TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "warning('off', 'MATLAB:rmpath:DirNotFound'); rmpath(genpath('/home/m/ecModels-dependencies/RAVEN')); rmpath(genpath('/home/m/actions-runner')); addpath(genpath('.')); checkInstallation; cd('testing/unit_tests'); runtests(struct2table(dir('*.m')).name); exit;" | awk 'NR>13 && !/^(___|===|---)/')
+          PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}"
+          echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT
+
+      - name: Post comment
+        uses: NejcZdovc/comment-pr@v2
+        with:
+          file: "commentsFromTests.md"
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          TEST_RESULTS: ${{steps.matlab-test.outputs.results}}
+          GH_ACTION_RUN: ${{github.run_id}}

INIT/ftINITFillGapsForAllTasks.m

@@ -43,7 +43,7 @@
     rxnScores=ones(numel(refModel.rxns),1)*-1;
 end
 
-if isempty(taskStructure) && ~(exist(inputFile,'file')==2)
+if isempty(taskStructure) && ~isfile(inputFile)
     error('Task file %s cannot be found',string(inputFile));
 end
 

README.md

@@ -1,39 +1,33 @@
-# ![The RAVEN Toolbox 2](RAVEN2.png)
+<img src="./RAVEN2.png" width="200px">
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3689518.svg)](https://doi.org/10.5281/zenodo.3689518) [![GitHub release](https://img.shields.io/github/release/SysBioChalmers/RAVEN/all.svg)](https://GitHub.com/SysBioChalmers/RAVEN/releases/) [![Join the chat at https://gitter.im/SysBioChalmers/RAVEN](https://badges.gitter.im/SysBioChalmers/RAVEN.svg)](https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![View RAVEN Toolbox on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/112330-raven-toolbox)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3689518.svg)](https://doi.org/10.5281/zenodo.3689518)
+[![GitHub release](https://img.shields.io/github/release/SysBioChalmers/RAVEN/all.svg)](https://GitHub.com/SysBioChalmers/RAVEN/releases/)
+[![Tests 
+passing](https://github.com/SysBioChalmers/RAVEN/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/SysBioChalmers/RAVEN/actions)
+[![Join the chat at https://gitter.im/SysBioChalmers/RAVEN](https://badges.gitter.im/SysBioChalmers/RAVEN.svg)](https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![View RAVEN Toolbox on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/112330-raven-toolbox)
 
 The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.
 
 
 ## Documentation
-The information about downloading, installing and developing RAVEN is included in the [Wiki](https://github.com/SysBioChalmers/RAVEN/wiki)
+The information about downloading, installing and developing RAVEN is included in the [Wiki](https://github.com/SysBioChalmers/RAVEN/wiki). The source code documentation is also available 
+[online](http://sysbiochalmers.github.io/RAVEN/doc/).
 
 
 ## Cite Us
-If you use RAVEN 2.0 in your scientific work, please cite:
+If you use RAVEN 2 in your scientific work, please cite:
 > Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on _Streptomyces coelicolor_. PLoS Comput Biol 14(10): e1006541. doi:[10.1371/journal.pcbi.1006541](https://doi.org/10.1371/journal.pcbi.1006541).
 
 Starting with RAVEN v2.3.1, all the releases are also archived in [Zenodo](https://doi.org/10.5281/zenodo.3689518), for you to cite the specific version of RAVEN that you used in your study
 
+If you use ftINIT in your scientific work, please cite:
+> Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:[10.1073/pnas.2217868120](https://doi.org/10.1073/pnas.2217868120)
 
-If you use any of the following functions, please also cite the relevant paper:
-
-* `getInitModel` and similar _INIT_ functions:
-  >Agren R _et al_. (2012) PLoS Comput Biol 8(5): e1002518. doi:[10.1371/journal.pcbi.1002518](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002518).
-  
-* `getInitModel` with a `taskFile` and similar _tINIT_ functions:
-  >Agren R _et al_. (2014) Mol Syst Biol 10(3): 721. doi:[10.1002/msb.145122](http://msb.embopress.org/content/10/3/721).
-
-* `randomSampling`:
-  >Bordel S _et al_. (2010) PLoS Comput Biol 6(7): e1000859. doi:[10.1371/journal.pcbi.1000859](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000859).
-
-* If you only use RAVEN 1.0 in your scientific work, please cite:
-  >Agren R _et al_. (2013) PLoS Comput Biol 9(3): e1002980. doi:[10.1371/journal.pcbi.1002980](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002980).
-
+For crediting supporting work, please cite doi:[10.1002/msb.145122](http://msb.embopress.org/content/10/3/721) (`tInit`); doi:[10.1371/journal.pcbi.1000859](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000859) (`randomsampling`). For crediting RAVEN 1, cite doi:[10.1371/journal.pcbi.1002980](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002980). For more details, see [wiki#cite-us](https://github.com/SysBioChalmers/RAVEN/wiki#cite-us).
 
 ## Contact Us
-For support, technical issues, bug reports etc., please [![Join the chat at https://gitter.im/SysBioChalmers/RAVEN](https://badges.gitter.im/SysBioChalmers/RAVEN.svg)](https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge). For other issues, please contact [Eduard Kerkhoven](https://github.com/edkerk).
-
+For support, technical issues, bug reports etc., please [![Join the chat at https://gitter.im/SysBioChalmers/RAVEN](https://badges.gitter.im/SysBioChalmers/RAVEN.svg)](https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge). For other issues, please contact [Eduard Kerkhoven](https://www.chalmers.se/en/persons/eduardk/).
 
 ## More from SysBio Chalmers
 For more systems biology related software and recently published genome-scale models from the Systems and Synthetic Biology group at Chalmers University of Technology, please visit the [GitHub page](https://github.com/SysBioChalmers). For more information and publications by the Systems and Synthetic Biology please visit [SysBio](https://www.sysbio.se/).

_config.yml

@@ -0,0 +1,4 @@
+theme: jekyll-theme-minimal
+logo: RAVEN2.png
+show_downloads: true
+keep_files: ["doc/"]

core/addRxns.m

@@ -214,7 +214,11 @@
     for i = 1:length(rxnsToAdd.mets)
         mets         = rxnsToAdd.mets{i};
         stoichCoeffs = rxnsToAdd.stoichCoeffs{i};
-        isrev        = rxnsToAdd.lb(i) < 0;
+        if isfield(rxnsToAdd,'ub')
+            isrev        = rxnsToAdd.lb(i) < 0 && rxnsToAdd.ub(i) > 0;
+        else
+            isrev        = rxnsToAdd.lb(i) < 0;
+        end
         rxnsToAdd.equations{i} = buildEquation(mets,stoichCoeffs,isrev);
     end
 end

core/findRAVENroot.m

@@ -7,15 +7,11 @@
 
 ST=dbstack('-completenames');
 prevDir = pwd();
-if length(ST)>1
-    ravenPath=ST(2).file; % In case findRAVENroot is run via another function
-else
-    ravenPath=ST(1).file;
-end
+ravenPath = ST(strcmp({ST.name},'findRAVENroot')).file;
 rootFound = 0;
 while rootFound == 0
-    isRoot = exist(fullfile(ravenPath,'RAVEN2.png'),'file');
-    if isRoot == 2
+    isRoot = isfile(fullfile(ravenPath,'RAVEN2.png'));
+    if isRoot
         rootFound = 1;
     else
         ravenPathOld = ravenPath;

core/fitTasks.m

@@ -53,7 +53,7 @@
     params=[];
 end
 
-if isempty(taskStructure) && ~(exist(inputFile,'file')==2)
+if isempty(taskStructure) && ~isfile(inputFile)
     error('Task file %s cannot be found',string(inputFile));
 end
 

core/getAllowedBounds.m

@@ -26,39 +26,72 @@
 minFluxes=zeros(numel(rxns),1);
 maxFluxes=zeros(numel(rxns),1);
 exitFlags=zeros(numel(rxns),2);
-
 c=zeros(numel(model.rxns),1);
-hsSolMin=[];
-hsSolMax=[];
-fprintf('Getting minimal and maximal fluxes...   0%% complete');
-for i=1:numel(rxns)
-    model.c=c;
-
-    %Get minimal flux
-    model.c(rxns(i))=-1;
-    [solution, hsSolMin]=solveLP(model,0,[],hsSolMin);
-    exitFlags(i,1)=solution.stat;
-    if ~isempty(solution.f)
-        minFluxes(i)=solution.x(rxns(i));
-    else
-        minFluxes(i)=NaN;
-    end
-
-    %Get maximal flux
-    model.c(rxns(i))=1;
-    [solution, hsSolMax]=solveLP(model,0,[],hsSolMax);
-    exitFlags(i,2)=solution.stat;
-    if ~isempty(solution.f)
-        maxFluxes(i)=solution.x(rxns(i));
-    else
-        maxFluxes(i)=NaN;
+
+N = numel(rxns);
+p = 1;
+h = waitbar(0, 'Please wait ...');
+
+addonList = matlab.addons.installedAddons;
+if any(strcmpi(addonList.Name,'Parallel Computing Toolbox'))
+    D = parallel.pool.DataQueue;
+    afterEach(D, @nUpdateWaitbar);
+
+    parfor i=1:N
+        tmpModel=model;
+        tmpModel.c=c;
+
+        %Get minimal flux
+        tmpModel.c(rxns(i))=-1;
+        solMin=solveLP(tmpModel);
+        if ~isempty(solMin.f)
+            minFluxes(i)=solMin.x(rxns(i));
+        else
+            minFluxes(i)=NaN;
+        end
+
+        %Get maximal flux
+        tmpModel.c(rxns(i))=1;
+        solMax=solveLP(tmpModel);
+        exitFlags(i,:)=[solMin.stat solMax.stat];
+        if ~isempty(solMax.f)
+            maxFluxes(i)=solMax.x(rxns(i));
+        else
+            maxFluxes(i)=NaN;
+        end
+        send(D, i);
     end
-    %Print the progress every 25 reactions
-    if rem(i-1,25) == 0
-        progress=num2str(floor(100*i/numel(rxns)));
-        progress=pad(progress,3,'left');
-        fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
+else
+    for i=1:N
+        tmpModel=model;
+        tmpModel.c=c;
+
+        %Get minimal flux
+        tmpModel.c(rxns(i))=-1;
+        solMin=solveLP(tmpModel);
+        if ~isempty(solMin.f)
+            minFluxes(i)=solMin.x(rxns(i));
+        else
+            minFluxes(i)=NaN;
+        end
+
+        %Get maximal flux
+        tmpModel.c(rxns(i))=1;
+        solMax=solveLP(tmpModel);
+        exitFlags(i,:)=[solMin.stat solMax.stat];
+        if ~isempty(solMax.f)
+            maxFluxes(i)=solMax.x(rxns(i));
+        else
+            maxFluxes(i)=NaN;
+        end
+        nUpdateWaitbar;
     end
 end
-fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+
+close(h)
+
+    function nUpdateWaitbar(~)
+        waitbar(p/N, h);
+        p = p + 1;
+    end
 end

core/parseTaskList.m

@@ -109,7 +109,7 @@
 %
 %   Usage: taskStruct=parseTaskList(inputFile)
 
-if ~(exist(inputFile,'file')==2)
+if ~isfile(inputFile)
     error('Task list %s cannot be found',string(inputFile));
 end
 

doc/INIT/ftINITFillGapsForAllTasks.html

@@ -125,7 +125,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0043     rxnScores=ones(numel(refModel.rxns),1)*-1;
 0044 <span class="keyword">end</span>
 0045 
-0046 <span class="keyword">if</span> isempty(taskStructure) &amp;&amp; ~(exist(inputFile,<span class="string">'file'</span>)==2)
+0046 <span class="keyword">if</span> isempty(taskStructure) &amp;&amp; ~isfile(inputFile)
 0047     error(<span class="string">'Task file %s cannot be found'</span>,string(inputFile));
 0048 <span class="keyword">end</span>
 0049