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Remove everything icy related to make Clij3 compile #64

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merged 5 commits into from
Sep 12, 2024
Merged

Remove everything icy related to make Clij3 compile #64

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3b7ff0d
remove everything icy related
carlosuc3m Sep 11, 2024
be0b1d6
change to stable version 0.12.1
carlosuc3m Sep 11, 2024
cb83f38
reuse forks for testing
carlosuc3m Sep 11, 2024
4b000b7
do not redirect test output and do not reuse forks
carlosuc3m Sep 11, 2024
f195def
try to increase memory for the tests
carlosuc3m Sep 11, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@


lib/
libs/
native/cppbuild

# from CLIJ2
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2 changes: 1 addition & 1 deletion native/clesperantoj/CMakeLists.txt
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Expand Up @@ -22,7 +22,7 @@ set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON) # Export all symbols for shared library
option(BUILD_TESTING OFF)
option(BUILD_BENCHMARK OFF)
option(BUILD_SHARED_LIBS ON)
set(CLIC_REPO_TAG master) # branch name for dev
set(CLIC_REPO_TAG 0.12.1) # branch name for dev
set(CLIC_REPO_URL https://github.com/clEsperanto/CLIc_prototype.git)
add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/clic)

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128 changes: 92 additions & 36 deletions pom.xml
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@@ -1,23 +1,20 @@
<?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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<parent>
<groupId>net.haesleinhuepf</groupId>
<artifactId>clij-parent-pom</artifactId>
<version>2.2.0.14</version>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>38.0.1</version>
<relativePath />
</parent>

<groupId>net.clesperanto</groupId>
<artifactId>clesperantoj_</artifactId>
<version>0.0.0.1</version>
<artifactId>clesperantoj</artifactId>
<version>0.0.1-SNAPSHOT</version>

<name>clesperantoj_</name>
<description>clesperantoj</description>
<name>clesperantoj</name>
<description>Java wrapper for Clesperanto</description>
<url>http://haesleinhuepf.net</url>
<inceptionYear>2022</inceptionYear>
<organization>
Expand All @@ -26,22 +23,57 @@
</organization>
<licenses>
<license>
<name>Simplified BSD License</name>
<name>BSD 3-Clause License</name>
<url>https://opensource.org/license/bsd-3-clause</url>
<distribution>repo</distribution>
</license>
</licenses>

<developers>
<developer>
<id>haesleinhuepf</id>
<name>Robert Haase`</name>
<name>Robert Haase</name>
<url>http://haesleinhuepf.net</url>
<organization>PoL TUD</organization>
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<id>StRigaud</id>
<name>Stephane Rigaud</name>
<url>https://github.com/StRigaud</url>
<organization>Institut Pasteur</organization>
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<id>carlosuc3m</id>
<name>Carlos Javier Garcia Lopez de Haro</name>
<url>https://github.com/carlosuc3m</url>
<roles>
<role>developer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>Robert Haase</name>
<url>http://haesleinhuepf.net</url>
<properties><id>haesleinhuepf</id></properties>
</contributor>
<contributor>
<name>Stephane Rigaud</name>
<url>https://github.com/StRigaud</url>
<properties><id>StRigaud</id></properties>
</contributor>
<contributor>
<name>Carlos Javier Garcia Lopez de Haro</name>
<url>https://github.com/carlosuc3m</url>
<properties><id>carlosuc3m</id></properties>
</contributor>
</contributors>

<mailingLists>
<mailingList>
Expand All @@ -50,15 +82,29 @@
</mailingList>
</mailingLists>

<scm>
<connection>scm:git:https://github.com/clEsperanto/clesperantoj_prototype</connection>
<developerConnection>scm:git:[email protected]:clEsperanto/clesperantoj_prototype</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/clEsperanto/clesperantoj_prototype</url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github.com/clEsperanto/clesperantoj_prototype/issues</url>
</issueManagement>
<ciManagement>
<system>GitHub Actions</system>
<url>https://github.com/clEsperanto/clesperantoj_prototype/actions</url>
</ciManagement>

<properties>
<package-name>net.haesleinhuepf</package-name>
<package-name>net.clesperanto</package-name>
<license.licenseName>bsd_3</license.licenseName>
<license.copyrightOwners>Robert Haase, MPI CBG</license.copyrightOwners>
<!-- <scijava.app.directory>/PATH/TO/YOUR/FIJI/Fiji.app/</scijava.app.directory> -->
<scijava.app.directory>/home/stephane/Libraries/Fiji.app/</scijava.app.directory>
<!-- specify your cuda version (for windows users) -->
<cuda.version>11.2</cuda.version>
<license.copyrightOwners>Robert Haase, MPI CBG and Stephane Rigaud, Institut Pasteur</license.copyrightOwners>
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
</properties>

<profiles>
<profile>
<id>win</id>
Expand Down Expand Up @@ -102,11 +148,6 @@


<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>icy-kernel</artifactId>
<version>2.5.1</version>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
Expand All @@ -121,6 +162,7 @@
<dependency>
<groupId>org.bytedeco</groupId>
<artifactId>javacpp</artifactId>
<!-- TODO check if we can work with the scijava pom version -->
<version>1.5.10</version>
</dependency>
<dependency>
Expand All @@ -130,13 +172,11 @@
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.7.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>5.7.0</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand All @@ -146,10 +186,6 @@
<id>scijava.public</id>
<url>https://maven.scijava.org/content/groups/public</url>
</repository>
<repository>
<id>icy</id>
<url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
</repository>
</repositories>

<build>
Expand Down Expand Up @@ -177,7 +213,7 @@
<!-- Execute cppbuild.sh to build cleperantoj a wrapper to clesperato.hpp -->
<plugin>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
<!-- TODO remove <version>1.6.0</version> -->
<groupId>org.codehaus.mojo</groupId>
<executions>
<execution>
Expand All @@ -197,7 +233,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.3.0</version>
<!-- TODO remove <version>3.3.0</version> -->
<executions>
<execution>
<id>add-source</id>
Expand All @@ -215,7 +251,7 @@
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.12.1</version>
<!-- TODO remove <version>3.12.1</version> -->
<configuration>
<source>1.8</source>
<target>1.8</target>
Expand Down Expand Up @@ -309,14 +345,34 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.2</version>
<!-- TODO remove <version>2.22.2</version> -->
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
<forkCount>1</forkCount>
<reuseForks>false</reuseForks>
<argLine>-Xmx1024m</argLine>
</configuration>
</plugin>

<plugin>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>copy</id>
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.basedir}/target/classes/net/clesperanto</outputDirectory>
<resources>
<resource>
<directory>${project.basedir}/libs</directory>
<filtering>false</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

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