Add fly cells and accompanying proliferation module

.github/config/checks.xml

@@ -33,11 +33,13 @@
         <property name="id" value="LineLength"/>
         <property name="fileExtensions" value="java" />
         <property name="max" value="100"/>
+        <property name="severity" value="warning"/>
     </module>
     <module name="LineLength">
         <property name="id" value="LineLengthTest"/>
         <property name="fileExtensions" value=".java" />
         <property name="max" value="120"/>
+        <property name="severity" value="error"/>
     </module>
 
     <!-- Checks for whitespace -->

.github/workflows/lint.yml

@@ -15,12 +15,12 @@ jobs:
         fetch-depth: 0
 
     - name: Lint code base
-      uses: dbelyaev/action-checkstyle@v0.9.5
+      uses: dbelyaev/action-checkstyle@v3.0.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check
         checkstyle_config: .github/config/checks.xml
-        fail_on_error: true
+        fail_level: error
 
   update-lint-badges:
     if: ${{ always() && github.ref == 'refs/heads/main' }}

build.gradle

@@ -62,8 +62,8 @@ jacocoTestReport {
         })
     }
     reports {
-        xml.enabled true
-        html.enabled true
+        xml.required.set(true)
+        html.required.set(true)
     }
 }
 
@@ -161,6 +161,8 @@ task updateVersion (group: "versioning", description: "Syncs gradle version with
 
 build.dependsOn copyJar
 
+copyJar.mustRunAfter check, jacocoTestReport
+
 test.finalizedBy jacocoTestReport
 
 bumpMajor.finalizedBy updateVersion

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

setup/gmc.xml

@@ -0,0 +1,28 @@
+<set prefix="2024-10-25-04">
+    <series name="dd" start="1" end="1"
+            ds=".3" margin="0" height="1" length="302" width="302"
+            dt=".083" ticks="576" interval="4">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.term id="surface" />
+            <!-- <potts.term id="persistence" /> -->
+            <!-- <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-neuron:*"/>
+            <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-gmc:*"/> -->
+        </potts>
+        <agents>
+            <populations>
+                <population id="fly-gmc" class="fly-gmc" init="1">
+                 <population.link id="fly-neuron" weight="1"/>
+                 <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                 <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                </population>
+                <population id="fly-neuron" class="fly-neuron" init="0">
+                <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
+                <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                </population>
+            </populations>
+        </agents>
+    </series>
+</set>

setup/nb.xml

@@ -0,0 +1,42 @@
+<set prefix="2025-10-23-01">
+    <series name="dd" start="1" end="1"
+            ds=".3" margin="0" height="1" length="802" width="802"
+            dt=".083" ticks="576" interval="4">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.term id="surface" />
+        </potts>
+        <agents>
+            <populations>
+                <population id="fly-stem-wt" class="fly-stem-wt" init="1" >
+                    <population.link id="fly-gmc" weight="1"/>
+                    <population.parameter id="proliferation/SIZE_TARGET" value="1.2" />
+                    <population.parameter id="CRITICAL_VOLUME" value="52" units="um^3" conversion="DS^-3" />
+                    <population.parameter id="proliferation/CELL_GROWTH_RATE" value="5" units="um^3/hour" conversion="DS^-3DT"/>
+                    <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                    <population.parameter id="proliferation/DIV_ROTATION_DISTRIBUTION" value="NORMAL(MU=36,SIGMA=30)" />
+                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET" value="location" />
+                    <population.parameter id="proliferation/DIFFERENTIATION_RULESET_EQUALITY_RANGE" value="10" />
+                    <population.parameter id="proliferation/APICAL_AXIS_RULESET" value="uniform" />
+                    <population.parameter id="proliferation/APICAL_AXIS_ROTATION_DISTRIBUTION" value="UNIFORM(MIN=0,MAX=360)" />
+                    <population.parameter id= "proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
+                    <population.parameter id= "proliferation/DYNAMIC_GROWTH_RATE_NB_CONTACT" value="0" />
+                    <population.parameter id= "proliferation/VOLUME_BASED_CRITICAL_VOLUME" value="1" />
+                </population>
+                <population id="fly-gmc" class="fly-gmc" init="0">
+                 <population.link id="fly-neuron" weight="1"/>
+                 <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                 <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                 <population.parameter id="proliferation/CELL_GROWTH_RATE" value="1.22" units="um^2/hour" conversion="DS^-2.DT"/>
+                 <population.parameter id= "proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="0" />
+                </population>
+                <population id="fly-neuron" class="fly-neuron" init="0">
+                <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
+                <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                </population>
+            </populations>
+        </agents>
+    </series>
+</set>

setup/neuron.xml

@@ -0,0 +1,23 @@
+<set prefix="2024-10-25-04">
+    <series name="dd" start="1" end="1"
+            ds=".3" margin="0" height="1" length="502" width="502"
+            dt=".083" ticks="576" interval="4">
+        <potts>
+            <potts.term id="volume" />
+            <potts.term id="adhesion" />
+            <potts.term id="surface" />
+            <potts.term id="persistence" />
+            <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-neuron:*"/>
+        </potts>
+        <agents>
+            <populations>
+                <population id="fly-neuron" class="fly-neuron" init="1">
+                <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
+                <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
+                <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
+                </population>
+
+            </populations>
+        </agents>
+    </series>
+</set>