Util 4.1.0 (#18)

* Addded array indexers * move test resource helper * Added default serialVersionUID to IOExceptionFile * Added tuple generator to ms-util * Bump the standard-plugins group with 3 updates (#11) Bumps the standard-plugins group with 3 updates: [org.apache.maven.plugins:maven-surefire-plugin](https://github.com/apache/maven-surefire), [org.apache.maven.plugins:maven-source-plugin](https://github.com/apache/maven-source-plugin) and [org.apache.maven.plugins:maven-javadoc-plugin](https://github.com/apache/maven-javadoc-plugin). Updates `org.apache.maven.plugins:maven-surefire-plugin` from 3.0.0-M5 to 3.2.5 - [Release notes](https://github.com/apache/maven-surefire/releases) - [Commits](apache/maven-surefire@surefire-3.0.0-M5...surefire-3.2.5) Updates `org.apache.maven.plugins:maven-source-plugin` from 3.2.1 to 3.3.0 - [Commits](apache/maven-source-plugin@maven-source-plugin-3.2.1...maven-source-plugin-3.3.0) Updates `org.apache.maven.plugins:maven-javadoc-plugin` from 3.5.0 to 3.6.3 - [Release notes](https://github.com/apache/maven-javadoc-plugin/releases) - [Commits](apache/maven-javadoc-plugin@maven-javadoc-plugin-3.5.0...maven-javadoc-plugin-3.6.3) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-surefire-plugin dependency-type: direct:production update-type: version-update:semver-minor dependency-group: standard-plugins - dependency-name: org.apache.maven.plugins:maven-source-plugin dependency-type: direct:production update-type: version-update:semver-minor dependency-group: standard-plugins - dependency-name: org.apache.maven.plugins:maven-javadoc-plugin dependency-type: direct:production update-type: version-update:semver-minor dependency-group: standard-plugins ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump the test-dependencies group with 3 updates (#12) Bumps the test-dependencies group with 3 updates: [org.junit.jupiter:junit-jupiter-engine](https://github.com/junit-team/junit5), [org.junit.jupiter:junit-jupiter-api](https://github.com/junit-team/junit5) and [org.jacoco:jacoco-maven-plugin](https://github.com/jacoco/jacoco). Updates `org.junit.jupiter:junit-jupiter-engine` from 5.8.2 to 5.10.1 - [Release notes](https://github.com/junit-team/junit5/releases) - [Commits](junit-team/junit5@r5.8.2...r5.10.1) Updates `org.junit.jupiter:junit-jupiter-api` from 5.8.2 to 5.10.1 - [Release notes](https://github.com/junit-team/junit5/releases) - [Commits](junit-team/junit5@r5.8.2...r5.10.1) Updates `org.jacoco:jacoco-maven-plugin` from 0.8.9 to 0.8.11 - [Release notes](https://github.com/jacoco/jacoco/releases) - [Commits](jacoco/jacoco@v0.8.9...v0.8.11) --- updated-dependencies: - dependency-name: org.junit.jupiter:junit-jupiter-engine dependency-type: direct:production update-type: version-update:semver-minor dependency-group: test-dependencies - dependency-name: org.junit.jupiter:junit-jupiter-api dependency-type: direct:production update-type: version-update:semver-minor dependency-group: test-dependencies - dependency-name: org.jacoco:jacoco-maven-plugin dependency-type: direct:development update-type: version-update:semver-patch dependency-group: test-dependencies ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * refactor package structure (#13) * move path validator (#14) * update workflows * update workflows * test-commit * Update dev_build.yml * Update pr_build.yml * update workflow * update workflows * add text table reader (#17) * Bump the test-dependencies group with 2 updates (#16) Bumps the test-dependencies group with 2 updates: [org.junit.jupiter:junit-jupiter-engine](https://github.com/junit-team/junit5) and [org.junit.jupiter:junit-jupiter-api](https://github.com/junit-team/junit5). Updates `org.junit.jupiter:junit-jupiter-engine` from 5.10.1 to 5.10.2 - [Release notes](https://github.com/junit-team/junit5/releases) - [Commits](junit-team/junit5@r5.10.1...r5.10.2) Updates `org.junit.jupiter:junit-jupiter-api` from 5.10.1 to 5.10.2 - [Release notes](https://github.com/junit-team/junit5/releases) - [Commits](junit-team/junit5@r5.10.1...r5.10.2) --- updated-dependencies: - dependency-name: org.junit.jupiter:junit-jupiter-engine dependency-type: direct:production update-type: version-update:semver-patch dependency-group: test-dependencies - dependency-name: org.junit.jupiter:junit-jupiter-api dependency-type: direct:production update-type: version-update:semver-patch dependency-group: test-dependencies ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update pom.xml --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: shawnhatch <[email protected]> Co-authored-by: shawnhatch <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
HHS · Feb 20, 2024 · 839be6d · 839be6d
1 parent 7d1b1fe
commit 839be6d
Show file tree

Hide file tree

Showing 154 changed files with 1,908 additions and 435 deletions.
diff --git a/pom.xml b/pom.xml
@@ -7,8 +7,8 @@
     <!-- Artifact -->
     <groupId>gov.hhs.aspr.ms</groupId>
     <artifactId>util</artifactId>
-    <version>4.0.0</version>
-    <packaging>jar</packaging>
+    <version>4.1.0</version>
+    <packaging>jar</packaging> 
 
     <name>Modeling Utils</name>
     <description>A suite of utility methods that are useful for simulation frameworks.</description>
@@ -53,15 +53,15 @@
         <maven.compiler.target>17</maven.compiler.target>
 
         <!-- plugin versions -->
-        <maven-surefire-plugin.version>3.0.0-M5</maven-surefire-plugin.version>
-        <maven-source-plugin.version>3.2.1</maven-source-plugin.version>
-        <maven-javadoc-plugin.version>3.5.0</maven-javadoc-plugin.version>
+        <maven-surefire-plugin.version>3.2.5</maven-surefire-plugin.version>
+        <maven-source-plugin.version>3.3.0</maven-source-plugin.version>
+        <maven-javadoc-plugin.version>3.6.3</maven-javadoc-plugin.version>
 
         <!-- dependency versions-->
         <commons-math3.version>3.6.1</commons-math3.version>
         <jcip-annotations.version>1.0</jcip-annotations.version>
-        <junit-jupiter-engine.version>5.8.2</junit-jupiter-engine.version>
-        <jacoco-maven-plugin.version>0.8.9</jacoco-maven-plugin.version>
+        <junit-jupiter-engine.version>5.10.2</junit-jupiter-engine.version>
+        <jacoco-maven-plugin.version>0.8.11</jacoco-maven-plugin.version>
     </properties>
 
     <!-- Dependencies -->
@@ -215,4 +215,4 @@
         </profile>
     </profiles>
 
-</project>
+</project>
diff --git a/src/main/java/util/annotations/UnitTag.java → ...hhs/aspr/ms/util/annotations/UnitTag.java b/src/main/java/util/annotations/UnitTag.java → ...hhs/aspr/ms/util/annotations/UnitTag.java
@@ -1,4 +1,4 @@
-package util.annotations;
+package gov.hhs.aspr.ms.util.annotations;
 
 public enum UnitTag {
 	/*

diff --git a/...util/annotations/UnitTestConstructor.java → ...util/annotations/UnitTestConstructor.java b/...util/annotations/UnitTestConstructor.java → ...util/annotations/UnitTestConstructor.java
@@ -1,4 +1,4 @@
-package util.annotations;
+package gov.hhs.aspr.ms.util.annotations;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

diff --git a/.../java/util/annotations/UnitTestField.java → ...pr/ms/util/annotations/UnitTestField.java b/.../java/util/annotations/UnitTestField.java → ...pr/ms/util/annotations/UnitTestField.java
@@ -1,4 +1,4 @@
-package util.annotations;
+package gov.hhs.aspr.ms.util.annotations;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

diff --git a/...util/annotations/UnitTestForCoverage.java → ...util/annotations/UnitTestForCoverage.java b/...util/annotations/UnitTestForCoverage.java → ...util/annotations/UnitTestForCoverage.java
@@ -1,4 +1,4 @@
-package util.annotations;
+package gov.hhs.aspr.ms.util.annotations;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

diff --git a/...java/util/annotations/UnitTestMethod.java → ...r/ms/util/annotations/UnitTestMethod.java b/...java/util/annotations/UnitTestMethod.java → ...r/ms/util/annotations/UnitTestMethod.java
@@ -1,4 +1,4 @@
-package util.annotations;
+package gov.hhs.aspr.ms.util.annotations;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

diff --git a/src/main/java/gov/hhs/aspr/ms/util/combinatorics/TupleGenerator.java b/src/main/java/gov/hhs/aspr/ms/util/combinatorics/TupleGenerator.java
@@ -0,0 +1,98 @@
+package gov.hhs.aspr.ms.util.combinatorics;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Utility class for generating tuples from a fixed set of finite ranges of the
+ * form [0,n). Uses a standard builder pattern for construction.
+ */
+public final class TupleGenerator {
+	private final int[] moduli;
+	private final int[] dimensions;
+	private final int size;
+
+	private TupleGenerator(List<Integer> dimensionSizes) {
+		dimensions = new int[dimensionSizes.size()];
+		moduli = new int[dimensionSizes.size()];
+
+		int count = 1;
+		for (int i = 0; i < dimensionSizes.size(); i++) {
+			int dimSize = dimensionSizes.get(i);
+			dimensions[i] = dimSize;
+			moduli[i] = count;
+			count *= dimSize;
+		}
+		size = count;
+	}
+
+	/**
+	 * Returns the number of dimensions in this {@link TupleGenerator}.
+	 */
+	public int dimensions() {
+		return dimensions.length;
+	}
+
+	/**
+	 * Returns the number of tuples that can be generated by this {@link TupleGenerator}
+	 */
+	public int size() {
+		return size;
+	}
+
+	/**
+	 * Fills the given tuple with the values that correspond to the given index.
+	 * 
+	 * @throws IndexOutOfBoundsException
+	 *                                   <ul>
+	 *                                   <li>if index &lt; 0</li>
+	 *                                   <li>if index &gt;= size()</li>
+	 *                                   </ul>
+	 * @throws IllegalArgumentException
+	 *                                   <ul>
+	 *                                   <li>if the tuple is null</li>
+	 *                                   <li>if the tuple's length is not equal to
+	 *                                   dimensions()</li>
+	 *                                   </ul>
+	 */
+	public void fillTuple(int index, int[] tuple) {
+		if ((index < 0) || (index >= size)) {
+			throw new IndexOutOfBoundsException("index out of bounds");
+		}
+
+		if (tuple == null) {
+			throw new IllegalArgumentException("null array");
+		}
+
+		if (tuple.length != dimensions.length) {
+			throw new IllegalArgumentException("wrong number of dimensions");
+		}
+
+		for (int i = 0; i < dimensions.length; i++) {
+			tuple[i] = (index / moduli[i]) % dimensions[i];
+		}
+	}
+
+	public static Builder builder() {
+		return new Builder();
+	}
+
+	public static class Builder {
+		private List<Integer> dimensionSizes = new ArrayList<>();
+
+		private Builder() {
+		}
+
+		public TupleGenerator build() {
+			return new TupleGenerator(dimensionSizes);
+		}
+
+		public Builder addDimension(int dimensionSize) {
+			if (dimensionSize <= 0) {
+				throw new IllegalArgumentException("Non positive dimension size");
+			}
+			dimensionSizes.add(dimensionSize);
+			return this;
+		}
+	}
+}
diff --git a/...java/util/delaunay/GeoDelaunaySolver.java → ...r/ms/util/delaunay/GeoDelaunaySolver.java b/...java/util/delaunay/GeoDelaunaySolver.java → ...r/ms/util/delaunay/GeoDelaunaySolver.java
@@ -1,4 +1,4 @@
-package util.delaunay;
+package gov.hhs.aspr.ms.util.delaunay;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -10,10 +10,10 @@
 import org.apache.commons.math3.util.FastMath;
 import org.apache.commons.math3.util.Pair;
 
-import util.dimensiontree.VolumetricDimensionTree;
-import util.earth.LatLon;
-import util.vector.MutableVector3D;
-import util.vector.Vector3D;
+import gov.hhs.aspr.ms.util.dimensiontree.VolumetricDimensionTree;
+import gov.hhs.aspr.ms.util.earth.LatLon;
+import gov.hhs.aspr.ms.util.vector.MutableVector3D;
+import gov.hhs.aspr.ms.util.vector.Vector3D;
 
 public class GeoDelaunaySolver<T> {
 

diff --git a/...a/util/delaunay/PlanarDelaunaySolver.java → ...s/util/delaunay/PlanarDelaunaySolver.java b/...a/util/delaunay/PlanarDelaunaySolver.java → ...s/util/delaunay/PlanarDelaunaySolver.java
@@ -1,4 +1,4 @@
-package util.delaunay;
+package gov.hhs.aspr.ms.util.delaunay;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -10,10 +10,10 @@
 import org.apache.commons.math3.util.FastMath;
 import org.apache.commons.math3.util.Pair;
 
-import util.dimensiontree.VolumetricDimensionTree;
-import util.spherical.Chirality;
-import util.vector.MutableVector2D;
-import util.vector.Vector2D;
+import gov.hhs.aspr.ms.util.dimensiontree.VolumetricDimensionTree;
+import gov.hhs.aspr.ms.util.spherical.Chirality;
+import gov.hhs.aspr.ms.util.vector.MutableVector2D;
+import gov.hhs.aspr.ms.util.vector.Vector2D;
 
 public class PlanarDelaunaySolver<T> {
 

diff --git a/...ava/util/dimensiontree/DimensionTree.java → .../ms/util/dimensiontree/DimensionTree.java b/...ava/util/dimensiontree/DimensionTree.java → .../ms/util/dimensiontree/DimensionTree.java
@@ -1,4 +1,4 @@
-package util.dimensiontree;
+package gov.hhs.aspr.ms.util.dimensiontree;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -9,7 +9,7 @@
 
 import org.apache.commons.math3.util.FastMath;
 
-import util.errors.ContractException;
+import gov.hhs.aspr.ms.util.errors.ContractException;
 
 /**
  * <p>

diff --git a/...til/dimensiontree/DimensionTreeError.java → ...til/dimensiontree/DimensionTreeError.java b/...til/dimensiontree/DimensionTreeError.java → ...til/dimensiontree/DimensionTreeError.java
@@ -1,7 +1,7 @@
-package util.dimensiontree;
+package gov.hhs.aspr.ms.util.dimensiontree;
 
-import util.errors.ContractError;
-import util.errors.ContractException;
+import gov.hhs.aspr.ms.util.errors.ContractError;
+import gov.hhs.aspr.ms.util.errors.ContractException;
 
 /**
  * An enumeration supporting {@link ContractException} that acts as a general

diff --git a/...imensiontree/VolumetricDimensionTree.java → ...imensiontree/VolumetricDimensionTree.java b/...imensiontree/VolumetricDimensionTree.java → ...imensiontree/VolumetricDimensionTree.java
@@ -1,4 +1,4 @@
-package util.dimensiontree;
+package gov.hhs.aspr.ms.util.dimensiontree;
 
 import java.util.ArrayList;
 import java.util.Arrays;

diff --git a/src/main/java/util/earth/Earth.java → ...ava/gov/hhs/aspr/ms/util/earth/Earth.java b/src/main/java/util/earth/Earth.java → ...ava/gov/hhs/aspr/ms/util/earth/Earth.java
@@ -1,8 +1,8 @@
-package util.earth;
+package gov.hhs.aspr.ms.util.earth;
 
 import org.apache.commons.math3.util.FastMath;
 
-import util.vector.Vector3D;
+import gov.hhs.aspr.ms.util.vector.Vector3D;
 
 /**
  * A spherical geo-model for converting various coordinate representations and

diff --git a/src/main/java/util/earth/EarthGrid.java → ...gov/hhs/aspr/ms/util/earth/EarthGrid.java b/src/main/java/util/earth/EarthGrid.java → ...gov/hhs/aspr/ms/util/earth/EarthGrid.java
@@ -1,10 +1,10 @@
-package util.earth;
+package gov.hhs.aspr.ms.util.earth;
 
 import org.apache.commons.math3.util.FastMath;
 
-import util.vector.MutableVector3D;
-import util.vector.Vector2D;
-import util.vector.Vector3D;
+import gov.hhs.aspr.ms.util.vector.MutableVector3D;
+import gov.hhs.aspr.ms.util.vector.Vector2D;
+import gov.hhs.aspr.ms.util.vector.Vector3D;
 
 /**
  * A utility class for converting (x,y) two dimensional grid coordinates to and

diff --git a/src/main/java/util/earth/LatLon.java → ...va/gov/hhs/aspr/ms/util/earth/LatLon.java b/src/main/java/util/earth/LatLon.java → ...va/gov/hhs/aspr/ms/util/earth/LatLon.java
@@ -1,4 +1,4 @@
-package util.earth;
+package gov.hhs.aspr.ms.util.earth;
 
 import net.jcip.annotations.Immutable;
 

diff --git a/src/main/java/util/earth/LatLonAlt.java → ...gov/hhs/aspr/ms/util/earth/LatLonAlt.java b/src/main/java/util/earth/LatLonAlt.java → ...gov/hhs/aspr/ms/util/earth/LatLonAlt.java
@@ -1,6 +1,6 @@
-package util.earth;
+package gov.hhs.aspr.ms.util.earth;
 
-import util.vector.Vector3D;
+import gov.hhs.aspr.ms.util.vector.Vector3D;
 
 public class LatLonAlt {
 

diff --git a/src/main/java/util/errors/ContractError.java → ...hs/aspr/ms/util/errors/ContractError.java b/src/main/java/util/errors/ContractError.java → ...hs/aspr/ms/util/errors/ContractError.java
@@ -1,5 +1,5 @@
 
-package util.errors;
+package gov.hhs.aspr.ms.util.errors;
 
 /**
  * Marker interface for the descriptions of runtime exceptions where the source

diff --git a/...n/java/util/errors/ContractException.java → ...spr/ms/util/errors/ContractException.java b/...n/java/util/errors/ContractException.java → ...spr/ms/util/errors/ContractException.java
@@ -1,4 +1,4 @@
-package util.errors;
+package gov.hhs.aspr.ms.util.errors;
 
 /**
  * A {@link RuntimeException} that indicates that the cause of the error as a

diff --git a/...main/java/util/geolocator/GeoLocator.java → ...s/aspr/ms/util/geolocator/GeoLocator.java b/...main/java/util/geolocator/GeoLocator.java → ...s/aspr/ms/util/geolocator/GeoLocator.java
@@ -1,4 +1,4 @@
-package util.geolocator;
+package gov.hhs.aspr.ms.util.geolocator;
 
 import java.util.ArrayList;
 import java.util.Comparator;
@@ -9,11 +9,11 @@
 import org.apache.commons.math3.util.FastMath;
 import org.apache.commons.math3.util.Pair;
 
-import util.dimensiontree.DimensionTree;
-import util.earth.Earth;
-import util.earth.LatLonAlt;
-import util.vector.Vector2D;
-import util.vector.Vector3D;
+import gov.hhs.aspr.ms.util.dimensiontree.DimensionTree;
+import gov.hhs.aspr.ms.util.earth.Earth;
+import gov.hhs.aspr.ms.util.earth.LatLonAlt;
+import gov.hhs.aspr.ms.util.vector.Vector2D;
+import gov.hhs.aspr.ms.util.vector.Vector3D;
 
 /**
  * A generics-based utility class for managing point locations on a spherical

diff --git a/src/main/java/util/graph/Graph.java → ...ava/gov/hhs/aspr/ms/util/graph/Graph.java b/src/main/java/util/graph/Graph.java → ...ava/gov/hhs/aspr/ms/util/graph/Graph.java
@@ -1,4 +1,4 @@
-package util.graph;
+package gov.hhs.aspr.ms.util.graph;
 
 import java.util.List;
 

diff --git a/.../java/util/graph/GraphDepthEvaluator.java → ...pr/ms/util/graph/GraphDepthEvaluator.java b/.../java/util/graph/GraphDepthEvaluator.java → ...pr/ms/util/graph/GraphDepthEvaluator.java
@@ -1,4 +1,4 @@
-package util.graph;
+package gov.hhs.aspr.ms.util.graph;
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;

diff --git a/src/main/java/util/graph/Graphs.java → ...va/gov/hhs/aspr/ms/util/graph/Graphs.java b/src/main/java/util/graph/Graphs.java → ...va/gov/hhs/aspr/ms/util/graph/Graphs.java
@@ -1,4 +1,4 @@
-package util.graph;
+package gov.hhs.aspr.ms.util.graph;
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -9,8 +9,8 @@
 import java.util.Optional;
 import java.util.Set;
 
-import util.path.Path;
-import util.path.Paths;
+import gov.hhs.aspr.ms.util.path.Path;
+import gov.hhs.aspr.ms.util.path.Paths;
 
 public final class Graphs {
 

diff --git a/src/main/java/util/graph/MutableGraph.java → .../hhs/aspr/ms/util/graph/MutableGraph.java b/src/main/java/util/graph/MutableGraph.java → .../hhs/aspr/ms/util/graph/MutableGraph.java
@@ -1,4 +1,4 @@
-package util.graph;
+package gov.hhs.aspr.ms.util.graph;
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;