diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index da75498d03564066d5eb9a5f09364b645f4ae3db..c72903aac967482a5f6afd71527cbf614a99af97 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,6 +8,7 @@ cache:
paths:
- .m2/repository/
- target/
+ - coverage/
build:
stage: build
@@ -17,12 +18,10 @@ build:
test:
stage: test
script:
- - mvn test
+ - mvn clean test
+ - cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
+
-verify:
- stage: test
- script:
- - mvn verify
deploySnapshot:
stage: deploy
diff --git a/README.md b/README.md
index 6412c84c2e573dabfd40b7a00ef59d33e3eda131..e4609e25b846f20047cfff1ca49f844d9b9bd3ff 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,11 @@
## Java library for metabolic networks
+
+[](https://forgemia.inra.fr/metexplore/met4j/-/commits/ci_coverage2)
+
+[](https://forgemia.inra.fr/metexplore/met4j/-/commits/ci_coverage2)
+
### Modules
Met4j is composed by several maven modules:
diff --git a/coverage/pom.xml b/coverage/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c8a195135f249617469a6b74e8537994f93c8556
--- /dev/null
+++ b/coverage/pom.xml
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ ~ Copyright INRAE (2021)
+ ~
+ ~ contact-metexplore@inrae.fr
+ ~
+ ~ This software is a computer program whose purpose is to [describe
+ ~ functionalities and technical features of your software].
+ ~
+ ~ This software is governed by the CeCILL license under French law and
+ ~ abiding by the rules of distribution of free software. You can use,
+ ~ modify and/ or redistribute the software under the terms of the CeCILL
+ ~ license as circulated by CEA, CNRS and INRIA at the following URL
+ ~ "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ ~
+ ~ As a counterpart to the access to the source code and rights to copy,
+ ~ modify and redistribute granted by the license, users are provided only
+ ~ with a limited warranty and the software's author, the holder of the
+ ~ economic rights, and the successive licensors have only limited
+ ~ liability.
+ ~
+ ~ In this respect, the user's attention is drawn to the risks associated
+ ~ with loading, using, modifying and/or developing or reproducing the
+ ~ software by the user in light of its specific status of free software,
+ ~ that may mean that it is complicated to manipulate, and that also
+ ~ therefore means that it is reserved for developers and experienced
+ ~ professionals having in-depth computer knowledge. Users are therefore
+ ~ encouraged to load and test the software's suitability as regards their
+ ~ requirements in conditions enabling the security of their systems and/or
+ ~ data to be ensured and, more generally, to use and operate it in the
+ ~ same conditions as regards security.
+ ~
+ ~ The fact that you are presently reading this means that you have had
+ ~ knowledge of the CeCILL license and that you accept its terms.
+ ~
+ -->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+ http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <parent>
+ <groupId>fr.inrae.toulouse.metexplore</groupId>
+ <artifactId>met4j</artifactId>
+ <version>0.7.6-SNAPSHOT</version>
+ <relativePath>../pom.xml</relativePath>
+ </parent>
+
+ <artifactId>coverage</artifactId>
+ <name>coverage</name>
+ <description>Compute aggregated test code coverage</description>
+
+ <properties>
+ <maven.deploy.skip>true</maven.deploy.skip>
+ </properties>
+
+ <dependencies>
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>met4j-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>met4j-io</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>met4j-graph</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>met4j-mapping</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.5</version>
+ <executions>
+ <execution>
+ <id>report-aggregate</id>
+ <phase>test</phase>
+ <goals>
+ <goal>report-aggregate</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
\ No newline at end of file
diff --git a/met4j-chemUtils/pom.xml b/met4j-chemUtils/pom.xml
index d293d42bc7521558a560b169a72a0855ebc55fc2..d3cf05061e41083fc197ed62ff2dce974637b04b 100644
--- a/met4j-chemUtils/pom.xml
+++ b/met4j-chemUtils/pom.xml
@@ -1,46 +1,6 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-<!-- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <configuration>
- <source>11</source>
- <target>11</target>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
- <executions>
- <execution>
- <id>attach-javadocs</id>
- <goals>
- <goal>jar</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
- <executions>
- <execution>
- <id>attach-sources</id>
- <goals>
- <goal>jar</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
<parent>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -48,69 +8,71 @@
<version>0.7.6-SNAPSHOT</version>
</parent>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
- </properties>
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <maven.compiler.source>11</maven.compiler.source>
+ <maven.compiler.target>11</maven.compiler.target>
+ </properties>
- <artifactId>met4j-chemUtils</artifactId>
- <packaging>jar</packaging>
+ <artifactId>met4j-chemUtils</artifactId>
+ <packaging>jar</packaging>
- <name>met4j-chemUtils</name>
- <url>http://maven.apache.org</url>
+ <name>met4j-chemUtils</name>
+ <url>http://maven.apache.org</url>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.12</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.openscience.cdk</groupId>
- <artifactId>cdk-bundle</artifactId>
- <version>1.5.14</version>
- </dependency>
- <dependency>
- <groupId>fr.inrae.toulouse.metexplore</groupId>
- <artifactId>met4j-core</artifactId>
- <version>0.7.6-SNAPSHOT</version>
- </dependency>
- <!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-core</artifactId>
- <version>3.0.0</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-<!-- <profiles>
- <profile>
- <id>release-sign-artifacts</id>
- <activation>
- <property>
- <name>performRelease</name>
- <value>true</value>
- </property>
- </activation>
- <build>
+ <dependencies>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.12</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.openscience.cdk</groupId>
+ <artifactId>cdk-bundle</artifactId>
+ <version>1.5.14</version>
+ </dependency>
+ <dependency>
+ <groupId>fr.inrae.toulouse.metexplore</groupId>
+ <artifactId>met4j-core</artifactId>
+ <version>0.7.6-SNAPSHOT</version>
+ </dependency>
+ <!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-core</artifactId>
+ <version>3.0.0</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+
+ <build>
<plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-gpg-plugin</artifactId>
- <executions>
- <execution>
- <id>sign-artifacts</id>
- <phase>verify</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
+ <plugin>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
+ <executions>
+ <!-- to avoid bugs in some situations -->
+ <execution>
+ <id>default-prepare-agent</id>
+ <goals>
+ <goal>prepare-agent</goal>
+ </goals>
+ </execution>
+
+ <!-- create report during maven verify phase -->
+ <execution>
+ <id>report</id>
+ <phase>verify</phase>
+ <goals>
+ <goal>report</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
</plugins>
- </build>
- </profile>
- </profiles>-->
+ </build>
+
</project>
diff --git a/met4j-core/pom.xml b/met4j-core/pom.xml
index d01259ea96b6051a8b075e1b29ff18606eb1c220..3796367958867efe4b4691c1e2bd17ab5751a097 100644
--- a/met4j-core/pom.xml
+++ b/met4j-core/pom.xml
@@ -1,5 +1,6 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
<parent>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -7,97 +8,64 @@
<version>0.7.6-SNAPSHOT</version>
</parent>
- <scm>
- <developerConnection>scm:git:ssh://git@forgemia.inra.fr/metexplore/met4j.git</developerConnection>
- <tag>met4j-0.1.2</tag>
- <url>https://forgemia.inra.fr/metexplore/met4j/-/tree/master</url>
- </scm>
+ <scm>
+ <developerConnection>scm:git:ssh://git@forgemia.inra.fr/metexplore/met4j.git</developerConnection>
+ <tag>met4j-0.1.2</tag>
+ <url>https://forgemia.inra.fr/metexplore/met4j/-/tree/master</url>
+ </scm>
- <artifactId>met4j-core</artifactId>
- <packaging>jar</packaging>
+ <artifactId>met4j-core</artifactId>
+ <packaging>jar</packaging>
- <name>met4j-core</name>
- <url>http://maven.apache.org</url>
+ <name>met4j-core</name>
+ <url>http://maven.apache.org</url>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
- </properties>
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <maven.compiler.source>11</maven.compiler.source>
+ <maven.compiler.target>11</maven.compiler.target>
+ </properties>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>4.12</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>commons-lang3</artifactId>
- <version>3.0</version>
- </dependency>
- </dependencies>
+ <dependencies>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.12</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-lang3</artifactId>
+ <version>3.0</version>
+ </dependency>
+ </dependencies>
-<!-- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
- <executions>
- <execution>
- <id>attach-javadocs</id>
- <goals>
- <goal>jar</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
- <executions>
- <execution>
- <id>attach-sources</id>
- <goals>
- <goal>jar</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>-->
- <!--<profiles>
- <profile>
- <id>release-sign-artifacts</id>
- <activation>
- <property>
- <name>performRelease</name>
- <value>true</value>
- </property>
- </activation>
- <build>
+ <build>
<plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-gpg-plugin</artifactId>
- <executions>
- <execution>
- <id>sign-artifacts</id>
- <phase>verify</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
+ <plugin>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
+ <executions>
+ <!-- to avoid bugs in some situations -->
+ <execution>
+ <id>default-prepare-agent</id>
+ <goals>
+ <goal>prepare-agent</goal>
+ </goals>
+ </execution>
+
+ <!-- create report during maven verify phase -->
+ <execution>
+ <id>report</id>
+ <phase>verify</phase>
+ <goals>
+ <goal>report</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
</plugins>
- </build>
- </profile>
- </profiles>-->
+ </build>
+
</project>
diff --git a/met4j-graph/pom.xml b/met4j-graph/pom.xml
index 0275128d8e6ebd6e5d6f4ffd33e6f79798e29e19..f57172db2fcc680b6ab232e2b574d9ce44173b29 100644
--- a/met4j-graph/pom.xml
+++ b/met4j-graph/pom.xml
@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
@@ -57,65 +58,33 @@
<version>0.7.6-SNAPSHOT</version>
</dependency>
</dependencies>
-<!-- <build>
+
+ <build>
<plugins>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
<executions>
+ <!-- to avoid bugs in some situations -->
<execution>
- <id>attach-javadocs</id>
+ <id>default-prepare-agent</id>
<goals>
- <goal>jar</goal>
+ <goal>prepare-agent</goal>
</goals>
</execution>
- </executions>
- <configuration>
- <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
- <executions>
+
+ <!-- create report during maven verify phase -->
<execution>
- <id>attach-sources</id>
+ <id>report</id>
+ <phase>verify</phase>
<goals>
- <goal>jar</goal>
+ <goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
- <profiles>
- <profile>
- <id>release-sign-artifacts</id>
- <activation>
- <property>
- <name>performRelease</name>
- <value>true</value>
- </property>
- </activation>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-gpg-plugin</artifactId>
- <executions>
- <execution>
- <id>sign-artifacts</id>
- <phase>verify</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
- </profile>
- </profiles>-->
+
</project>
diff --git a/met4j-io/pom.xml b/met4j-io/pom.xml
index dcd65fa5b8dcce1e0cdab6d44dc8f9f0b3471b1e..fa4e1a1b359bbcb47e0f477c65b8f3012cf72768 100644
--- a/met4j-io/pom.xml
+++ b/met4j-io/pom.xml
@@ -1,5 +1,6 @@
<?xml version="1.0"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
@@ -20,47 +21,6 @@
<maven.compiler.target>11</maven.compiler.target>
</properties>
-<!-- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <configuration>
- <source>11</source>
- <target>11</target>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
- <executions>
- <execution>
- <id>attach-javadocs</id>
- <goals>
- <goal>jar</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
- <executions>
- <execution>
- <id>attach-sources</id>
- <goals>
- <goal>jar</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>-->
<dependencies>
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -102,32 +62,33 @@
</dependency>
</dependencies>
-<!-- <profiles>
- <profile>
- <id>release-sign-artifacts</id>
- <activation>
- <property>
- <name>performRelease</name>
- <value>true</value>
- </property>
- </activation>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-gpg-plugin</artifactId>
- <executions>
- <execution>
- <id>sign-artifacts</id>
- <phase>verify</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
- </profile>
- </profiles>-->
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
+ <executions>
+ <!-- to avoid bugs in some situations -->
+ <execution>
+ <id>default-prepare-agent</id>
+ <goals>
+ <goal>prepare-agent</goal>
+ </goals>
+ </execution>
+
+ <!-- create report during maven verify phase -->
+ <execution>
+ <id>report</id>
+ <phase>verify</phase>
+ <goals>
+ <goal>report</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
</project>
diff --git a/met4j-mapping/pom.xml b/met4j-mapping/pom.xml
index 5136e81647f6eed410252126cfdf3bee7b598b7b..8fb5e803d34221047b00f161c8416b6b3d175151 100644
--- a/met4j-mapping/pom.xml
+++ b/met4j-mapping/pom.xml
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>met4j</artifactId>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -22,66 +23,33 @@
</dependency>
</dependencies>
-<!-- <build>
+ <build>
<plugins>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
<executions>
+ <!-- to avoid bugs in some situations -->
<execution>
- <id>attach-javadocs</id>
+ <id>default-prepare-agent</id>
<goals>
- <goal>jar</goal>
+ <goal>prepare-agent</goal>
</goals>
</execution>
- </executions>
- <configuration>
- <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
- <executions>
+
+ <!-- create report during maven verify phase -->
<execution>
- <id>attach-sources</id>
+ <id>report</id>
+ <phase>verify</phase>
<goals>
- <goal>jar</goal>
+ <goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
- <profiles>
- <profile>
- <id>release-sign-artifacts</id>
- <activation>
- <property>
- <name>performRelease</name>
- <value>true</value>
- </property>
- </activation>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-gpg-plugin</artifactId>
- <executions>
- <execution>
- <id>sign-artifacts</id>
- <phase>verify</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
- </profile>
- </profiles>-->
+
</project>
\ No newline at end of file
diff --git a/met4j-mathUtils/pom.xml b/met4j-mathUtils/pom.xml
index f598d1e8a5bc5aa5a032cf9c59812b0ed271d920..f8a0fd52d8fe9538ed0c67a03f2c22277183e37d 100644
--- a/met4j-mathUtils/pom.xml
+++ b/met4j-mathUtils/pom.xml
@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
@@ -39,65 +40,32 @@
</dependency>
</dependencies>
-<!-- <build>
+ <build>
<plugins>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
<executions>
+ <!-- to avoid bugs in some situations -->
<execution>
- <id>attach-javadocs</id>
+ <id>default-prepare-agent</id>
<goals>
- <goal>jar</goal>
+ <goal>prepare-agent</goal>
</goals>
</execution>
- </executions>
- <configuration>
- <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
- <executions>
+
+ <!-- create report during maven verify phase -->
<execution>
- <id>attach-sources</id>
+ <id>report</id>
+ <phase>verify</phase>
<goals>
- <goal>jar</goal>
+ <goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
- <profiles>
- <profile>
- <id>release-sign-artifacts</id>
- <activation>
- <property>
- <name>performRelease</name>
- <value>true</value>
- </property>
- </activation>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-gpg-plugin</artifactId>
- <executions>
- <execution>
- <id>sign-artifacts</id>
- <phase>verify</phase>
- <goals>
- <goal>sign</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
- </profile>
- </profiles>-->
+
</project>
diff --git a/met4j-toolbox/pom.xml b/met4j-toolbox/pom.xml
index 1ae965b7f8fd229100fbd1695cdf955679cb9c44..62ebd973570dbb0a226db22f1d280e7c11239a0c 100644
--- a/met4j-toolbox/pom.xml
+++ b/met4j-toolbox/pom.xml
@@ -1,5 +1,6 @@
<?xml version="1.0"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -86,6 +87,30 @@
</configuration>
<version>2.2-beta-5</version>
</plugin>
+ <plugin>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.7</version>
+ <executions>
+ <!-- to avoid bugs in some situations -->
+ <execution>
+ <id>default-prepare-agent</id>
+ <goals>
+ <goal>prepare-agent</goal>
+ </goals>
+ </execution>
+
+ <!-- create report during maven verify phase -->
+ <execution>
+ <id>report</id>
+ <phase>verify</phase>
+ <goals>
+ <goal>report</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
</plugins>
</build>
+
</project>
diff --git a/pom.xml b/pom.xml
index e5bea6bae76cd35256dadfb5c640eb7efb994219..c753225a60d84bb5a97c7b3e8ddf5fe6ef3ba39f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -100,6 +100,11 @@
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.19.1</version>
+ </plugin>
</plugins>
</build>
<profiles>
@@ -169,6 +174,7 @@
<module>met4j-graph</module>
<module>met4j-toolbox</module>
<module>met4j-mapping</module>
+ <module>coverage</module>
</modules>
<dependencies>