Deploy to scijava

.github/build.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-build.sh
+sh ci-build.sh

.github/setup.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/main/ci-setup-github-actions.sh
+sh ci-setup-github-actions.sh

.github/workflows/build.yaml

@@ -1,85 +1,164 @@
+---
 name: build
-
 on:
   push:
-    branches: [ main ]
+    branches:
+      - main
+      - deploy-to-scijava
+    tags:
+      - "*-[0-9]+.*"
+    paths-ignore:
+      - .github/workflows/build_fast.yaml
   pull_request:
-    branches: [ main ]
-
-
+    branches:
+      - main
 env:
-  opencl-icd-loader-git-tag: "v2023.04.17"
-  opencl-headers-git-tag: "v2023.04.17"
-
+  opencl-icd-loader-git-tag: v2023.04.17
+  opencl-headers-git-tag: v2023.04.17
 jobs:
-  build:
+  build-os:
     strategy:
       fail-fast: false
       matrix:
-        name: [ubuntu, windows, macos]
+        name:
+          - ubuntu
+          - windows
+          - macos
         include:
           - name: ubuntu
             os: ubuntu-latest
-            c-compiler: "gcc"
-            cxx-compiler: "g++"
-            cmake-build-type: "Release"
+            c-compiler: gcc
+            cxx-compiler: g++
+            cmake-build-type: Release
             cmake-build-flag: ""
           - name: windows
             os: windows-latest
-            c-compiler: "cl.exe"
-            cxx-compiler: "cl.exe"
-            cmake-build-type: "Release"
-            cmake-build-flag: "-A x64"
+            c-compiler: cl.exe
+            cxx-compiler: cl.exe
+            cmake-build-type: Release
+            cmake-build-flag: -A x64
           - name: macos
-            os: macos-13
-            c-compiler: "clang"
-            cxx-compiler: "clang++"
-            cmake-build-type: "Release"
+            os: macos-14
+            c-compiler: clang
+            cxx-compiler: clang++
+            cmake-build-type: Release
             cmake-build-flag: ""
     runs-on: ${{ matrix.os }}
-
     steps:
-    - uses: actions/checkout@v2
-    - uses: ilammy/msvc-dev-cmd@v1
+      - uses: actions/checkout@v4
+      - uses: ilammy/msvc-dev-cmd@v1
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: "11"
+          distribution: adopt
+      - name: Install ocl-icd-loader - windows
+        if: runner.os == 'Windows'
+        run: |
+          cd ..
 
-    - name: Set up JDK
-      uses: actions/setup-java@v2
-      with:
-        java-version: '11'
-        distribution: 'adopt'
+          git clone --branch ${{ env.opencl-icd-loader-git-tag }} https://github.com/KhronosGroup/OpenCL-ICD-Loader
 
-    - name: Install ocl-icd-loader - windows
-      if: runner.os == 'Windows'
-      run: |
-        cd ..
-        git clone --branch ${{ env.opencl-icd-loader-git-tag }} https://github.com/KhronosGroup/OpenCL-ICD-Loader
-        git clone --branch ${{ env.opencl-headers-git-tag }} https://github.com/KhronosGroup/OpenCL-Headers
-        cmake -S "./OpenCL-Headers" -B "./OpenCL-Headers/build"
-        cmake --build "./OpenCL-Headers/build" --parallel 6 --target install
-        cmake -D CMAKE_PREFIX_PATH="./OpenCL-Headers" -D OPENCL_ICD_LOADER_HEADERS_DIR="./OpenCL-Headers/" -S "./OpenCL-ICD-Loader" -B "./OpenCL-ICD-Loader/build" -A x64
-        cmake --build "./OpenCL-ICD-Loader/build" --parallel 6 --target install --config Release
-      shell: bash -l {0}
+          git clone --branch ${{ env.opencl-headers-git-tag }} https://github.com/KhronosGroup/OpenCL-Headers
+
+          cmake -S "./OpenCL-Headers" -B "./OpenCL-Headers/build"
+
+          cmake --build "./OpenCL-Headers/build" --parallel 6 --target install
+
+          cmake -D CMAKE_PREFIX_PATH="./OpenCL-Headers" -D OPENCL_ICD_LOADER_HEADERS_DIR="./OpenCL-Headers/" -S "./OpenCL-ICD-Loader" -B "./OpenCL-ICD-Loader/build" -A x64
+
+          cmake --build "./OpenCL-ICD-Loader/build" --parallel 6 --target install --config Release
+        shell: bash -l {0}
+      - name: Increase swapfile on Ubuntu
+        if: runner.os == 'Linux'
+        run: |
+          sudo swapoff -a
+          sudo fallocate -l 15G /swapfile
+          sudo chmod 600 /swapfile
+          sudo mkswap /swapfile
+          sudo swapon /swapfile
+          sudo swapon --show
+      - name: Install openCL on Ubuntu
+        if: runner.os == 'Linux'
+        run: sudo apt install ocl-icd-opencl-dev
+      - name: Build with Maven
+        run: mvn clean install -DskipTests
+        shell: bash
+      - name: Run Java class (only possible on MacOS intel)
+        if: contains(matrix.os, 'macos')
+        run: >
+          if [[ $(uname -m) == 'x86_64' ]]; then
+            mvn dependency:build-classpath -Dmdep.outputFile=classpath.txt
+            java -cp target/classes:$(cat classpath.txt) net.clesperanto.ClesperantoJ
+          fi
+      - name: Get Maven Version and Upload Artifact
+        shell: bash
+        run: |
+          MVN_VERSION=$(mvn -q \
+            -Dexec.executable=echo \
+            -Dexec.args='${project.version}' \
+            --non-recursive \
+            exec:exec)
+          MVN_NAME=$(mvn -q \
+            -Dexec.executable=echo \
+            -Dexec.args='${project.name}' \
+            --non-recursive \
+            exec:exec)
+          echo "version=${MVN_VERSION}" >> $GITHUB_OUTPUT
+          echo "name=${MVN_NAME}" >> $GITHUB_OUTPUT
+        id: mvn_info
+      - name: Upload native library
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.name }}-artifact
+          path: target/${{steps.mvn_info.outputs.name}}-${{steps.mvn_info.outputs.version}}.jar
+  build:
+    needs: build-os
+    runs-on: macos-13
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 8
+        uses: actions/setup-java@v4
+        with:
+          java-version: "8"
+          distribution: zulu
+          cache: maven
+      - name: Download all platform-specific JAR files
+        uses: actions/download-artifact@v4
+      - name: Get Maven Version
+        run: |
+          MVN_VERSION=$(mvn -q \
+            -Dexec.executable=echo \
+            -Dexec.args='${project.version}' \
+            --non-recursive \
+            exec:exec)
+          MVN_NAME=$(mvn -q \
+            -Dexec.executable=echo \
+            -Dexec.args='${project.name}' \
+            --non-recursive \
+            exec:exec)
+          echo "version=${MVN_VERSION}" >> $GITHUB_OUTPUT
+          echo "name=${MVN_NAME}" >> $GITHUB_OUTPUT
+        id: mvn_info
+      - name: Extract compiled native libraries to target fodler libs
+        run: |
+          jar xf ubuntu-artifact/${{steps.mvn_info.outputs.name}}-${{steps.mvn_info.outputs.version}}.jar net/clesperanto/linux-x86_64
 
-    - name: Increase swapfile on Ubuntu
-      if: runner.os == 'Linux'
-      run: |
-        sudo swapoff -a
-        sudo fallocate -l 15G /swapfile
-        sudo chmod 600 /swapfile
-        sudo mkswap /swapfile
-        sudo swapon /swapfile
-        sudo swapon --show
+          jar xf windows-artifact/${{steps.mvn_info.outputs.name}}-${{steps.mvn_info.outputs.version}}.jar net/clesperanto/windows-x86_64
 
-    - name: Install openCL on Ubuntu
-      if: runner.os == 'Linux'
-      run: sudo apt install ocl-icd-opencl-dev
+          jar xf macos-artifact/${{steps.mvn_info.outputs.name}}-${{steps.mvn_info.outputs.version}}.jar net/clesperanto/macosx-arm64
 
-    - name: Build with Maven
-      run:  mvn clean install -DskipTests
-      shell: bash
+          mkdir -p libs
 
-    - name: Run Java class (only possible on MacOS)
-      if: contains(matrix.os, 'macos')
-      run: |
-        mvn dependency:build-classpath -Dmdep.outputFile=classpath.txt
-        java -cp target/classes:$(cat classpath.txt) net.clesperanto.ClesperantoJ
+          mv net/clesperanto/* libs/
+      - name: Set up CI environment
+        run: .github/setup.sh
+      - name: Execute the build
+        run: .github/build.sh
+        env:
+          GPG_KEY_NAME: ${{ secrets.GPG_KEY_NAME }}
+          GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
+          MAVEN_USER: ${{ secrets.MAVEN_USER }}
+          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+          OSSRH_PASS: ${{ secrets.OSSRH_PASS }}
+          SIGNING_ASC: ${{ secrets.SIGNING_ASC }}

.github/workflows/build_fast.yaml

@@ -0,0 +1,44 @@
+name: build fast
+on:
+  push:
+    branches:
+      - main
+      - deploy-to-scijava
+    tags:
+      - "*-[0-9]+.*"
+  pull_request:
+    branches:
+      - main
+env:
+  opencl-icd-loader-git-tag: v2023.04.17
+  opencl-headers-git-tag: v2023.04.17
+jobs:
+  build:
+    runs-on: macos-13
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 8
+        uses: actions/setup-java@v4
+        with:
+          java-version: "8"
+          distribution: zulu
+          cache: maven
+      - name: Check secrets are set
+        run: |
+          if [ -z "$GPG_KEY_NAME" ]; then echo "GPG_KEY_NAME is not set"; fi
+          if [ -z "$GPG_PASSPHRASE" ]; then echo "GPG_PASSPHRASE is not set"; fi
+          if [ -z "$MAVEN_USER" ]; then echo "MAVEN_USER is not set"; fi
+          if [ -z "$MAVEN_PASS" ]; then echo "MAVEN_PASS is not set"; fi
+          if [ -z "$OSSRH_PASS" ]; then echo "OSSRH_PASS is not set"; fi
+          if [ -z "$SIGNING_ASC" ]; then echo "SIGNING_ASC is not set"; fi
+      - name: Set up CI environment
+        run: .github/setup.sh
+      - name: Execute the build
+        run: .github/build.sh
+        env:
+          GPG_KEY_NAME: ${{ secrets.GPG_KEY_NAME }}
+          GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
+          MAVEN_USER: ${{ secrets.MAVEN_USER }}
+          MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+          OSSRH_PASS: ${{ secrets.OSSRH_PASS }}
+          SIGNING_ASC: ${{ secrets.SIGNING_ASC }}

.github/workflows/test.yaml

@@ -1,6 +1,10 @@
 name: ClesperantoJ tests
 
-on: [push]
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
 
 jobs:
   test:

LICENSE.txt

@@ -0,0 +1,27 @@
+Copyright 2024 Stéphane Rigaud, Robert Haase, Institut Pasteur Paris, Max Planck Institute for Molecular Cell Biology and Genetics Dresden, ScaDS.AI, Leipzig University
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

pom.xml

@@ -106,7 +106,6 @@
 		<url>https://github.com/clEsperanto/clesperantoj_prototype/actions</url>
 	</ciManagement>
 
-
 
     <profiles>
         <profile>

src/main/java/net/clesperanto/ClesperantoJ.java

@@ -1,3 +1,36 @@
+
+/*
+ * Copyright 2024 Stéphane Rigaud, Robert Haase, Institut Pasteur Paris,
+ * Max Planck Institute for Molecular Cell Biology and Genetics Dresden,
+ * ScaDS.AI, Leipzig University
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * 3. Neither the name of the copyright holder nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package net.clesperanto;
 
 import net.clesperanto.core.*;

src/main/java/net/clesperanto/ImagePlusClesperantoJExample.java

@@ -1,3 +1,35 @@
+/*
+ * Copyright 2024 Stéphane Rigaud, Robert Haase, Institut Pasteur Paris,
+ * Max Planck Institute for Molecular Cell Biology and Genetics Dresden,
+ * ScaDS.AI, Leipzig University
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * 3. Neither the name of the copyright holder nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package net.clesperanto;
 
 import ij.IJ;