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Commit 222f30a5 authored by Ludovic Cottret's avatar Ludovic Cottret
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Add coverage module

parent e3385e04
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Inline Side-by-side
.gitlab-ci.yml
View file @ 222f30a5
......@@ -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
......
README.md
View file @ 222f30a5
......@@ -2,6 +2,11 @@
## Java library for metabolic networks
[![pipeline status](https://forgemia.inra.fr/metexplore/met4j/badges/ci_coverage2/pipeline.svg)](https://forgemia.inra.fr/metexplore/met4j/-/commits/ci_coverage2)
[![coverage report](https://forgemia.inra.fr/metexplore/met4j/badges/ci_coverage2/coverage.svg)](https://forgemia.inra.fr/metexplore/met4j/-/commits/ci_coverage2)
### Modules
Met4j is composed by several maven modules:
......
coverage/pom.xml 0 → 100644
View file @ 222f30a5
<?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
met4j-chemUtils/pom.xml
View file @ 222f30a5
<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>
met4j-core/pom.xml
View file @ 222f30a5
<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>
met4j-graph/pom.xml
View file @ 222f30a5
<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>${java.home}/bin/javadoc</javadocExecutable>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
<executions>
<!-- create report during maven verify phase -->
<execution>
<id>attach-sources</id>
<id>report</id>
<phase>verify</phase>
<goals>
<goal>jar</goal>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<id>release-sign-artifacts</id>
<activation>
<property>
<name>performRelease</name>
<value>true</value>
</property>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>-->
</project>
met4j-io/pom.xml
View file @ 222f30a5
<?xml version="1.0"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
......@@ -20,47 +21,6 @@
<maven.compiler.target>11</maven.compiler.target>
</properties>
<!-- <build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
<configuration>
<javadocExecutable>${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>