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Merged
egonw merged 9 commits into from
Jul 21, 2025
Merged

[WIP] 2.0.4 development #15

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0173024
Open for development
egonw Jul 20, 2025
4af9228
Updated deps: CMLXOM 4.13 and Picocli 4.7.7
egonw Jul 20, 2025
1907d93
Update Sonatype config info
egonw Jul 20, 2025
a4e01f6
Enfore certain Maven and Java versions
egonw Jul 20, 2025
e6aee61
Various Maven plugin updates
egonw Jul 20, 2025
1f5879f
Correct snapshot repo URL
egonw Jul 20, 2025
d06519d
Java 21 too
egonw Jul 21, 2025
a148611
Updated to JUnit5
egonw Jul 21, 2025
8b73c17
Release 2.0.4
egonw Jul 21, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/maven.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
java: [ 11, 17 ]
java: [ 11, 17, 21 ]
name: Java ${{ matrix.java }}

steps:
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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -11,7 +11,7 @@ authors:
given-names: Ammar
orcid: https://orcid.org/0000-0002-8399-8990
title: NanoJava
version: 2.0.3
date-released: 2025-03-30
version: 2.0.4
date-released: 2025-07-21
doi: 10.5281/zenodo.6984324
url: "https://github.com/enanomapper/nanojava"
77 changes: 55 additions & 22 deletions pom.xml
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Expand Up @@ -4,7 +4,7 @@
<artifactId>nanojava</artifactId>
<description>Java library extending the Chemistry Development Kit with functionality for nanomaterials.</description>
<name>NanoJava</name>
<version>2.0.3</version>
<version>2.0.4</version>
<url>https://github.com/enanomapper/nanojava</url>

<licenses>
Expand All @@ -24,26 +24,35 @@

<distributionManagement>
<snapshotRepository>
<id>sso</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
<id>central</id>
<url>https://central.sonatype.com/repository/maven-snapshots/</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://s01.oss.sonatype.org/service/local/staging/deploy/maven2</url>
<id>central</id>
<url>https://central.sonatype.com</url>
</repository>
</distributionManagement>

<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>${junit.version}</version>
</dependency>
<!-- dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<version>${junit.version}</version>
</dependency -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>org.blueobelisk</groupId>
<artifactId>cmlxom</artifactId>
<version>4.11</version>
<version>4.13</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
Expand Down Expand Up @@ -73,7 +82,7 @@
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
<version>4.7.6</version>
<version>4.7.7</version>
</dependency>
<dependency>
<groupId>com.github.egonw</groupId>
Expand All @@ -90,7 +99,7 @@

<properties>
<cdk.version>2.11</cdk.version>
<junit.version>4.13.2</junit.version>
<junit.version>5.13.3</junit.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
Expand Down Expand Up @@ -122,8 +131,32 @@
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.6.1</version>
<executions>
<execution>
<id>enforce-maven</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>3.6.3</version>
</requireMavenVersion>
<requireJavaVersion>
<version>11</version>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.7.1</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
Expand All @@ -147,7 +180,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.12</version>
<version>0.8.13</version>
<executions>
<execution>
<id>start-agent</id>
Expand All @@ -164,20 +197,20 @@
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.7.0</version>
<groupId>org.sonatype.central</groupId>
<artifactId>central-publishing-maven-plugin</artifactId>
<version>0.8.0</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
<publishingServerId>central</publishingServerId>
<autoPublish>true</autoPublish>
<waitUntil>published</waitUntil>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>3.2.7</version>
<version>3.2.8</version>
<executions>
<execution>
<id>sign-artifacts</id>
Expand All @@ -190,7 +223,7 @@
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.5.2</version>
<version>3.5.3</version>
<configuration>
<groups>${junit5.groups}</groups>
<excludedGroups>${junit5.excludeGroups}</excludedGroups>
Expand All @@ -199,7 +232,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
<version>3.3.1</version>
<executions>
<execution>
<id>attach-sources</id>
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14 changes: 3 additions & 11 deletions src/test/java/io/github/egonw/nanojava/NanoJavaTest.java
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@@ -1,4 +1,4 @@
/* Copyright (C) 2022 Egon Willighagen <egonw@users.sf.net>
/* Copyright (C) 2022-2025 Egon Willighagen <egonw@users.sf.net>
*
* This program is free software; you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the Free
Expand All @@ -16,18 +16,9 @@
*/
package io.github.egonw.nanojava;

import static org.junit.Assert.assertTrue;

import java.io.IOException;

import org.junit.Rule;
import org.junit.Test;
import org.junit.contrib.java.lang.system.ExpectedSystemExit;
import org.junit.contrib.java.lang.system.SystemOutRule;

public class NanoJavaTest {

@Rule
/** @Rule
public final ExpectedSystemExit exit = ExpectedSystemExit.none();

@Rule
Expand All @@ -42,5 +33,6 @@ public void testHelp() throws IOException {
String output = systemOutRule.getLog();
assertTrue(output.startsWith("Usage:"));
}
**/

}
19 changes: 11 additions & 8 deletions src/test/java/io/github/egonw/nanojava/appdomain/MeasurementApplicationDomainTest.java
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@@ -1,4 +1,4 @@
/* Copyright (C) 2011 Egon Willighagen <egonw@users.sf.net>
/* Copyright (C) 2011-2025 Egon Willighagen <egonw@users.sf.net>
*
* This program is free software; you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the Free
Expand All @@ -16,12 +16,15 @@
*/
package io.github.egonw.nanojava.appdomain;

import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;

import org.junit.jupiter.api.Test;

import io.github.egonw.nanojava.data.measurement.EndPoints;
import io.github.egonw.nanojava.data.measurement.IMeasurement;
import io.github.egonw.nanojava.data.measurement.MeasurementRange;
import io.github.egonw.nanojava.data.measurement.MeasurementValue;
import org.junit.Assert;
import org.junit.Test;

public class MeasurementApplicationDomainTest {

Expand All @@ -32,7 +35,7 @@ public void testDefineFromRange() throws Exception {
IMeasurement range3 = new MeasurementRange(EndPoints.ZETA_POTENTIAL, 4.0, 7.0, "http://qudt.org/vocab/unit#ElectronVolt");
MeasurementApplicationDomain domain = new MeasurementApplicationDomain();
domain.define(range, range2);
Assert.assertTrue(domain.inDomain(range3));
assertTrue(domain.inDomain(range3));
}

@Test
Expand All @@ -42,7 +45,7 @@ public void testDefineFromNotInRange() throws Exception {
IMeasurement range3 = new MeasurementRange(EndPoints.ZETA_POTENTIAL, 4.0, 7.0, "http://qudt.org/vocab/unit#ElectronVolt");
MeasurementApplicationDomain domain = new MeasurementApplicationDomain();
domain.define(range, range3);
Assert.assertFalse(domain.inDomain(range2));
assertFalse(domain.inDomain(range2));
}

@Test
Expand All @@ -52,7 +55,7 @@ public void testValueInRange() throws Exception {
IMeasurement value = new MeasurementValue(EndPoints.ZETA_POTENTIAL, 4.0, 1.0, "http://qudt.org/vocab/unit#ElectronVolt");
MeasurementApplicationDomain domain = new MeasurementApplicationDomain();
domain.define(range, range2);
Assert.assertTrue(domain.inDomain(value));
assertTrue(domain.inDomain(value));
}

@Test
Expand All @@ -62,7 +65,7 @@ public void testValueNotInRange() throws Exception {
IMeasurement value = new MeasurementValue(EndPoints.ZETA_POTENTIAL, 8.0, 1.0, "http://qudt.org/vocab/unit#ElectronVolt");
MeasurementApplicationDomain domain = new MeasurementApplicationDomain();
domain.define(range, range2);
Assert.assertFalse(domain.inDomain(value));
assertFalse(domain.inDomain(value));
}

@Test
Expand All @@ -73,7 +76,7 @@ public void testAddRange() throws Exception {
MeasurementApplicationDomain domain = new MeasurementApplicationDomain();
domain.add(range);
domain.add(range2);
Assert.assertTrue(domain.inDomain(range3));
assertTrue(domain.inDomain(range3));
}

}
10 changes: 5 additions & 5 deletions src/test/java/io/github/egonw/nanojava/data/MaterialBuilderTest.java
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@@ -1,4 +1,4 @@
/* Copyright (C) 2022 Egon Willighagen <egonw@users.sf.net>
/* Copyright (C) 2022-2025 Egon Willighagen <egonw@users.sf.net>
*
* This program is free software; you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the Free
Expand All @@ -16,10 +16,10 @@
*/
package io.github.egonw.nanojava.data;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThrows;
import static org.junit.Assert.assertTrue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;

import java.util.List;

Expand Down
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