Merge pull request #240 from HHS/dev

4.2.2
HHS · Jun 17, 2024 · 9bdeaec · 9bdeaec
2 parents af8336e + d4de9b1
commit 9bdeaec
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diff --git a/.github/workflows/dev_build.yml b/.github/workflows/dev_build.yml
@@ -11,8 +11,6 @@ name: GCM Development Build
 on:
   push:
     branches: [ "dev" ]
-  pull_request:
-    branches: [ "dev" ]
 
 jobs:
   dev-build:

diff --git a/.github/workflows/dev_pr_build.yml b/.github/workflows/dev_pr_build.yml
@@ -0,0 +1,50 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: GCM Development PR Build
+
+on:
+  pull_request:
+    branches-ignore: ["main", "master"]
+
+jobs:
+  dev-build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout GCM
+      uses: actions/checkout@v4
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+        cache: maven
+
+    - name: Get Util Version
+      run: |
+        echo "util_version=v$(mvn help:evaluate -Dexpression=util.version -q -DforceStdout --file pom.xml)" >> "$GITHUB_ENV"
+
+    - name: Checkout Util
+      if: ${{ endsWith(env.util_version, 'SNAPSHOT') }}
+      uses: actions/checkout@v4
+      with:
+        repository: HHS/ASPR-ms-util
+        path: util
+        ref: dev
+
+    - name: Build Util
+      if: ${{ endsWith(env.util_version, 'SNAPSHOT') }}
+      run: mvn clean install -DskipTests --file util/pom.xml
+
+    - name: Build GCM
+      run: mvn clean install --file pom.xml
+
+    # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
+   # - name: Update dependency graph
+     # uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6
diff --git a/pom.xml b/pom.xml
@@ -51,28 +51,28 @@
 
     <!-- Properties -->
     <properties>
-        <revision>4.2.1</revision>
+        <revision>4.2.2</revision>
 
         <!-- basic project properties -->
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>17</maven.compiler.source>
         <maven.compiler.target>17</maven.compiler.target>
 
         <!-- plugin versions -->
-        <flatten-maven-plugin.version>1.3.0</flatten-maven-plugin.version>
-        <maven-surefire-plugin.version>3.0.0-M5</maven-surefire-plugin.version>
-        <maven-failsafe-plugin.version>3.0.0-M5</maven-failsafe-plugin.version>
-        <maven-source-plugin.version>3.2.1</maven-source-plugin.version>
-        <maven-install-plugin.version>3.1.1</maven-install-plugin.version>
-        <maven-deploy-plugin.version>3.1.1</maven-deploy-plugin.version>
-        <maven-javadoc-plugin.version>3.5.0</maven-javadoc-plugin.version>
-        <maven-gpg-plugin.version>3.2.2</maven-gpg-plugin.version>
+        <flatten-maven-plugin.version>1.6.0</flatten-maven-plugin.version>
+        <maven-surefire-plugin.version>3.2.5</maven-surefire-plugin.version>
+        <maven-failsafe-plugin.version>3.2.5</maven-failsafe-plugin.version>
+        <maven-source-plugin.version>3.3.1</maven-source-plugin.version>
+        <maven-install-plugin.version>3.1.2</maven-install-plugin.version>
+        <maven-deploy-plugin.version>3.1.2</maven-deploy-plugin.version>
+        <maven-javadoc-plugin.version>3.7.0</maven-javadoc-plugin.version>
+        <maven-gpg-plugin.version>3.2.4</maven-gpg-plugin.version>
         <central-publishing-maven-plugin.version>0.4.0</central-publishing-maven-plugin.version>
 
         <!-- dependency versions -->
         <util.version>4.2.0</util.version>
-        <jacoco-maven-plugin.version>0.8.9</jacoco-maven-plugin.version>
-        <junit-jupiter-engine.version>5.8.2</junit-jupiter-engine.version>
+        <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
+        <junit-jupiter-engine.version>5.10.2</junit-jupiter-engine.version>
     </properties>
 
     <dependencyManagement>

diff --git a/.../aspr/ms/gcm/simulation/plugins/partitions/support/DegeneratePopulationPartitionImpl.java b/.../aspr/ms/gcm/simulation/plugins/partitions/support/DegeneratePopulationPartitionImpl.java
@@ -9,12 +9,12 @@
 import org.apache.commons.math3.random.RandomGenerator;
 
 import gov.hhs.aspr.ms.gcm.simulation.nucleus.Event;
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers.BasePeopleContainer;
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers.PeopleContainer;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.filters.Filter;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.filters.TrueFilter;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers.BasePeopleContainer;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers.PeopleContainer;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.stochastics.datamanagers.StochasticsDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.stochastics.support.RandomNumberGeneratorId;
 import gov.hhs.aspr.ms.util.errors.ContractException;
@@ -67,10 +67,11 @@ public DegeneratePopulationPartitionImpl(final PartitionsContext partitionsConte
 			}
 			list.add(filterSensitivity);
 		}
-
-		peopleContainer = new BasePeopleContainer(partitionsContext, supportRunContinuity);
-
+
 		final PeopleDataManager peopleDataManager = partitionsContext.getDataManager(PeopleDataManager.class);
+		peopleContainer = new BasePeopleContainer(peopleDataManager, supportRunContinuity);
+
+
 		final int personIdLimit = peopleDataManager.getPersonIdLimit();
 		for (int i = 0; i < personIdLimit; i++) {
 			if (peopleDataManager.personIndexExists(i)) {

diff --git a/...va/gov/hhs/aspr/ms/gcm/simulation/plugins/partitions/support/PopulationPartitionImpl.java b/...va/gov/hhs/aspr/ms/gcm/simulation/plugins/partitions/support/PopulationPartitionImpl.java
@@ -16,12 +16,12 @@
 
 import gov.hhs.aspr.ms.gcm.simulation.nucleus.Event;
 import gov.hhs.aspr.ms.gcm.simulation.nucleus.NucleusError;
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers.BasePeopleContainer;
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers.PeopleContainer;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.filters.Filter;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.filters.TrueFilter;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers.BasePeopleContainer;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers.PeopleContainer;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.stochastics.datamanagers.StochasticsDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.stochastics.support.RandomNumberGeneratorId;
 import gov.hhs.aspr.ms.util.combinatorics.TupleGenerator;
@@ -426,7 +426,8 @@ private void addPerson(final PersonId personId) {
 			cleanedKey = new Key(key);
 			cleanedKey.calculateHashCode();
 			keyMap.put(cleanedKey, cleanedKey);
-			final BasePeopleContainer basePeopleContainer = new BasePeopleContainer(partitionsContext,
+
+			final BasePeopleContainer basePeopleContainer = new BasePeopleContainer(peopleDataManager,
 					supportRunContinuity);
 			keyToPeopleMap.put(cleanedKey, basePeopleContainer);
 			final LabelSet labelSet = getLabelSet(cleanedKey);
@@ -1020,7 +1021,7 @@ private void move(final Key currentKey, final Key newKey, final PersonId personI
 		if (cleanedNewKey == null) {
 			cleanedNewKey = newKey;
 			keyMap.put(cleanedNewKey, cleanedNewKey);
-			keyToPeopleMap.put(cleanedNewKey, new BasePeopleContainer(partitionsContext, supportRunContinuity));
+			keyToPeopleMap.put(cleanedNewKey, new BasePeopleContainer(peopleDataManager, supportRunContinuity));
 			final LabelSet labelSet = getLabelSet(cleanedNewKey);
 			labelSetInfoMap.put(cleanedNewKey, labelSet);
 		}

diff --git a/...tion/src/main/java/gov/hhs/aspr/ms/gcm/simulation/plugins/people/support/PersonError.java b/...tion/src/main/java/gov/hhs/aspr/ms/gcm/simulation/plugins/people/support/PersonError.java
@@ -21,7 +21,7 @@ public enum PersonError implements ContractError {
 	NULL_PERSON_RANGE("Null person range"),// 
 	PERSON_ASSIGNMENT_TIME_IN_FUTURE("The person assignment time from the plugin data is greater than the current time in the simulation"),//
 	UNKNOWN_PERSON_ID("Unknown person id"),//
-
+	NULL_PEOPLE_DATA_MANAGER("Null people data manager"),//
 	;
 
 	private final String description;

diff --git a/...pport/containers/BasePeopleContainer.java → ...pport/containers/BasePeopleContainer.java b/...pport/containers/BasePeopleContainer.java → ...pport/containers/BasePeopleContainer.java
@@ -1,10 +1,9 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import java.util.List;
 
 import org.apache.commons.math3.random.RandomGenerator;
 
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.PartitionsContext;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
 
@@ -32,8 +31,8 @@ private static enum PeopleContainerMode {
 
 	private final boolean supportRunContinuity;
 
-	public BasePeopleContainer(PartitionsContext partitionsContext, boolean supportRunContinuity) {
-		this.peopleDataManager = partitionsContext.getDataManager(PeopleDataManager.class);
+	public BasePeopleContainer(PeopleDataManager peopleDataManager, boolean supportRunContinuity) {
+		this.peopleDataManager = peopleDataManager;
 		this.supportRunContinuity = supportRunContinuity;
 
 		if (supportRunContinuity) {

diff --git a/...ort/containers/IntSetPeopleContainer.java → ...ort/containers/IntSetPeopleContainer.java b/...ort/containers/IntSetPeopleContainer.java → ...ort/containers/IntSetPeopleContainer.java
@@ -1,4 +1,4 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/...s/support/containers/PeopleContainer.java → ...e/support/containers/PeopleContainer.java b/...s/support/containers/PeopleContainer.java → ...e/support/containers/PeopleContainer.java
@@ -1,4 +1,4 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import java.util.List;
 

diff --git a/...containers/TreeBitSetPeopleContainer.java → ...containers/TreeBitSetPeopleContainer.java b/...containers/TreeBitSetPeopleContainer.java → ...containers/TreeBitSetPeopleContainer.java
@@ -1,4 +1,4 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import java.util.ArrayList;
 import java.util.BitSet;
@@ -7,8 +7,8 @@
 import org.apache.commons.math3.random.RandomGenerator;
 import org.apache.commons.math3.util.FastMath;
 
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.PartitionError;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonError;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
 import gov.hhs.aspr.ms.util.errors.ContractException;
 
@@ -38,12 +38,12 @@ public class TreeBitSetPeopleContainer implements PeopleContainer {
 	/**
 	 * Constructs the people container
 	 * 
-	 * @throws ContractException {@linkplain PartitionError#NULL_PEOPLE_DATA_MANAGER}
+	 * @throws ContractException {@linkplain PersonError#NULL_PEOPLE_DATA_MANAGER}
 	 *                           if the person data view is null
 	 */
 	public TreeBitSetPeopleContainer(PeopleDataManager personDataManger) {
 		if (personDataManger == null) {
-			throw new ContractException(PartitionError.NULL_PEOPLE_DATA_MANAGER);
+			throw new ContractException(PersonError.NULL_PEOPLE_DATA_MANAGER);
 		}
 		blockSize = 63;
 		this.peopleDataManager = personDataManger;

diff --git a/...rt/containers/AT_BasePeopleContainer.java → ...rt/containers/AT_BasePeopleContainer.java b/...rt/containers/AT_BasePeopleContainer.java → ...rt/containers/AT_BasePeopleContainer.java
@@ -1,21 +1,21 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import org.apache.commons.math3.random.RandomGenerator;
 import org.junit.jupiter.api.Test;
 
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.PartitionsContext;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
 import gov.hhs.aspr.ms.util.annotations.UnitTestConstructor;
 import gov.hhs.aspr.ms.util.annotations.UnitTestMethod;
 
 public class AT_BasePeopleContainer {
 
-	private PeopleContainer getPeopleContainer(PartitionsContext partitionsContext) {
-		return new BasePeopleContainer(partitionsContext,false);
+	private PeopleContainer getPeopleContainer(PeopleDataManager peopleDataManager) {
+		return new BasePeopleContainer(peopleDataManager,false);
 	}
 
 	@Test
-	@UnitTestConstructor(target = BasePeopleContainer.class, args = { PartitionsContext.class, boolean.class})
+	@UnitTestConstructor(target = BasePeopleContainer.class, args = { PeopleDataManager.class, boolean.class})
 	public void testConstructor() {
 		// nothing to test
 	}

diff --git a/.../containers/AT_IntSetPeopleContainer.java → .../containers/AT_IntSetPeopleContainer.java b/.../containers/AT_IntSetPeopleContainer.java → .../containers/AT_IntSetPeopleContainer.java
@@ -1,12 +1,12 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 
 import org.apache.commons.math3.random.RandomGenerator;
 import org.junit.jupiter.api.Test;
 
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.PartitionsContext;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
 import gov.hhs.aspr.ms.util.annotations.UnitTestConstructor;
 import gov.hhs.aspr.ms.util.annotations.UnitTestField;
@@ -20,7 +20,7 @@ public void testDefaultTargetDepth() {
 		assertEquals(80, IntSetPeopleContainer.DEFAULT_TARGET_DEPTH);
 	}
 
-	private PeopleContainer getPeopleContainer(PartitionsContext context) {
+	private PeopleContainer getPeopleContainer(PeopleDataManager peopleDataManager) {
 		return new IntSetPeopleContainer();
 	}
 

diff --git a/...tainers/AT_TreeBitSetPeopleContainer.java → ...tainers/AT_TreeBitSetPeopleContainer.java b/...tainers/AT_TreeBitSetPeopleContainer.java → ...tainers/AT_TreeBitSetPeopleContainer.java
@@ -1,14 +1,13 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
 import org.apache.commons.math3.random.RandomGenerator;
 import org.junit.jupiter.api.Test;
 
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.PartitionError;
-import gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.PartitionsContext;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.datamanagers.PeopleDataManager;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonError;
 import gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.PersonId;
 import gov.hhs.aspr.ms.util.annotations.UnitTestConstructor;
 import gov.hhs.aspr.ms.util.annotations.UnitTestMethod;
@@ -18,15 +17,15 @@
 public class AT_TreeBitSetPeopleContainer {
 
 
-	private PeopleContainer getPeopleContainer(PartitionsContext context) {
-		return new TreeBitSetPeopleContainer(context.getDataManager(PeopleDataManager.class));
+	private PeopleContainer getPeopleContainer(PeopleDataManager peopleDataManager) {
+		return new TreeBitSetPeopleContainer(peopleDataManager);
 	}
 
 	@Test
 	@UnitTestConstructor(target = TreeBitSetPeopleContainer.class,args = {PeopleDataManager.class})
 	public void testConstructor() {
 		ContractException contractException = assertThrows(ContractException.class,()->new TreeBitSetPeopleContainer(null));
-		assertEquals(PartitionError.NULL_PEOPLE_DATA_MANAGER, contractException.getErrorType());
+		assertEquals(PersonError.NULL_PEOPLE_DATA_MANAGER, contractException.getErrorType());
 	}
 
 	@Test

diff --git a/...ns/support/containers/MT_ArrayIntSet.java → ...le/support/containers/MT_ArrayIntSet.java b/...ns/support/containers/MT_ArrayIntSet.java → ...le/support/containers/MT_ArrayIntSet.java
@@ -1,4 +1,4 @@
-package gov.hhs.aspr.ms.gcm.simulation.plugins.partitions.support.containers;
+package gov.hhs.aspr.ms.gcm.simulation.plugins.people.support.containers;
 
 /*
  * Manual performance tuning test turned off until adoption of JOL or another memory assessment tool for post-8 java