Adding fly stem cells

.github/config/checks.xml

@@ -44,6 +44,7 @@
         <property name="id" value="LineLengthTest"/>
         <property name="fileExtensions" value=".java" />
         <property name="max" value="120"/>
+        <property name="severity" value="error"/>
     </module>
 
     <!-- Checks for whitespace -->

.gitignore

@@ -12,3 +12,4 @@ docs/javadoc
 working/
 .DS_Store
 MANIFEST.MF
+setup/

build.gradle

@@ -62,8 +62,8 @@ jacocoTestReport {
         })
     }
     reports {
-        xml.enabled true
-        html.enabled true
+        xml.required.set(true)
+        html.required.set(true)
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/arcade/potts/agent/cell/PottsCellContainer.java

@@ -176,6 +176,10 @@ public Cell convert(
                 return new PottsCellFlyNeuron(this, location, parameters, links);
             case "fly-gmc":
                 return new PottsCellFlyGMC(this, location, parameters, links);
+            case "fly-stem-wt":
+                return new PottsCellFlyStem(this, location, parameters, links);
+            case "fly-stem-mudmut":
+                return new PottsCellFlyStem(this, location, parameters, links);
             default:
             case "stem":
                 return new PottsCellStem(this, location, parameters, links);

src/arcade/potts/agent/cell/PottsCellFactory.java

@@ -1,5 +1,6 @@
 package arcade.potts.agent.cell;
 
+import java.security.InvalidParameterException;
 import java.util.ArrayList;
 import java.util.EnumMap;
 import java.util.HashMap;
@@ -213,8 +214,13 @@ void parseValues(Series series) {
             if (linkKeys.size() > 0) {
                 links = new GrabBag();
                 for (String linkKey : linkKeys) {
-                    int popLink = series.populations.get(linkKey).getInt("CODE");
-                    links.add(popLink, linksBox.getDouble(linkKey));
+                    try {
+                        int popLink = series.populations.get(linkKey).getInt("CODE");
+                        links.add(popLink, linksBox.getDouble(linkKey));
+                    } catch (Exception e) {
+                        throw new InvalidParameterException(
+                                "A population link is set that references a population that does not exist.");
+                    }
                 }
             }
 

src/arcade/potts/agent/cell/PottsCellFlyGMC.java

@@ -12,7 +12,9 @@
 /**
  * Implementation of {@link PottsCell} for fly GMC agents. These cells divide into two {@link
  * PottsCellFlyNeuron} cells. The links must be set in the setup file so that 100% of the daughter
- * cells are Neurons. The basal apoptosis rate of this cell should be set to 0 in the setup file.
+ * cells are Neurons. The differentiation of the parent cell is handled by the {@link
+ * PottsModuleProliferationVolumeBasedDivision} module. The basal apoptosis rate of this cell should
+ * be set to 0 in the setup file.
  */
 public class PottsCellFlyGMC extends PottsCell {