Fix minor formatting and move remaining make test to PottsCellStem

bagherilab · Jul 30, 2024 · 20cd228 · 20cd228
1 parent 56d0281
commit 20cd228
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Showing 6 changed files with 48 additions and 57 deletions.
diff --git a/src/arcade/potts/agent/cell/PottsCell.java b/src/arcade/potts/agent/cell/PottsCell.java
@@ -308,7 +308,7 @@ public void setState(CellState newState) {
      * @param newState  the cell state
      */
     abstract void setStateModule(CellState newState);
-
+    
     @Override
     public void schedule(Schedule schedule) {
         stopper = schedule.scheduleRepeating(this, Ordering.CELLS.ordinal(), 1);

diff --git a/src/arcade/potts/agent/cell/PottsCellStem.java b/src/arcade/potts/agent/cell/PottsCellStem.java
@@ -38,25 +38,25 @@ public final class PottsCellStem extends PottsCell {
      * @param criticalRegionHeights  the map of critical heights for regions
      */
     public PottsCellStem(int id, int parent, int pop, CellState state, int age, int divisions,
-            Location location, boolean hasRegions, MiniBox parameters,
-            double criticalVolume, double criticalHeight,
-            EnumMap<Region, Double> criticalRegionVolumes,
-            EnumMap<Region, Double> criticalRegionHeights) {
+                         Location location, boolean hasRegions, MiniBox parameters,
+                         double criticalVolume, double criticalHeight,
+                         EnumMap<Region, Double> criticalRegionVolumes,
+                         EnumMap<Region, Double> criticalRegionHeights) {
         super(id, parent, pop, state, age, divisions, location, hasRegions, parameters,
                 criticalVolume, criticalHeight, criticalRegionVolumes, criticalRegionHeights);
     }
 
     @Override
     public PottsCell make(int newID, CellState newState, Location newLocation,
-                    MersenneTwisterFast random) {
+                          MersenneTwisterFast random) {
         divisions++;
         return new PottsCellStem(newID, id, pop, newState, age, divisions, newLocation,
-                            hasRegions, parameters, criticalVolume, criticalHeight,
-                            criticalRegionVolumes, criticalRegionHeights);
+                hasRegions, parameters, criticalVolume, criticalHeight,
+                criticalRegionVolumes, criticalRegionHeights);
     }
-
+    
     @Override
-    public void setStateModule(CellState newState) {
+    void setStateModule(CellState newState) {
         switch ((State) newState) {
             case QUIESCENT:
                 module = new PottsModuleQuiescence(this);

diff --git a/src/arcade/potts/sim/PottsSeries.java b/src/arcade/potts/sim/PottsSeries.java
@@ -19,7 +19,7 @@ public final class PottsSeries extends Series {
 
     /** Default cell class. */
     public static final String DEFAULT_CELL_CLASS = "stem";
-
+    
     /** Map of potts settings. */
     public MiniBox potts;
 
@@ -190,8 +190,9 @@ protected void updatePopulations(ArrayList<Box> populationsBox, MiniBox populati
             if (populationClass == null) {
                 populationClass = DEFAULT_CELL_CLASS;
             }
-            //TODO: Use logger to print message when default class is used.
-
+
+            // TODO: Use logger to print message when default class is used.
+
             // Create new population and update code.
             MiniBox population = new MiniBox();
             population.put("CODE", code++);

diff --git a/test/arcade/potts/agent/cell/PottsCellStemTest.java b/test/arcade/potts/agent/cell/PottsCellStemTest.java
@@ -56,12 +56,6 @@ public class PottsCellStemTest {
 
     static State cellState = State.QUIESCENT;
 
-    static PottsCell cellDefault;
-
-    static PottsCell cellWithRegions;
-
-    static PottsCell cellWithoutRegions;
-
     static EnumSet<Region> regionList;
 
     static MiniBox parametersMock;
@@ -176,6 +170,32 @@ public void setState_invalidState_setsNull() {
         assertNull(cell.getModule());
     }
 
+    @Test
+    public void make_noRegions_setsFields() {
+        double criticalVolume = randomDoubleBetween(10, 100);
+        double criticalHeight = randomDoubleBetween(10, 100);
+        MiniBox parameters = mock(MiniBox.class);
+        Location location1 = mock(PottsLocation.class);
+        Location location2 = mock(PottsLocation.class);
+
+        PottsCellStem cell1 = new PottsCellStem(cellID, cellParent, cellPop, cellState, cellAge, cellDivisions,
+                location1, false, parameters, criticalVolume, criticalHeight,
+                null, null);
+        PottsCellStem cell2 = (PottsCellStem) cell1.make(cellID + 1, State.QUIESCENT, location2, null);
+
+        assertEquals(cellID + 1, cell2.id);
+        assertEquals(cellID, cell2.parent);
+        assertEquals(cellPop, cell2.pop);
+        assertEquals(cellAge, cell2.getAge());
+        assertEquals(cellDivisions + 1, cell1.getDivisions());
+        assertEquals(cellDivisions + 1, cell2.getDivisions());
+        assertFalse(cell2.hasRegions());
+        assertEquals(location2, cell2.getLocation());
+        assertEquals(cell2.parameters, parameters);
+        assertEquals(criticalVolume, cell2.getCriticalVolume(), EPSILON);
+        assertEquals(criticalHeight, cell2.getCriticalHeight(), EPSILON);
+    }
+
     @Test
     public void make_hasRegions_setsFields() {
         double criticalVolume = randomDoubleBetween(10, 100);

diff --git a/test/arcade/potts/agent/cell/PottsCellTest.java b/test/arcade/potts/agent/cell/PottsCellTest.java
@@ -75,28 +75,27 @@ public class PottsCellTest {
     static EnumSet<Region> regionList;
 
     static MiniBox parametersMock;
-
+    
     static class PottsCellMock extends PottsCell {
         PottsCellMock(int id, int parent, int pop, CellState state, int age, int divisions,
                       Location location, boolean hasRegions, MiniBox parameters,
                       double criticalVolume, double criticalHeight,
                       EnumMap<Region, Double> criticalRegionVolumes,
                       EnumMap<Region, Double> criticalRegionHeights) {
             super(id, parent, pop, state, age, divisions, location, hasRegions, parameters,
-            criticalVolume, criticalHeight, criticalRegionVolumes, criticalRegionHeights);
-
+                    criticalVolume, criticalHeight, criticalRegionVolumes, criticalRegionHeights);
         }
 
         @Override
         public PottsCellMock make(int newID, CellState newState, Location newLocation,
-                              MersenneTwisterFast random) {
+                                  MersenneTwisterFast random) {
             return new PottsCellMock(newID, id, pop, newState, age, divisions, newLocation,
-                            hasRegions, parameters, criticalVolume, criticalHeight,
-                            criticalRegionVolumes, criticalRegionHeights);
+                    hasRegions, parameters, criticalVolume, criticalHeight,
+                    criticalRegionVolumes, criticalRegionHeights);
         }
 
         @Override
-        public void setStateModule(CellState newState) {
+        void setStateModule(CellState newState) {
             module = mock(PottsModule.class);
         }
     }
@@ -162,7 +161,7 @@ static PottsCell make(boolean regions) {
         return make(locationMock, regions);
     }
 
-    static PottsCellMock make(Location location, boolean regions) {
+    static PottsCell make(Location location, boolean regions) {
         if (!regions) {
             return new PottsCellMock(cellID, cellParent, cellPop, cellState, cellAge, cellDivisions,
                     location, false, parametersMock, cellCriticalVolume, cellCriticalHeight,
@@ -587,32 +586,6 @@ public void stop_called_callsMethod() {
         verify(cell.stopper).stop();
     }
 
-    @Test
-    public void make_noRegions_setsFields() {
-        double criticalVolume = randomDoubleBetween(10, 100);
-        double criticalHeight = randomDoubleBetween(10, 100);
-        MiniBox parameters = mock(MiniBox.class);
-        Location location1 = mock(PottsLocation.class);
-        Location location2 = mock(PottsLocation.class);
-
-        PottsCell cell1 = new PottsCellStem(cellID, cellParent, cellPop, cellState, cellAge, cellDivisions,
-                location1, false, parameters, criticalVolume, criticalHeight,
-                null, null);
-        PottsCell cell2 = (PottsCellStem) cell1.make(cellID + 1, State.QUIESCENT, location2, null);
-
-        assertEquals(cellID + 1, cell2.id);
-        assertEquals(cellID, cell2.parent);
-        assertEquals(cellPop, cell2.pop);
-        assertEquals(cellAge, cell2.getAge());
-        assertEquals(cellDivisions + 1, cell1.getDivisions());
-        assertEquals(cellDivisions + 1, cell2.getDivisions());
-        assertFalse(cell2.hasRegions());
-        assertEquals(location2, cell2.getLocation());
-        assertEquals(cell2.parameters, parameters);
-        assertEquals(criticalVolume, cell2.getCriticalVolume(), EPSILON);
-        assertEquals(criticalHeight, cell2.getCriticalHeight(), EPSILON);
-    }
-
     @Test
     public void schedule_validInput_callsMethod() {
         Schedule schedule = spy(mock(Schedule.class));
@@ -1047,9 +1020,8 @@ public void convert_noRegions_createsContainer() {
         PottsCell cell = new PottsCellMock(id, parent, pop, state, age, divisions, location,
                 false, parameters, criticalVolume, criticalHeight,
                 null, null);
-
         doReturn(phase).when((PottsModule) cell.getModule()).getPhase();
-
+        
         int voxels = randomIntBetween(1, 100);
         doReturn((double) voxels).when(location).getVolume();
 
@@ -1094,7 +1066,6 @@ public void convert_withRegions_createsContainer() {
         PottsCell cell = new PottsCellMock(id, parent, pop, state, age, divisions, location, true,
                 parameters, criticalVolume, criticalHeight,
                 criticalRegionVolumes, criticalRegionHeights);
-
         doReturn(phase).when((PottsModule) cell.getModule()).getPhase();
 
         int voxels = randomIntBetween(1, 100);

diff --git a/test/arcade/potts/sim/PottsSeriesTest.java b/test/arcade/potts/sim/PottsSeriesTest.java
@@ -12,7 +12,6 @@
 import arcade.core.util.MiniBox;
 import arcade.potts.vis.PottsVisualization;
 import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.*;
 import static arcade.core.ARCADETestUtilities.*;
 import static arcade.core.util.MiniBox.TAG_SEPARATOR;