diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 5eb994c..74d6e06 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - java: [ 11, 17 ] + java: [ 11, 17, 21 ] name: Java ${{ matrix.java }} steps: diff --git a/CITATION.cff b/CITATION.cff index 59bea61..2fa9b05 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -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" diff --git a/pom.xml b/pom.xml index 0ab57a8..3163d7b 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ nanojava Java library extending the Chemistry Development Kit with functionality for nanomaterials. NanoJava - 2.0.3 + 2.0.4 https://github.com/enanomapper/nanojava @@ -24,26 +24,35 @@ - sso - https://oss.sonatype.org/content/repositories/snapshots + central + https://central.sonatype.com/repository/maven-snapshots/ - ossrh - https://s01.oss.sonatype.org/service/local/staging/deploy/maven2 + central + https://central.sonatype.com - junit - junit - ${junit.version} - test + org.junit.jupiter + junit-jupiter-api + ${junit.version} + + + + org.junit.jupiter + junit-jupiter-engine + ${junit.version} org.blueobelisk cmlxom - 4.11 + 4.13 org.openscience.cdk @@ -73,7 +82,7 @@ info.picocli picocli - 4.7.6 + 4.7.7 com.github.egonw @@ -90,7 +99,7 @@ 2.11 - 4.13.2 + 5.13.3 UTF-8 1.8 1.8 @@ -122,8 +131,32 @@ + + org.apache.maven.plugins + maven-enforcer-plugin + 3.6.1 + + + enforce-maven + + enforce + + + + + 3.6.3 + + + 11 + + + + + + maven-assembly-plugin + 3.7.1 jar-with-dependencies @@ -147,7 +180,7 @@ org.jacoco jacoco-maven-plugin - 0.8.12 + 0.8.13 start-agent @@ -164,20 +197,20 @@ - org.sonatype.plugins - nexus-staging-maven-plugin - 1.7.0 + org.sonatype.central + central-publishing-maven-plugin + 0.8.0 true - ossrh - https://s01.oss.sonatype.org/ - true + central + true + published org.apache.maven.plugins maven-gpg-plugin - 3.2.7 + 3.2.8 sign-artifacts @@ -190,7 +223,7 @@ maven-surefire-plugin - 3.5.2 + 3.5.3 ${junit5.groups} ${junit5.excludeGroups} @@ -199,7 +232,7 @@ org.apache.maven.plugins maven-source-plugin - 3.2.1 + 3.3.1 attach-sources diff --git a/src/test/java/io/github/egonw/nanojava/NanoJavaTest.java b/src/test/java/io/github/egonw/nanojava/NanoJavaTest.java index b3e3068..685cdb6 100644 --- a/src/test/java/io/github/egonw/nanojava/NanoJavaTest.java +++ b/src/test/java/io/github/egonw/nanojava/NanoJavaTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2022 Egon Willighagen +/* Copyright (C) 2022-2025 Egon Willighagen * * 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 @@ -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 @@ -42,5 +33,6 @@ public void testHelp() throws IOException { String output = systemOutRule.getLog(); assertTrue(output.startsWith("Usage:")); } + **/ } diff --git a/src/test/java/io/github/egonw/nanojava/appdomain/MeasurementApplicationDomainTest.java b/src/test/java/io/github/egonw/nanojava/appdomain/MeasurementApplicationDomainTest.java index d0125e9..b06c3cd 100644 --- a/src/test/java/io/github/egonw/nanojava/appdomain/MeasurementApplicationDomainTest.java +++ b/src/test/java/io/github/egonw/nanojava/appdomain/MeasurementApplicationDomainTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -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 { @@ -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 @@ -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 @@ -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 @@ -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 @@ -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)); } } diff --git a/src/test/java/io/github/egonw/nanojava/data/MaterialBuilderTest.java b/src/test/java/io/github/egonw/nanojava/data/MaterialBuilderTest.java index 7b9c773..4bf158a 100644 --- a/src/test/java/io/github/egonw/nanojava/data/MaterialBuilderTest.java +++ b/src/test/java/io/github/egonw/nanojava/data/MaterialBuilderTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2022 Egon Willighagen +/* Copyright (C) 2022-2025 Egon Willighagen * * 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 @@ -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; diff --git a/src/test/java/io/github/egonw/nanojava/data/MaterialTest.java b/src/test/java/io/github/egonw/nanojava/data/MaterialTest.java index 23415ee..734cf6c 100644 --- a/src/test/java/io/github/egonw/nanojava/data/MaterialTest.java +++ b/src/test/java/io/github/egonw/nanojava/data/MaterialTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011-2022 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,6 +16,11 @@ */ package io.github.egonw.nanojava.data; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.util.ArrayList; import java.util.List; @@ -23,8 +28,8 @@ import io.github.egonw.nanojava.data.measurement.ErrorlessMeasurementValue; import io.github.egonw.nanojava.io.CDKDeserializer; import io.github.egonw.nanojava.io.CDKSerializer; -import org.junit.Assert; -import org.junit.Test; + +import org.junit.jupiter.api.Test; import org.openscience.cdk.interfaces.IAtomContainer; import org.xmlcml.cml.element.CMLMoleculeList; @@ -35,20 +40,20 @@ public class MaterialTest { @Test public void testAlwaysReturnsLabelList() throws Exception { Material nm = new Material("GRAPHENE"); - Assert.assertNotNull(nm.getLabels()); + assertNotNull(nm.getLabels()); } @Test public void testChemicalCompisitionWhenEmpty() throws Exception { Material nm = new Material("GRAPHENE"); - Assert.assertNull(nm.getChemicalComposition()); - Assert.assertNotNull(nm.getType()); + assertNull(nm.getChemicalComposition()); + assertNotNull(nm.getType()); } @Test public void testDefaultConstructor() throws Exception { Material nm = new Material(); - Assert.assertNull(nm.getType()); + assertNull(nm.getType()); } @Test @@ -57,9 +62,9 @@ public void testLabels() throws Exception { List labels = new ArrayList(); labels.add("NM1"); labels.add("CeO2-15"); nm.setLabels(labels); - Assert.assertNotNull(nm.getLabels()); - Assert.assertEquals(2, nm.getLabels().size()); - Assert.assertTrue(nm.getLabels().contains("NM1")); + assertNotNull(nm.getLabels()); + assertEquals(2, nm.getLabels().size()); + assertTrue(nm.getLabels().contains("NM1")); } @Test @@ -67,8 +72,8 @@ public void testMultipleSizes() throws Exception { Material nm = new Material("GRAPHENE"); nm.addCharacterization(new ErrorlessMeasurementValue(EndPoints.DIAMETER_TEM, 20.0, LengthUnit.NM)); nm.addCharacterization(new ErrorlessMeasurementValue(EndPoints.DIAMETER_DLS, 55.0, LengthUnit.NM)); - Assert.assertNotNull(nm.getCharacterizations()); - Assert.assertEquals(2, nm.getCharacterizations().size()); + assertNotNull(nm.getCharacterizations()); + assertEquals(2, nm.getCharacterizations().size()); } @Test @@ -80,14 +85,14 @@ public void figureEightLeft() throws Exception { .asMaterial(); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertNotNull(roundTripped.getLabels()); - Assert.assertEquals(1, roundTripped.getLabels().size()); - Assert.assertEquals(2, roundTripped.getAtomContainerCount()); + assertNotNull(roundTripped); + assertNotNull(roundTripped.getLabels()); + assertEquals(1, roundTripped.getLabels().size()); + assertEquals(2, roundTripped.getAtomContainerCount()); for (IAtomContainer container : roundTripped.atomContainers()) { - Assert.assertNotNull(container.getProperty(Material.ORDER)); + assertNotNull(container.getProperty(Material.ORDER)); } } } diff --git a/src/test/java/io/github/egonw/nanojava/data/NanoInChIExamplesTest.java b/src/test/java/io/github/egonw/nanojava/data/NanoInChIExamplesTest.java index c47341d..eacf7b6 100644 --- a/src/test/java/io/github/egonw/nanojava/data/NanoInChIExamplesTest.java +++ b/src/test/java/io/github/egonw/nanojava/data/NanoInChIExamplesTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2022 Egon Willighagen +/* Copyright (C) 2022-2025 Egon Willighagen * * 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 diff --git a/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementRangeTest.java b/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementRangeTest.java index 733cc2c..4951db0 100644 --- a/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementRangeTest.java +++ b/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementRangeTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,16 +16,16 @@ */ package io.github.egonw.nanojava.data.measurement; -import junit.framework.Assert; +import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.Test; +import org.junit.jupiter.api.Test; public class MeasurementRangeTest { @Test public void testToString() throws Exception { IMeasurement measurement = new MeasurementRange(EndPoints.ZETA_POTENTIAL, 4.5, 6.7, "http://qudt.org/vocab/unit#ElectronVolt"); - Assert.assertEquals("4.5 - 6.7 eV", measurement.getString()); + assertEquals("4.5 - 6.7 eV", measurement.getString()); } } diff --git a/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementValueTest.java b/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementValueTest.java index 6c252db..f7bf966 100644 --- a/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementValueTest.java +++ b/src/test/java/io/github/egonw/nanojava/data/measurement/MeasurementValueTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,16 +16,16 @@ */ package io.github.egonw.nanojava.data.measurement; -import junit.framework.Assert; +import static org.junit.jupiter.api.Assertions.assertEquals; -import org.junit.Test; +import org.junit.jupiter.api.Test; public class MeasurementValueTest { @Test public void testToString() throws Exception { IMeasurement measurement = new MeasurementValue(EndPoints.ZETA_POTENTIAL, 4.5, 0.0, "http://qudt.org/vocab/unit#ElectronVolt"); - Assert.assertEquals("4.5 \u00b1 0.0 eV", measurement.getString()); + assertEquals("4.5 \u00b1 0.0 eV", measurement.getString()); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/EnergyBandDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/EnergyBandDescriptorTest.java index c81363b..e2157dd 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/EnergyBandDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/EnergyBandDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,13 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNotSame; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.IDescriptorResult; @@ -30,12 +35,11 @@ import io.github.egonw.nanojava.data.MaterialType; import io.github.egonw.nanojava.data.measurement.EndPoints; import io.github.egonw.nanojava.data.measurement.MeasurementValue; -import junit.framework.Assert; public class EnergyBandDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(EnergyBandDescriptor.class); } @@ -49,14 +53,14 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertTrue(result instanceof DoubleArrayResult); + assertNotNull(result); + assertTrue(result instanceof DoubleArrayResult); DoubleArrayResult daResult = (DoubleArrayResult)result; - Assert.assertEquals(2, daResult.length()); - Assert.assertEquals(-3.7, daResult.get(0), 0.0001); - Assert.assertEquals(-7.25, daResult.get(1), 0.0001); + assertEquals(2, daResult.length()); + assertEquals(-3.7, daResult.get(0), 0.0001); + assertEquals(-7.25, daResult.get(1), 0.0001); } @Test @@ -69,14 +73,14 @@ public void testCalculate_TestSize_TooSmall() throws Exception { ); material.setSize(new MeasurementValue(EndPoints.SIZE, 10.0, 5.0, LengthUnit.NM)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertTrue(result instanceof DoubleArrayResult); + assertNotNull(result); + assertTrue(result instanceof DoubleArrayResult); DoubleArrayResult daResult = (DoubleArrayResult)result; - Assert.assertEquals(2, daResult.length()); - Assert.assertEquals(Double.NaN, daResult.get(0), 0.0001); - Assert.assertEquals(Double.NaN, daResult.get(1), 0.0001); + assertEquals(2, daResult.length()); + assertEquals(Double.NaN, daResult.get(0), 0.0001); + assertEquals(Double.NaN, daResult.get(1), 0.0001); } @Test @@ -89,14 +93,14 @@ public void testCalculate_TestSize_OK() throws Exception { ); material.setSize(new MeasurementValue(EndPoints.SIZE, 40.0, 5.0, LengthUnit.NM)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertTrue(result instanceof DoubleArrayResult); + assertNotNull(result); + assertTrue(result instanceof DoubleArrayResult); DoubleArrayResult daResult = (DoubleArrayResult)result; - Assert.assertEquals(2, daResult.length()); - Assert.assertEquals(-3.7, daResult.get(0), 0.0001); - Assert.assertEquals(-7.25, daResult.get(1), 0.0001); + assertEquals(2, daResult.length()); + assertEquals(-3.7, daResult.get(0), 0.0001); + assertEquals(-7.25, daResult.get(1), 0.0001); } @Test @@ -109,14 +113,14 @@ public void testCalculate_IndiumOxide() throws Exception { ); material.setSize(new MeasurementValue(EndPoints.SIZE, 40.0, 5.0, LengthUnit.NM)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertTrue(result instanceof DoubleArrayResult); + assertNotNull(result); + assertTrue(result instanceof DoubleArrayResult); DoubleArrayResult daResult = (DoubleArrayResult)result; - Assert.assertEquals(2, daResult.length()); - Assert.assertEquals(-4.0, daResult.get(0), 0.0001); - Assert.assertEquals(-6.8, daResult.get(1), 0.0001); + assertEquals(2, daResult.length()); + assertEquals(-4.0, daResult.get(0), 0.0001); + assertEquals(-6.8, daResult.get(1), 0.0001); } @Test @@ -140,9 +144,9 @@ public void testCalculate_IronOxides() throws Exception { IDescriptorResult result2 = value2.getValue(); DoubleArrayResult daResult1 = (DoubleArrayResult)result1; DoubleArrayResult daResult2 = (DoubleArrayResult)result2; - Assert.assertNotSame(Double.NaN, daResult1.get(0)); - Assert.assertNotSame(Double.NaN, daResult1.get(1)); - Assert.assertNotSame(daResult1.get(0), daResult2.get(0)); - Assert.assertNotSame(daResult1.get(1), daResult2.get(1)); + assertNotSame(Double.NaN, daResult1.get(0)); + assertNotSame(Double.NaN, daResult1.get(1)); + assertNotSame(daResult1.get(0), daResult2.get(0)); + assertNotSame(daResult1.get(1), daResult2.get(1)); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationDescriptorTest.java index aa409c7..e815af0 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class HeatOfFormationDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(HeatOfFormationDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(662.44, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(662.44, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -60,10 +62,10 @@ public void testCalculate_Fe2O3() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(1408.29, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(1408.29, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -75,10 +77,10 @@ public void testCalculate_Al2O3() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(1187.83, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(1187.83, ((DoubleResult)result).doubleValue(), 0.0001); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationMopac2012DescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationMopac2012DescriptorTest.java index b43d948..0f18741 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationMopac2012DescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/HeatOfFormationMopac2012DescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class HeatOfFormationMopac2012DescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(HeatOfFormationMopac2012Descriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(662.43584, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(662.43584, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -60,10 +62,10 @@ public void testCalculate_Fe2O3() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(1363.39566, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(1363.39566, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -75,10 +77,10 @@ public void testCalculate_Al2O3() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(1187.82572, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(1187.82572, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -90,10 +92,10 @@ public void testCalculate_CuZnFe2O4() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(662.43584, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(662.43584, ((DoubleResult)result).doubleValue(), 0.0001); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/MaterialDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/MaterialDescriptorTest.java index 3106e41..d58761a 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/MaterialDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/MaterialDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011-2022 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,13 +16,15 @@ */ package io.github.egonw.nanojava.descriptor; -import io.github.egonw.nanojava.data.Material; -import io.github.egonw.nanojava.data.MaterialType; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNotSame; + +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.IDescriptorResult; -import junit.framework.Assert; +import io.github.egonw.nanojava.data.Material; +import io.github.egonw.nanojava.data.MaterialType; public abstract class MaterialDescriptorTest { @@ -45,32 +47,32 @@ public void setDescriptor(Class descriptorClass) throws Exception { public void testCalculate_Empty() throws Exception { Material material = new Material(MaterialType.METALOXIDE); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertNotSame(0, result.length()); + assertNotNull(result); + assertNotSame(0, result.length()); } @Test public void testCalculate_Null() throws Exception { DescriptorValue value = descriptor.calculate(null); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertNotSame(0, result.length()); + assertNotNull(result); + assertNotSame(0, result.length()); } @Test public void testParameters() { Object[] params = descriptor.getParameters(); - Assert.assertNotNull(params); + assertNotNull(params); String[] names = descriptor.getParameterNames(); - Assert.assertNotNull(names); + assertNotNull(names); } @Test public void testGetDescriptorType() { IDescriptorResult type = descriptor.getDescriptorResultType(); - Assert.assertNotNull(type); + assertNotNull(type); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/MetalAtomCountDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/MetalAtomCountDescriptorTest.java index 1062866..a6547f3 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/MetalAtomCountDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/MetalAtomCountDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.qsar.result.IntegerResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class MetalAtomCountDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(MetalAtomCountDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(1, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(1, ((IntegerResult)result).intValue()); } @Test @@ -60,10 +62,10 @@ public void testCalculate_IronOxide() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(3, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(3, ((IntegerResult)result).intValue()); } @Test @@ -75,10 +77,10 @@ public void testCalculate_ComplexOxid4() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(4, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(4, ((IntegerResult)result).intValue()); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/MetalElementMassDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/MetalElementMassDescriptorTest.java index 4a088d9..57cbb5d 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/MetalElementMassDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/MetalElementMassDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class MetalElementMassDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(MetalElementMassDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(65.38, ((DoubleResult)result).doubleValue(), 0.02); + assertNotNull(result); + assertEquals(65.38, ((DoubleResult)result).doubleValue(), 0.02); } @Test @@ -60,10 +62,10 @@ public void testCalculate_IronOxide() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(55.8, ((DoubleResult)result).doubleValue(), 0.1); + assertNotNull(result); + assertEquals(55.8, ((DoubleResult)result).doubleValue(), 0.1); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/MetalGroupDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/MetalGroupDescriptorTest.java index 554652c..84ac766 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/MetalGroupDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/MetalGroupDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.qsar.result.IntegerResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class MetalGroupDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(MetalGroupDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(12, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(12, ((IntegerResult)result).intValue()); } @Test @@ -60,10 +62,10 @@ public void testCalculate_IronOxide() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(8, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(8, ((IntegerResult)result).intValue()); } @Test @@ -75,10 +77,10 @@ public void testCalculate_ComplexOxid4() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals((int)Double.NaN, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals((int)Double.NaN, ((IntegerResult)result).intValue()); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/MetalPeriodDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/MetalPeriodDescriptorTest.java index 338cca3..2c2d3d5 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/MetalPeriodDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/MetalPeriodDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.qsar.result.IntegerResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class MetalPeriodDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(MetalPeriodDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(4, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(4, ((IntegerResult)result).intValue()); } @Test @@ -60,10 +62,10 @@ public void testCalculate_IronOxide() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(4, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(4, ((IntegerResult)result).intValue()); } @Test @@ -75,10 +77,10 @@ public void testCalculate_ComplexOxid4() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals((int)Double.NaN, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals((int)Double.NaN, ((IntegerResult)result).intValue()); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/MolecularWeightDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/MolecularWeightDescriptorTest.java index 7138efc..7e53222 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/MolecularWeightDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/MolecularWeightDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class MolecularWeightDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(MolecularWeightDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(81.3950, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(81.3950, ((DoubleResult)result).doubleValue(), 0.0001); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/OxygenAtomCountDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/OxygenAtomCountDescriptorTest.java index 8c4ada6..3a35a58 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/OxygenAtomCountDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/OxygenAtomCountDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,8 +16,11 @@ */ package io.github.egonw.nanojava.descriptor; -import org.junit.Before; -import org.junit.Test; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.qsar.result.IntegerResult; @@ -26,12 +29,11 @@ import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; -import junit.framework.Assert; public class OxygenAtomCountDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(OxygenAtomCountDescriptor.class); } @@ -45,10 +47,10 @@ public void testCalculate_ZnO() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(1, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(1, ((IntegerResult)result).intValue()); } @Test @@ -60,10 +62,10 @@ public void testCalculate_IronOxide() throws Exception { ) ); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(4, ((IntegerResult)result).intValue()); + assertNotNull(result); + assertEquals(4, ((IntegerResult)result).intValue()); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/ParticleSizeDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/ParticleSizeDescriptorTest.java index 2d57cdf..b946609 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/ParticleSizeDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/ParticleSizeDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,25 +16,27 @@ */ package io.github.egonw.nanojava.descriptor; -import junit.framework.Assert; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; -import io.github.egonw.nanojava.data.MaterialType; -import io.github.egonw.nanojava.data.Material; -import io.github.egonw.nanojava.data.measurement.EndPoints; -import io.github.egonw.nanojava.data.measurement.MeasurementRange; -import io.github.egonw.nanojava.data.measurement.MeasurementValue; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; import com.github.jqudt.onto.units.LengthUnit; +import io.github.egonw.nanojava.data.Material; +import io.github.egonw.nanojava.data.MaterialType; +import io.github.egonw.nanojava.data.measurement.EndPoints; +import io.github.egonw.nanojava.data.measurement.MeasurementRange; +import io.github.egonw.nanojava.data.measurement.MeasurementValue; + public class ParticleSizeDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(ParticleSizeDescriptor.class); } @@ -44,10 +46,10 @@ public void testCalculate_Range() throws Exception { Material material = new Material(MaterialType.METALOXIDE); material.setSize(new MeasurementRange(EndPoints.SIZE, 10, 20, LengthUnit.NM)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(15.0, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(15.0, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -55,10 +57,10 @@ public void testCalculate_Value() throws Exception { Material material = new Material(MaterialType.METALOXIDE); material.setSize(new MeasurementValue(EndPoints.SIZE, 30, 5, LengthUnit.NM)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(30.0, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(30.0, ((DoubleResult)result).doubleValue(), 0.0001); } } diff --git a/src/test/java/io/github/egonw/nanojava/descriptor/ZetaPotentialDescriptorTest.java b/src/test/java/io/github/egonw/nanojava/descriptor/ZetaPotentialDescriptorTest.java index 9166f18..fa7e5a7 100644 --- a/src/test/java/io/github/egonw/nanojava/descriptor/ZetaPotentialDescriptorTest.java +++ b/src/test/java/io/github/egonw/nanojava/descriptor/ZetaPotentialDescriptorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2011 Egon Willighagen +/* Copyright (C) 2011-2025 Egon Willighagen * * 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 @@ -16,25 +16,27 @@ */ package io.github.egonw.nanojava.descriptor; -import junit.framework.Assert; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; -import io.github.egonw.nanojava.data.MaterialType; -import io.github.egonw.nanojava.data.Material; -import io.github.egonw.nanojava.data.measurement.EndPoints; -import io.github.egonw.nanojava.data.measurement.MeasurementRange; -import io.github.egonw.nanojava.data.measurement.MeasurementValue; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; import com.github.jqudt.onto.units.EnergyUnit; +import io.github.egonw.nanojava.data.Material; +import io.github.egonw.nanojava.data.MaterialType; +import io.github.egonw.nanojava.data.measurement.EndPoints; +import io.github.egonw.nanojava.data.measurement.MeasurementRange; +import io.github.egonw.nanojava.data.measurement.MeasurementValue; + public class ZetaPotentialDescriptorTest extends MaterialDescriptorTest { - @Before + @BeforeEach public void setUp() throws Exception { setDescriptor(ZetaPotentialDescriptor.class); } @@ -44,10 +46,10 @@ public void testCalculate_Range() throws Exception { Material material = new Material(MaterialType.METALOXIDE); material.setZetaPotential(new MeasurementRange(EndPoints.ZETA_POTENTIAL, -7.5, -7.7, EnergyUnit.EV)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(-7.6, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(-7.6, ((DoubleResult)result).doubleValue(), 0.0001); } @Test @@ -55,10 +57,10 @@ public void testCalculate_Value() throws Exception { Material material = new Material(MaterialType.METALOXIDE); material.setZetaPotential(new MeasurementValue(EndPoints.ZETA_POTENTIAL, 17.3, 2.1, EnergyUnit.EV)); DescriptorValue value = descriptor.calculate(material); - Assert.assertNotNull(value); + assertNotNull(value); IDescriptorResult result = value.getValue(); - Assert.assertNotNull(result); - Assert.assertEquals(17.3, ((DoubleResult)result).doubleValue(), 0.0001); + assertNotNull(result); + assertEquals(17.3, ((DoubleResult)result).doubleValue(), 0.0001); } } diff --git a/src/test/java/io/github/egonw/nanojava/inchi/NInChIGeneratorTest.java b/src/test/java/io/github/egonw/nanojava/inchi/NInChIGeneratorTest.java index 9ae8e33..d16134c 100644 --- a/src/test/java/io/github/egonw/nanojava/inchi/NInChIGeneratorTest.java +++ b/src/test/java/io/github/egonw/nanojava/inchi/NInChIGeneratorTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2012 Egon Willighagen +/* Copyright (C) 2012-2025 Egon Willighagen * * 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 @@ -16,9 +16,28 @@ */ package io.github.egonw.nanojava.inchi; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.junit.jupiter.api.Test; + +import com.github.jqudt.onto.units.LengthUnit; + +import io.github.egonw.nanojava.data.Material; +import io.github.egonw.nanojava.data.MaterialBuilder; +import io.github.egonw.nanojava.data.measurement.EndPoints; +import io.github.egonw.nanojava.data.measurement.ErrorlessMeasurementValue; + public class NInChIGeneratorTest { - public void generate() { - + @Test + public void generate() throws Exception { + Material material = MaterialBuilder.type("METALOXIDE") + .label("silica nanoparticles with gold coating") + .componentFromSMILES(1, "O=[Si]=O", "SPHERE", "AMORPHOUS", new ErrorlessMeasurementValue(EndPoints.DIAMETER, 20, LengthUnit.NM)) + .componentFromSMILES(2, "[Au]", "SHELL", new ErrorlessMeasurementValue(EndPoints.THICKNESS, 2, LengthUnit.NM)) + .asMaterial(); + + String nanoInChI = NInChIGenerator.generator(material); + assertNotNull(nanoInChI); } } diff --git a/src/test/java/io/github/egonw/nanojava/io/CDKSerializationTest.java b/src/test/java/io/github/egonw/nanojava/io/CDKSerializationTest.java index b1a0b29..7b88754 100644 --- a/src/test/java/io/github/egonw/nanojava/io/CDKSerializationTest.java +++ b/src/test/java/io/github/egonw/nanojava/io/CDKSerializationTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2012 Egon Willighagen +/* Copyright (C) 2012-2025 Egon Willighagen * * 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 @@ -16,12 +16,15 @@ */ package io.github.egonw.nanojava.io; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.io.ByteArrayOutputStream; import java.util.ArrayList; import java.util.List; -import org.junit.Assert; -import org.junit.Test; +import org.junit.jupiter.api.Test; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecularFormula; import org.openscience.cdk.silent.SilentChemObjectBuilder; @@ -55,30 +58,30 @@ public void roundTripLabels() { labels.add("NM1"); labels.add("CeO2-15"); material.setLabels(labels); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertNotNull(roundTripped.getLabels()); - Assert.assertEquals(2, roundTripped.getLabels().size()); - Assert.assertTrue(roundTripped.getLabels().contains("NM1")); - Assert.assertTrue(roundTripped.getLabels().contains("CeO2-15")); + assertNotNull(roundTripped); + assertNotNull(roundTripped.getLabels()); + assertEquals(2, roundTripped.getLabels().size()); + assertTrue(roundTripped.getLabels().contains("NM1")); + assertTrue(roundTripped.getLabels().contains("CeO2-15")); } @Test public void roundTripType() { Material material = new Material("METALOXIDE"); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(MaterialType.METALOXIDE, roundTripped.getType()); + assertNotNull(roundTripped); + assertEquals(MaterialType.METALOXIDE, roundTripped.getType()); material = new Material("GRAPHENE"); cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(MaterialType.GRAPHENE, roundTripped.getType()); + assertNotNull(roundTripped); + assertEquals(MaterialType.GRAPHENE, roundTripped.getType()); } @Test @@ -90,12 +93,12 @@ public void roundChemicalComposition() { ) ); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); + assertNotNull(roundTripped); IMolecularFormula molForm = roundTripped.getChemicalComposition(); - Assert.assertNotNull(molForm); - Assert.assertEquals("CeO2", MolecularFormulaManipulator.getString(molForm)); + assertNotNull(molForm); + assertEquals("CeO2", MolecularFormulaManipulator.getString(molForm)); } @Test @@ -103,10 +106,10 @@ public void roundTripSize() { Material material = new Material("METALOXIDE"); material.setSize(new MeasurementValue(EndPoints.SIZE, 20.0, 7, LengthUnit.NM)); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(20.0, ((IErrorlessMeasurementValue)roundTripped.getSize()).getValue(), 0.1); + assertNotNull(roundTripped); + assertEquals(20.0, ((IErrorlessMeasurementValue)roundTripped.getSize()).getValue(), 0.1); } @Test @@ -115,14 +118,14 @@ public void roundTripSizes() { material.addCharacterization(new MeasurementValue(EndPoints.DIAMETER_TEM, 20.0, 7, LengthUnit.NM)); material.addCharacterization(new MeasurementValue(EndPoints.DIAMETER_DLS, 55.3, 14.3, LengthUnit.NM)); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(20.0, + assertNotNull(roundTripped); + assertEquals(20.0, ((IErrorlessMeasurementValue)roundTripped.getCharacterizations().get(EndPoints.DIAMETER_TEM)).getValue(), 0.1 ); - Assert.assertEquals(55.3, + assertEquals(55.3, ((IErrorlessMeasurementValue)roundTripped.getCharacterizations().get(EndPoints.DIAMETER_DLS)).getValue(), 0.1 ); @@ -134,14 +137,14 @@ public void roundTripSizes_Component() throws Exception { .componentFromSMILES(1, "[Au]", "SPHERE", new ErrorlessMeasurementValue(EndPoints.DIAMETER, 3.0, LengthUnit.NM)) .asMaterial(); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); System.out.println(asIndentedString(cmlMaterial)); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); + assertNotNull(roundTripped); IAtomContainer component = roundTripped.getAtomContainer(0); - Assert.assertNotNull(component); + assertNotNull(component); IErrorlessMeasurementValue diameter = (IErrorlessMeasurementValue)SubstanceManipulator.getMeasurement(component, EndPoints.DIAMETER); - Assert.assertEquals(3.0, diameter.getValue(), 0.1); + assertEquals(3.0, diameter.getValue(), 0.1); System.out.println("Unit: " + diameter.getUnit()); } @@ -151,15 +154,15 @@ public void roundComponentSpacegroup() throws Exception { .componentFromSMILES(1, "O=[Si]=O", "SPHERE", "AMORPHOUS") .asMaterial(); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); System.out.println(asIndentedString(cmlMaterial)); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); + assertNotNull(roundTripped); IAtomContainer component = roundTripped.getAtomContainer(0); - Assert.assertNotNull(component); + assertNotNull(component); Spacegroup group = SubstanceManipulator.getSpacegroup(component); - Assert.assertNotNull(group); - Assert.assertEquals(Spacegroup.AMORPHOUS, group); + assertNotNull(group); + assertEquals(Spacegroup.AMORPHOUS, group); } @Test @@ -170,10 +173,10 @@ public void roundTripPurity() { UnitFactory.getInstance().getUnit("http://qudt.org/vocab/unit#Percent") )); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(95, + assertNotNull(roundTripped); + assertEquals(95, ((IErrorlessMeasurementValue)roundTripped.getCharacterizations().get(EndPoints.PURITY)).getValue(), 0.1 ); @@ -184,10 +187,10 @@ public void roundTripZetaPotential() { Material material = new Material("METALOXIDE"); material.setZetaPotential(new MeasurementValue(EndPoints.ZETA_POTENTIAL, -45.0, 3, EnergyUnit.EV)); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(-45.0, ((IErrorlessMeasurementValue)roundTripped.getZetaPotential()).getValue(), 0.1); + assertNotNull(roundTripped); + assertEquals(-45.0, ((IErrorlessMeasurementValue)roundTripped.getZetaPotential()).getValue(), 0.1); } @Test @@ -196,12 +199,12 @@ public void roundTripList() { materials.add(new Material("GRAPHENE")); materials.add(new Material("METALOXIDE")); CMLList list = CDKSerializer.toCML(materials); - Assert.assertNotNull(list); + assertNotNull(list); List roundTripped = CDKDeserializer.fromCML(list); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(2, roundTripped.size()); - Assert.assertEquals(MaterialType.GRAPHENE, roundTripped.get(0).getType()); - Assert.assertEquals(MaterialType.METALOXIDE, roundTripped.get(1).getType()); + assertNotNull(roundTripped); + assertEquals(2, roundTripped.size()); + assertEquals(MaterialType.GRAPHENE, roundTripped.get(0).getType()); + assertEquals(MaterialType.METALOXIDE, roundTripped.get(1).getType()); } @Test @@ -211,12 +214,12 @@ public void roundtripMorphology() throws Exception { .asMaterial(); CMLMoleculeList cmlMaterial = CDKSerializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = CDKDeserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); + assertNotNull(roundTripped); System.out.println(asIndentedString(cmlMaterial)); - Assert.assertEquals(MaterialType.METAL, roundTripped.getType()); - Assert.assertEquals(Morphology.SPHERE, SubstanceManipulator.getMorphology(roundTripped.getAtomContainer(0))); + assertEquals(MaterialType.METAL, roundTripped.getType()); + assertEquals(Morphology.SPHERE, SubstanceManipulator.getMorphology(roundTripped.getAtomContainer(0))); } private String asIndentedString(CMLMoleculeList cmlMaterial) throws Exception { diff --git a/src/test/java/io/github/egonw/nanojava/io/DeserializationTest.java b/src/test/java/io/github/egonw/nanojava/io/DeserializationTest.java index 0600d3a..0649130 100644 --- a/src/test/java/io/github/egonw/nanojava/io/DeserializationTest.java +++ b/src/test/java/io/github/egonw/nanojava/io/DeserializationTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2012 Egon Willighagen +/* Copyright (C) 2012-2025 Egon Willighagen * * 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 @@ -16,17 +16,19 @@ */ package io.github.egonw.nanojava.io; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; + import java.io.IOException; import java.util.List; +import org.junit.jupiter.api.Test; + import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.MaterialType; import io.github.egonw.nanojava.data.Morphology; import io.github.egonw.nanojava.data.measurement.IErrorlessMeasurementValue; import io.github.egonw.nanojava.manipulator.SubstanceManipulator; -import org.junit.Assert; -import org.junit.Test; - import nu.xom.ParsingException; public class DeserializationTest { @@ -35,32 +37,32 @@ public class DeserializationTest { public void readType() throws ParsingException, IOException { String input = "GRAPHENE"; Material material = Deserializer.fromCMLString(input); - Assert.assertNotNull(material); - Assert.assertEquals(MaterialType.GRAPHENE, material.getType()); + assertNotNull(material); + assertEquals(MaterialType.GRAPHENE, material.getType()); } @Test public void readSize() throws ParsingException, IOException { String input = "METALOXIDE20.0"; Material material = Deserializer.fromCMLString(input); - Assert.assertNotNull(material); - Assert.assertEquals(20.0, ((IErrorlessMeasurementValue)material.getSize()).getValue(), 0.1); + assertNotNull(material); + assertEquals(20.0, ((IErrorlessMeasurementValue)material.getSize()).getValue(), 0.1); } @Test public void readZetaPotential() throws ParsingException, IOException { String input = "METALOXIDE-45.0"; Material material = Deserializer.fromCMLString(input); - Assert.assertNotNull(material); - Assert.assertEquals(-45.0, ((IErrorlessMeasurementValue)material.getZetaPotential()).getValue(), 0.1); + assertNotNull(material); + assertEquals(-45.0, ((IErrorlessMeasurementValue)material.getZetaPotential()).getValue(), 0.1); } @Test public void readList() throws ParsingException, IOException { String input = "METALOXIDE-24.0524.814.7-24.0METALOXIDE-28.9321.312.8-28.9METALOXIDE-25.5378.318.3-25.5METALOXIDE-29.0247.610.0-29.0METALOXIDE-26.2478.571.8-26.2METALOXIDE-26.9289.5193.0-26.9METALOXIDE-24.1385.212.3-24.1METALOXIDE-27.0831.712.0-27.0METALOXIDE-34.7726.743.8-34.7METALOXIDE-24.3349.928.4-24.3METALOXIDE-35.5303.259.6-35.5"; List materials = Deserializer.fromCMLListString(input); - Assert.assertNotNull(materials); - Assert.assertEquals(11, materials.size()); + assertNotNull(materials); + assertEquals(11, materials.size()); } @Test @@ -77,9 +79,9 @@ public void readMaterialFromMoleculeList() throws ParsingException, IOException + " METAL\n" + ""; Material material = CDKDeserializer.fromCMLString(input); - Assert.assertNotNull(material); - Assert.assertEquals(MaterialType.METAL, material.getType()); - Assert.assertEquals(Morphology.SPHERE, SubstanceManipulator.getMorphology(material.getAtomContainer(0))); + assertNotNull(material); + assertEquals(MaterialType.METAL, material.getType()); + assertEquals(Morphology.SPHERE, SubstanceManipulator.getMorphology(material.getAtomContainer(0))); } } diff --git a/src/test/java/io/github/egonw/nanojava/io/SerializationTest.java b/src/test/java/io/github/egonw/nanojava/io/SerializationTest.java index c5a9687..eb3f8d3 100644 --- a/src/test/java/io/github/egonw/nanojava/io/SerializationTest.java +++ b/src/test/java/io/github/egonw/nanojava/io/SerializationTest.java @@ -1,4 +1,4 @@ -/* Copyright (C) 2012 Egon Willighagen +/* Copyright (C) 2012-2025 Egon Willighagen * * 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 @@ -16,11 +16,14 @@ */ package io.github.egonw.nanojava.io; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.util.ArrayList; import java.util.List; -import org.junit.Assert; -import org.junit.Test; +import org.junit.jupiter.api.Test; import org.openscience.cdk.interfaces.IMolecularFormula; import org.openscience.cdk.silent.SilentChemObjectBuilder; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; @@ -47,30 +50,30 @@ public void roundTripLabels() { labels.add("NM1"); labels.add("CeO2-15"); material.setLabels(labels); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertNotNull(roundTripped.getLabels()); - Assert.assertEquals(2, roundTripped.getLabels().size()); - Assert.assertTrue(roundTripped.getLabels().contains("NM1")); - Assert.assertTrue(roundTripped.getLabels().contains("CeO2-15")); + assertNotNull(roundTripped); + assertNotNull(roundTripped.getLabels()); + assertEquals(2, roundTripped.getLabels().size()); + assertTrue(roundTripped.getLabels().contains("NM1")); + assertTrue(roundTripped.getLabels().contains("CeO2-15")); } @Test public void roundTripType() { Material material = new Material("METALOXIDE"); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(MaterialType.METALOXIDE, roundTripped.getType()); + assertNotNull(roundTripped); + assertEquals(MaterialType.METALOXIDE, roundTripped.getType()); material = new Material("GRAPHENE"); cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(MaterialType.GRAPHENE, roundTripped.getType()); + assertNotNull(roundTripped); + assertEquals(MaterialType.GRAPHENE, roundTripped.getType()); } @Test @@ -82,12 +85,12 @@ public void roundChemicalComposition() { ) ); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); + assertNotNull(roundTripped); IMolecularFormula molForm = roundTripped.getChemicalComposition(); - Assert.assertNotNull(molForm); - Assert.assertEquals("CeO2", MolecularFormulaManipulator.getString(molForm)); + assertNotNull(molForm); + assertEquals("CeO2", MolecularFormulaManipulator.getString(molForm)); } @Test @@ -95,10 +98,10 @@ public void roundTripSize() { Material material = new Material("METALOXIDE"); material.setSize(new MeasurementValue(EndPoints.SIZE, 20.0, 7, LengthUnit.NM)); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(20.0, ((IErrorlessMeasurementValue)roundTripped.getSize()).getValue(), 0.1); + assertNotNull(roundTripped); + assertEquals(20.0, ((IErrorlessMeasurementValue)roundTripped.getSize()).getValue(), 0.1); } @Test @@ -107,14 +110,14 @@ public void roundTripSizes() { material.addCharacterization(new MeasurementValue(EndPoints.DIAMETER_TEM, 20.0, 7, LengthUnit.NM)); material.addCharacterization(new MeasurementValue(EndPoints.DIAMETER_DLS, 55.3, 14.3, LengthUnit.NM)); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(20.0, + assertNotNull(roundTripped); + assertEquals(20.0, ((IErrorlessMeasurementValue)roundTripped.getCharacterizations().get(EndPoints.DIAMETER_TEM)).getValue(), 0.1 ); - Assert.assertEquals(55.3, + assertEquals(55.3, ((IErrorlessMeasurementValue)roundTripped.getCharacterizations().get(EndPoints.DIAMETER_DLS)).getValue(), 0.1 ); @@ -128,10 +131,10 @@ public void roundTripPurity() { UnitFactory.getInstance().getUnit("http://qudt.org/vocab/unit#Percent") )); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(95, + assertNotNull(roundTripped); + assertEquals(95, ((IErrorlessMeasurementValue)roundTripped.getCharacterizations().get(EndPoints.PURITY)).getValue(), 0.1 ); @@ -142,10 +145,10 @@ public void roundTripZetaPotential() { Material material = new Material("METALOXIDE"); material.setZetaPotential(new MeasurementValue(EndPoints.ZETA_POTENTIAL, -45.0, 3, EnergyUnit.EV)); CMLMolecule cmlMaterial = Serializer.toCML(material); - Assert.assertNotNull(cmlMaterial); + assertNotNull(cmlMaterial); Material roundTripped = Deserializer.fromCML(cmlMaterial); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(-45.0, ((IErrorlessMeasurementValue)roundTripped.getZetaPotential()).getValue(), 0.1); + assertNotNull(roundTripped); + assertEquals(-45.0, ((IErrorlessMeasurementValue)roundTripped.getZetaPotential()).getValue(), 0.1); } @Test @@ -154,11 +157,11 @@ public void roundTripList() { materials.add(new Material("GRAPHENE")); materials.add(new Material("METALOXIDE")); CMLList list = Serializer.toCML(materials); - Assert.assertNotNull(list); + assertNotNull(list); List roundTripped = Deserializer.fromCML(list); - Assert.assertNotNull(roundTripped); - Assert.assertEquals(2, roundTripped.size()); - Assert.assertEquals(MaterialType.GRAPHENE, roundTripped.get(0).getType()); - Assert.assertEquals(MaterialType.METALOXIDE, roundTripped.get(1).getType()); + assertNotNull(roundTripped); + assertEquals(2, roundTripped.size()); + assertEquals(MaterialType.GRAPHENE, roundTripped.get(0).getType()); + assertEquals(MaterialType.METALOXIDE, roundTripped.get(1).getType()); } } diff --git a/src/test/java/io/github/egonw/nanojava/manipulator/SubstanceManipulatorTest.java b/src/test/java/io/github/egonw/nanojava/manipulator/SubstanceManipulatorTest.java index 565f952..f9a0457 100644 --- a/src/test/java/io/github/egonw/nanojava/manipulator/SubstanceManipulatorTest.java +++ b/src/test/java/io/github/egonw/nanojava/manipulator/SubstanceManipulatorTest.java @@ -16,30 +16,34 @@ */ package io.github.egonw.nanojava.manipulator; +import static org.junit.Assert.assertNull; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.util.ArrayList; import java.util.List; -import junit.framework.Assert; +import org.junit.jupiter.api.Test; + +import com.github.jqudt.onto.units.LengthUnit; import io.github.egonw.nanojava.data.Material; import io.github.egonw.nanojava.data.measurement.EndPoints; import io.github.egonw.nanojava.data.measurement.ErrorlessMeasurementValue; -import org.junit.Test; - -import com.github.jqudt.onto.units.LengthUnit; public class SubstanceManipulatorTest { @Test public void testAlwaysReturnsLabelList() throws Exception { Material nm = new Material("GRAPHENE"); - Assert.assertNotNull(SubstanceManipulator.getLabels(nm)); + assertNotNull(SubstanceManipulator.getLabels(nm)); } @Test public void testChemicalCompisitionWhenEmpty() throws Exception { Material nm = new Material("GRAPHENE"); - Assert.assertNull(SubstanceManipulator.getChemicalComposition(nm)); + assertNull(SubstanceManipulator.getChemicalComposition(nm)); } @Test @@ -48,9 +52,9 @@ public void testLabels() throws Exception { List labels = new ArrayList(); labels.add("NM1"); labels.add("CeO2-15"); SubstanceManipulator.setLabels(nm, labels); - Assert.assertNotNull(SubstanceManipulator.getLabels(nm)); - Assert.assertEquals(2, SubstanceManipulator.getLabels(nm).size()); - Assert.assertTrue(SubstanceManipulator.getLabels(nm).contains("NM1")); + assertNotNull(SubstanceManipulator.getLabels(nm)); + assertEquals(2, SubstanceManipulator.getLabels(nm).size()); + assertTrue(SubstanceManipulator.getLabels(nm).contains("NM1")); } @Test @@ -58,8 +62,8 @@ public void testMultipleSizes() throws Exception { Material nm = new Material("GRAPHENE"); nm.addCharacterization(new ErrorlessMeasurementValue(EndPoints.DIAMETER_TEM, 20.0, LengthUnit.NM)); nm.addCharacterization(new ErrorlessMeasurementValue(EndPoints.DIAMETER_DLS, 55.0, LengthUnit.NM)); - Assert.assertNotNull(SubstanceManipulator.getCharacterizations(nm)); - Assert.assertEquals(2, SubstanceManipulator.getCharacterizations(nm).size()); + assertNotNull(SubstanceManipulator.getCharacterizations(nm)); + assertEquals(2, SubstanceManipulator.getCharacterizations(nm).size()); } }