From 334c7ae77d47cdf8a9b797e23493283c1b84546c Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 02:10:56 +0100
Subject: [PATCH 01/10] Remove compiled java

---
 ijplugin/.project                              |  17 -----------------
 ijplugin/ImageDecorrelationAnalysis_plugin.jar | Bin 22700 -> 0 bytes
 2 files changed, 17 deletions(-)
 delete mode 100644 ijplugin/.project
 delete mode 100644 ijplugin/ImageDecorrelationAnalysis_plugin.jar

diff --git a/ijplugin/.project b/ijplugin/.project
deleted file mode 100644
index 7c8be12..0000000
--- a/ijplugin/.project
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>ImDecorrAnalysis</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-	</natures>
-</projectDescription>
diff --git a/ijplugin/ImageDecorrelationAnalysis_plugin.jar b/ijplugin/ImageDecorrelationAnalysis_plugin.jar
deleted file mode 100644
index 796d36685177c64e746a80000e557b265a8afe2c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 59052cdd4b215bc90a617ede72e523262599522e Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 02:11:32 +0100
Subject: [PATCH 02/10] Move java files

---
 .../src/{ => main/java/imdecorr}/ImageDecorrelationAnalysis.java  | 0
 .../src/{ => main/java/imdecorr}/ImageDecorrelationAnalysis_.java | 0
 ijplugin/src/{ => main/java/imdecorr}/output.java                 | 0
 ijplugin/src/{ => main/java/imdecorr}/utils.java                  | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename ijplugin/src/{ => main/java/imdecorr}/ImageDecorrelationAnalysis.java (100%)
 rename ijplugin/src/{ => main/java/imdecorr}/ImageDecorrelationAnalysis_.java (100%)
 rename ijplugin/src/{ => main/java/imdecorr}/output.java (100%)
 rename ijplugin/src/{ => main/java/imdecorr}/utils.java (100%)

diff --git a/ijplugin/src/ImageDecorrelationAnalysis.java b/ijplugin/src/main/java/imdecorr/ImageDecorrelationAnalysis.java
similarity index 100%
rename from ijplugin/src/ImageDecorrelationAnalysis.java
rename to ijplugin/src/main/java/imdecorr/ImageDecorrelationAnalysis.java
diff --git a/ijplugin/src/ImageDecorrelationAnalysis_.java b/ijplugin/src/main/java/imdecorr/ImageDecorrelationAnalysis_.java
similarity index 100%
rename from ijplugin/src/ImageDecorrelationAnalysis_.java
rename to ijplugin/src/main/java/imdecorr/ImageDecorrelationAnalysis_.java
diff --git a/ijplugin/src/output.java b/ijplugin/src/main/java/imdecorr/output.java
similarity index 100%
rename from ijplugin/src/output.java
rename to ijplugin/src/main/java/imdecorr/output.java
diff --git a/ijplugin/src/utils.java b/ijplugin/src/main/java/imdecorr/utils.java
similarity index 100%
rename from ijplugin/src/utils.java
rename to ijplugin/src/main/java/imdecorr/utils.java

From 25ce14d9e0b25f0fc50e0a586d272e4ab067a874 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 02:51:48 +0100
Subject: [PATCH 03/10] Add Maven project file

---
 ijplugin/pom.xml | 89 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 ijplugin/pom.xml

diff --git a/ijplugin/pom.xml b/ijplugin/pom.xml
new file mode 100644
index 0000000..0197936
--- /dev/null
+++ b/ijplugin/pom.xml
@@ -0,0 +1,89 @@
+<?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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	
+	<groupId>org.springframeworkTODO</groupId>
+	<artifactId>ImageDecorrelationAnalysis</artifactId>
+	<packaging>jar</packaging>
+	<version>1.1.8</version>
+
+	<name>Image Decorrelation Analysis</name>
+	<description>Image Decorrelation Analysis plugin for ImageJ.</description>
+	<url>https://github.com/4ever2/ImDecorr</url>
+
+	<licenses>
+		<license>
+			<name>GNU General Public License v3</name>
+			<url>https://www.gnu.org/licenses/gpl.html</url>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+
+	<developers>
+		<developer>
+			<id>0000-0002-3101-6641</id>
+			<name>Adrien Descloux</name>
+			<email>adrien.descloux@epfl.ch</email>
+			<organization>École Polytechnique Fédérale de Lausanne</organization>
+			<roles>
+				<role>author</role>
+			</roles>
+		</developer>
+		<developer>
+			<id>0000-0003-4515-4356</id>
+			<name>Kristin Grußmayer</name>
+			<organization>École Polytechnique Fédérale de Lausanne</organization>
+			<roles>
+				<role>author</role>
+			</roles>
+		</developer>
+		<developer>
+			<id>0000-0001-8194-2785</id>
+			<name>Aleksandra Radenovic</name>
+			<email>aleksandra.radenovic@epfl.ch</email>
+			<organization>École Polytechnique Fédérale de Lausanne</organization>
+			<roles>
+				<role>author</role>
+			</roles>
+		</developer>
+	</developers>
+	<contributors>
+		<contributor>
+			<name>4ever2</name>
+			<url>https://github.com/4ever2</url>
+			<organization>Aarhus University</organization>
+			<roles><role>maintainer</role></roles>
+			<properties><id>4ever2</id></properties>
+		</contributor>
+	</contributors>
+
+	<issueManagement>
+		<system>GitHub</system>
+		<url>https://github.com/4ever2/ImDecorr/issues/</url>
+	</issueManagement>
+	<ciManagement>
+		<system>GitHub Actions</system>
+		<url>https://github.com/4ever2/ImDecorr/actions</url>
+	</ciManagement>
+	<scm>
+		<connection>scm:git:https://github.com/4ever2/ImDecorr</connection>
+		<developerConnection>scm:git:git@github.com:4ever2/ImDecorr</developerConnection>
+		<tag>HEAD</tag>
+		<url>https://github.com/4ever2/ImDecorr</url>
+	</scm>
+
+	<dependencies>
+		<!-- ImageJ dependencies -->
+		<dependency>
+			<groupId>net.imagej</groupId>
+			<artifactId>ij</artifactId>
+		</dependency>
+	</dependencies>
+
+	<properties>
+		<license.licenseName>gpl_v3</license.licenseName>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
+	</properties>
+</project>
\ No newline at end of file

From 4fb4ac377b6f227684ed4d7181d0066f92881884 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:00:19 +0100
Subject: [PATCH 04/10] Add build CI workflow for ImageJ plugin

---
 .github/workflows/build-java.yml | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 .github/workflows/build-java.yml

diff --git a/.github/workflows/build-java.yml b/.github/workflows/build-java.yml
new file mode 100644
index 0000000..4efd83a
--- /dev/null
+++ b/.github/workflows/build-java.yml
@@ -0,0 +1,27 @@
+name: 'Build ImageJ Plugin'
+on:
+  push:
+    branches:
+    - 'master'
+    paths:
+    - 'ijplugin/**/*'
+  pull_request:
+    paths:
+    - 'ijplugin/**/*'
+permissions:
+  contents: 'read'
+env:
+  THREADS: 2
+jobs:
+  build:
+    runs-on: 'ubuntu-latest'
+    steps:
+      - name: 'Checkout branch ${{ github.ref_name }}'
+        uses: actions/checkout@v4
+      - name: Set up JDK 11 for x64
+        uses: actions/setup-java@v3
+        with:
+          java-version: '8'
+          distribution: 'zulu'
+      - name: Build
+        run: cd ijplugin && mvn package

From bb8c8c1f50a119f261672e327f547ef0fde2a70e Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:17:27 +0100
Subject: [PATCH 05/10] Specifiy ImageJ library version

---
 ijplugin/pom.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ijplugin/pom.xml b/ijplugin/pom.xml
index 0197936..9909aaf 100644
--- a/ijplugin/pom.xml
+++ b/ijplugin/pom.xml
@@ -3,7 +3,7 @@
 	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>
 	
-	<groupId>org.springframeworkTODO</groupId>
+	<groupId>com.github.4ever2</groupId>
 	<artifactId>ImageDecorrelationAnalysis</artifactId>
 	<packaging>jar</packaging>
 	<version>1.1.8</version>
@@ -78,6 +78,7 @@
 		<dependency>
 			<groupId>net.imagej</groupId>
 			<artifactId>ij</artifactId>
+			<version>1.53t</version>
 		</dependency>
 	</dependencies>
 

From 0a6fda213117fe06db7f5df24e207461d7e2fac6 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:20:10 +0100
Subject: [PATCH 06/10] Cache maven dependencies

---
 .github/workflows/build-java.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build-java.yml b/.github/workflows/build-java.yml
index 4efd83a..0a43d87 100644
--- a/.github/workflows/build-java.yml
+++ b/.github/workflows/build-java.yml
@@ -23,5 +23,6 @@ jobs:
         with:
           java-version: '8'
           distribution: 'zulu'
+          cache: maven
       - name: Build
         run: cd ijplugin && mvn package

From 78bcd2b498808fc7c4fa209d2e368be8c3ee4092 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:24:26 +0100
Subject: [PATCH 07/10] Upload jar artifact

---
 .github/workflows/build-java.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-java.yml b/.github/workflows/build-java.yml
index 0a43d87..182f58e 100644
--- a/.github/workflows/build-java.yml
+++ b/.github/workflows/build-java.yml
@@ -16,7 +16,7 @@ jobs:
   build:
     runs-on: 'ubuntu-latest'
     steps:
-      - name: 'Checkout branch ${{ github.ref_name }}'
+      - name: Checkout branch ${{ github.ref_name }}
         uses: actions/checkout@v4
       - name: Set up JDK 11 for x64
         uses: actions/setup-java@v3
@@ -26,3 +26,10 @@ jobs:
           cache: maven
       - name: Build
         run: cd ijplugin && mvn package
+      - name: Prepare artifact
+        run: mkdir staging && cp ijplugin/target/*.jar staging
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: ImageDecorrelationAnalysis.jar
+          path: staging/*.jar

From dab591bce3aa6f05434481dd4cf5d13c81cf40f3 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:33:32 +0100
Subject: [PATCH 08/10] Set 1 week rention period for java artifacts

---
 .github/workflows/build-java.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-java.yml b/.github/workflows/build-java.yml
index 182f58e..06381f5 100644
--- a/.github/workflows/build-java.yml
+++ b/.github/workflows/build-java.yml
@@ -31,5 +31,6 @@ jobs:
       - name: Upload artifact
         uses: actions/upload-artifact@v3
         with:
-          name: ImageDecorrelationAnalysis.jar
+          name: Package
           path: staging/*.jar
+          retention-days: 7

From 442b5b85b73a4ef03d03f1200a6f247eddc2f153 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:36:58 +0100
Subject: [PATCH 09/10] Enable dependabot for github actions and maven

---
 .github/dependabot.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..344883a
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,14 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    labels:
+      - "part: dependencies"
+  - package-ecosystem: maven
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
\ No newline at end of file

From 24b0a05be28f26a2f8f8930e87e1fd40c9f7e325 Mon Sep 17 00:00:00 2001
From: 4ever2 <3417013+4ever2@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:46:52 +0100
Subject: [PATCH 10/10] Build and publish jar when version tag is pushed

---
 .github/workflows/build-java.yml   |  2 --
 .github/workflows/publish-java.yml | 23 +++++++++++++++++++++++
 ijplugin/pom.xml                   |  8 ++++++++
 3 files changed, 31 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/publish-java.yml

diff --git a/.github/workflows/build-java.yml b/.github/workflows/build-java.yml
index 06381f5..939e0d2 100644
--- a/.github/workflows/build-java.yml
+++ b/.github/workflows/build-java.yml
@@ -10,8 +10,6 @@ on:
     - 'ijplugin/**/*'
 permissions:
   contents: 'read'
-env:
-  THREADS: 2
 jobs:
   build:
     runs-on: 'ubuntu-latest'
diff --git a/.github/workflows/publish-java.yml b/.github/workflows/publish-java.yml
new file mode 100644
index 0000000..081fa63
--- /dev/null
+++ b/.github/workflows/publish-java.yml
@@ -0,0 +1,23 @@
+name: Publish package to GitHub Packages
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+permissions:
+  contents: 'read'
+jobs:
+  build:
+    runs-on: 'ubuntu-latest'
+    steps:
+      - name: Checkout branch ${{ github.ref_name }}
+        uses: actions/checkout@v4
+      - name: Set up JDK 11 for x64
+        uses: actions/setup-java@v3
+        with:
+          java-version: '8'
+          distribution: 'zulu'
+          cache: maven
+      - name: Publish package
+        run: mvn deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/ijplugin/pom.xml b/ijplugin/pom.xml
index 9909aaf..eeb07f4 100644
--- a/ijplugin/pom.xml
+++ b/ijplugin/pom.xml
@@ -87,4 +87,12 @@
 		<maven.compiler.source>1.8</maven.compiler.source>
 		<maven.compiler.target>1.8</maven.compiler.target>
 	</properties>
+
+	<distributionManagement>
+		<repository>
+		<id>github</id>
+		<name>GitHub Packages</name>
+		<url>https://maven.pkg.github.com/4ever2/ImDecorr</url>
+		</repository>
+	</distributionManagement>
 </project>
\ No newline at end of file