feat: support for alternative location of DLKcat in/output (#394)

* feat: alternative path of DLKcat in/output

* fix: avoid double output with printOrange function

* fix: remove mentions of Gitter

* doc: makeEcModel informative error noUniprof

* fix: check RAVEN version

.github/CONTRIBUTING.md

@@ -13,7 +13,7 @@ You can contribute in 2 main ways: by creating issues, and by sending pull reque
 * Lacking documentation.
 * Any type of feedback.
 
-If you are unsure about the issue, consider asking first in our [Gitter chat room](https://gitter.im/SysBioChalmers/GECKO).
+If you are unsure about the issue, consider asking first in the [GitHub Discussions page](https://github.com/SysBioChalmers/GECKO/discussions).
 
 When creating the issue, please make sure:
 

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
-  - name: Gitter Channel
-    url: https://gitter.im/SysBioChalmers/GECKO
-    about: You may also ask questions (or contribute with answers) at the GECKO Gitter channel.
+  - name: GitHub Discussions
+    url: https://github.com/SysBioChalmers/GECKO/discussions
+    about: You may also ask for support (or contribute with answers) at the GitHub Discussions page.

GECKOInstaller.m

@@ -66,14 +66,22 @@ function checkRAVENversion(minmVer)
             try
                 [currVer, installType] = checkInstallation('versionOnly');
                 if strcmp(currVer,'develop')
-                    printOrange('WARNING: Cannot determine your RAVEN version as it is in a development branch.\n')
+                    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)
-                            wrongVersion = true;
-                        end
+                    if currVerNum(1) < minmVerNum(1)
+                        wrongVersion = true;
+                    elseif currVerNum(1) > minmVerNum(1)
+                        wrongVersion = false;
+                    elseif currVerNum(2) < minmVerNum(2)
+                        wrongVersion = true;
+                    elseif currVerNum(2) > minmVerNum(2)
+                        wrongVersion = false;
+                    elseif currVerNum(3) < minmVerNum(3)
+                        wrongVersion = true;
+                    elseif currVerNum(3) >= minmVerNum(3)
+                        wrongVersion = false;
                     end
                 end
             catch

doc/src/geckomat/change_model/applyCustomKcats.html

@@ -287,7 +287,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0185     <span class="keyword">if</span> ~isempty(find(rxnToUpdate, 1))
 0186         model = <a href="applyKcatConstraints.html" class="code" title="function model = applyKcatConstraints(model,updateRxns)">applyKcatConstraints</a>(model, rxnToUpdate);
 0187     <span class="keyword">else</span>
-0188         printOrange(<span class="string">'WARNING: No matches found. Consider checking the IDs or proteins in customKcats.'</span>)
+0188         printOrange(<span class="string">'WARNING: No matches found. Consider checking the IDs or proteins in customKcats.'</span>);
 0189     <span class="keyword">end</span>
 0190 
 0191     rxnUpdated = model.ec.rxns(find(rxnToUpdate));

doc/src/geckomat/change_model/applyKcatConstraints.html

@@ -108,7 +108,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0046            <span class="string">' not a valid GECKO3 ecModel. First run makeEcModel(model).'</span>])
 0047 <span class="keyword">end</span>
 0048 <span class="keyword">if</span> all(model.ec.kcat==0)
-0049     printOrange(<span class="string">'WARNING: No kcat values are provided in model.ec.kcat, model remains unchanged.\n'</span>)
+0049     printOrange(<span class="string">'WARNING: No kcat values are provided in model.ec.kcat, model remains unchanged.\n'</span>);
 0050     <span class="keyword">return</span>
 0051 <span class="keyword">end</span>
 0052 

doc/src/geckomat/change_model/getComplexData.html

@@ -118,7 +118,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0044 
 0045 params = modelAdapter.params;
 0046 <span class="keyword">if</span> isempty(taxonomicID) <span class="comment">% Can be empty when gathered from model adapter</span>
-0047     printOrange(<span class="string">'WARNING: No taxonomicID specified.'</span>)
+0047     printOrange(<span class="string">'WARNING: No taxonomicID specified.'</span>);
 0048     <span class="keyword">return</span>
 0049 <span class="keyword">elseif</span> taxonomicID == 0
 0050     taxonomicID = [];

doc/src/geckomat/change_model/getKcatAcrossIsozymes.html

@@ -75,7 +75,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0018     error(<span class="string">'Provided model is a GECKO light version, this function is not relevant for such models'</span>)
 0019 <span class="keyword">end</span>
 0020 <span class="keyword">if</span> all(model.ec.kcat==0)
-0021     printOrange(<span class="string">'WARNING: No kcat values are provided in model.ec.kcat, model remains unchanged.\n'</span>)
+0021     printOrange(<span class="string">'WARNING: No kcat values are provided in model.ec.kcat, model remains unchanged.\n'</span>);
 0022     <span class="keyword">return</span>
 0023 <span class="keyword">end</span>
 0024