GECKO 3.1.0

.gitignore

@@ -17,6 +17,8 @@ geckopy/geckopy/data_files/*.xml
 *.ppt*
 # Only allowed .mat file
 !phylDist.mat
+# Ignore intermediate model files
+*_stage*.yml
 
 # Packages #
 ############

GECKOInstaller.m

@@ -1,14 +1,31 @@
 classdef GECKOInstaller
-% GECKOInstaller
-%   Support for installing and uninstalling
-%   Run GECKOInstaller.install to install (will set up the path in MATLAB)
-%   Run GECKOInstaller.uninstall to clear the path from MATLAB
-%   To install, you first need to cd to the GECKO root.
+    % GECKOInstaller
+    %   Support for installing and uninstalling
+    %   Run GECKOInstaller.install to install (will set up the path in MATLAB)
+    %   Run GECKOInstaller.uninstall to clear the path from MATLAB
+    %   To install, you first need to cd to the GECKO root.
 
     methods (Static)
         function install
             sourceDir = fileparts(which(mfilename));
             paths = GECKOInstaller.GetFilteredSubPaths(sourceDir, GECKOInstaller.FILE_FILTER);
+
+            GECKOInstaller.checkRAVENversion('2.8.3'); % Minimum RAVEN version
+
+            % Check unique function names
+            if ~exist("checkFunctionUniqueness.m")
+                error(['Cannot find RAVEN Toolbox in the MATLAB path. Make ' ...
+                    'sure you have installed RAVEN in accordance to the ' ...
+                    'following instructions, including running ''checkInstallation()'': ' ...
+                    'https://github.com/SysBioChalmers/RAVEN/wiki/Installation'])
+            else
+                status=checkFunctionUniqueness(paths);
+                if ~status
+                    error(['You might have multiple GECKO installations in your ' ...
+                        'MATLAB path. Rerun GECKOInstaller.install after ' ...
+                        'resolving the conflicting functions.'])
+                end
+            end
             addpath(paths);
             savepath;
         end
@@ -19,32 +36,54 @@
             savepath;
         end
         function path = getGECKOMainPath()
-			path = fileparts(which(mfilename));
-			path = strrep(path, '\', '/'); %get rid of backslashes in Windows
-			if ~endsWith(path, '/')
-				path = strcat(path,'/');
-			end
-		end
+            path = fileparts(which(mfilename));
+            path = strrep(path, '\', '/'); %get rid of backslashes in Windows
+            if ~endsWith(path, '/')
+                path = strcat(path,'/');
+            end
+        end
 
         function newPaths = GetFilteredSubPaths(path_, filter_)
             pathSep = pathsep();
-			%Check that there are no separators in the path - that will cause 
+            %Check that there are no separators in the path - that will cause
             %problems since the separator is used to separate paths in a string
-			if contains(path_, pathSep)
-				error('The path in which GECKO resides may not contain semicolons for this installation to work!');
-			end
+            if contains(path_, pathSep)
+                error('The path in which GECKO resides may not contain semicolons for this installation to work!');
+            end
             paths = genpath(path_);
             splitPaths = strsplit(paths, pathSep);
             %remove the last, it is empty
             splitPaths = splitPaths(1,1:end-1);
             matches = regexp(splitPaths, filter_, 'match');
             okPaths = cellfun(@isempty, matches);
             pathsLeft = splitPaths(1,okPaths);
-            newPaths = strcat(char(join(pathsLeft, pathSep)), pathSep);
+            newPaths = char(join(pathsLeft, pathSep));
+        end
+        function checkRAVENversion(minmVer)
+            try
+                currVer = checkInstallation('versionOnly');
+                if strcmp(currVer,'develop')
+                    printOrange('WARNING: Cannot determine your RAVEN version as it is in a development branch.\n')
+                else
+                    currVerNum = str2double(strsplit(currVer,'.'));
+                    minmVerNum = str2double(strsplit(minmVer,'.'));
+                    for i=1:3
+                        if currVerNum(i)<minmVerNum(i)
+                            error('Installed RAVEN version is %s, while the minimum is %s.',currVer,minmVer)
+                        end
+                    end
+                end
+            catch
+                warning(['Cannot find RAVEN Toolbox in the MATLAB path, or the version ' ...
+                    'is too old (before v' minmVer '). Make sure you have installed RAVEN in ' ...
+                    'accordance to the following instructions, including running ' ...
+                    '''checkInstallation()'': https://github.com/SysBioChalmers/RAVEN/wiki/Installation'])
+            end
+
         end
     end
-    
+
     properties (Constant)
-      FILE_FILTER = '.*\.git|.idea|userData.*';
-   end
+        FILE_FILTER = '.*\.git|.idea|tutorials.*|.github|_MACOSX|doc';
+    end
 end

README.md

@@ -10,6 +10,9 @@ The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzym
 
 💡 In the GECKO folder, `protocol.m` contains instructions on how to reconstruct and analyze an ecModel for _S. cerevisiae_. This demonstrates how many of GECKO's functions can be used.
 
+💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. The source code documentation is also available
+[online](http://sysbiochalmers.github.io/GECKO/doc/).
+
 _**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](#previous-versions-gecko-1-and-2)_.
 
 ### Citation
@@ -23,7 +26,7 @@ _**Note:** Regarding code and model compatibility with earlier GECKO versions, s
 #### Required software
 
 - MATLAB version 2019b or later, no additional MathWorks toolboxes are required.
-- [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.7.12 or later. The RAVEN Toolbox Wiki contains [installation instructions for both RAVEN](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) and [Gurobi](https://github.com/SysBioChalmers/RAVEN/wiki/Installation#solvers). Briefly, RAVEN is either downloaded via `git clone`, as ZIP-archive from GitHub, or installed as a [MATLAB AddOn](https://se.mathworks.com/matlabcentral/fileexchange/112330-raven-toolbox). After finishing all installation instructions, the user should run installation checks in MATLAB with: `checkInstallation`.
+- [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN). The RAVEN Toolbox Wiki contains [installation instructions for both RAVEN](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) and [Gurobi](https://github.com/SysBioChalmers/RAVEN/wiki/Installation#solvers). Briefly, RAVEN is either downloaded via `git clone`, as ZIP-archive from GitHub, or installed as a [MATLAB AddOn](https://se.mathworks.com/matlabcentral/fileexchange/112330-raven-toolbox). After finishing all installation instructions, the user should run installation checks in MATLAB with: `checkInstallation`.
 - [Gurobi Optimizer](https://www.gurobi.com/solutions/gurobi-optimizer/) is recommended for simulations (free academic license available). Alternatively, the open-source [GNU Linear Programming Kit](https://www.gnu.org/software/glpk/) (distributed with RAVEN) or SoPlex as part of the [SCIP Optimization Suite](https://scipopt.org/) can be used.
 - [Docker](https://www.docker.com/) for running DLKcat. Installation instructions are available at https://docs.docker.com/get-docker .
 

_config.yml

@@ -1,4 +1,5 @@
 theme: jekyll-theme-minimal
 logo: GECKO.png
-show_downloads: false
+show_downloads: true
 exclude: [.github, databases, src, test, userData]
+keep_files: ["doc/"]