Merge pull request #381 from SysBioChalmers/develop

GECKO 3.2.0
SysBioChalmers · May 27, 2024 · 0d8361f · 0d8361f
2 parents afa2334 + 10cfd74
commit 0d8361f
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,5 +1,10 @@
 name: Tests
 
+permissions:
+      contents: write
+      pull-requests: write
+      repository-projects: write
+
 on: [pull_request]
 
 jobs:
@@ -8,10 +13,10 @@ jobs:
 
     steps:
       - name: Fetch GECKO
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Fetch RAVEN
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: "SysBioChalmers/RAVEN"
           path: "RAVEN"

diff --git a/GECKOInstaller.m b/GECKOInstaller.m
@@ -10,7 +10,7 @@
             sourceDir = fileparts(which(mfilename));
             paths = GECKOInstaller.GetFilteredSubPaths(sourceDir, GECKOInstaller.FILE_FILTER);
 
-            GECKOInstaller.checkRAVENversion('2.8.3'); % Minimum RAVEN version
+            GECKOInstaller.checkRAVENversion('2.9.1'); % Minimum RAVEN version
 
             % Check unique function names
             if ~exist("checkFunctionUniqueness.m")
@@ -62,26 +62,42 @@
         end
 
         function checkRAVENversion(minmVer)
+            wrongVersion = false;
             try
-                currVer = checkInstallation('versionOnly');
+                [currVer, installType] = checkInstallation('versionOnly');
                 if strcmp(currVer,'develop')
                     printOrange('WARNING: Cannot determine your RAVEN version as it is in a development branch.\n')
-                else
+                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)
+                            wrongVersion = true;
                         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'])
+                    'is too old for this GECKO version (RAVEN ' minmVer ' is required). ' ...
+                    'Make sure you have installed RAVEN following the instructions available '...
+                    '<a href="https://github.com/SysBioChalmers/RAVEN/wiki/Installation#installation-instructions">here</a>, '...
+                    'including running ''checkInstallation()''.'])
+            end
+            if wrongVersion
+                switch installType
+                    case 0
+                        installType = 'advanced';
+                    case 1
+                        installType = 'easy';
+                    case 2
+                        installType = 'medium';
+                end
+                error(['Installed RAVEN version is %s, while the minimum is %s. '...
+                    'Upgrade RAVEN by following the instructions available ' ...
+                    '<a href="https://github.com/SysBioChalmers/RAVEN/wiki/Installation#upgrade-raven-after-' ...
+                    installType '-installation">here</a>. Do not attempt to run GECKO before upgrading.'], ...
+                    currVer,minmVer)
             end
-
         end
 
         function checkGECKOversion
@@ -113,7 +129,7 @@ function checkRAVENversion(minmVer)
                     fprintf('\n');
                 end
             else
-                fprintf('GECKO installed, unknown version (cannot find version.txt)\n')
+                fprintf('GECKO installed, unknown version (cannot find version.txt).\n')
             end
         end
     end

diff --git a/README.md b/README.md
@@ -10,6 +10,9 @@ The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzym
 
 💡 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. These two scripts complement the [protocols paper](#citation).
 
+### Significant changes since protocol publication
+- GECKO **3.2.0**: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects **Step 58** in the protocol, changing behaviour of `constrainEnzConcs` and making `updateProtPool` obsolete, `tutorials/full_ecModel/protocol.m` is updated to reflect this change. See [#357](https://github.com/SysBioChalmers/GECKO/issues/375) for more details.  
+
 _**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_.
 
 ## Cite us