Merge pull request #2 from HenriquesLab/AM_current

Major refactor
HenriquesLab · Feb 10, 2025 · d6db25b · d6db25b
2 parents 4cf8323 + 737382d
commit d6db25b
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Showing 59 changed files with 11,466 additions and 5,934 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,6 +10,13 @@ jobs:
         packages: write
 
     steps:
+      - name: Set up Xvfb
+        run: |
+          apt-get update
+          apt-get install -y xvfb
+          Xvfb :99 -screen 0 1024x768x24 &
+          export DISPLAY=:99
+
       - uses: actions/checkout@v4
       - name: Set up Java
         uses: actions/setup-java@v4

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -8,8 +8,8 @@ on:
       # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#onpushpull_requestpull_request_targetpathspaths-ignore
       - "src/**"
       - "pom.xml"
-    pull_request:
-        branches: ["main"]
+    # pull_request:
+    #     branches: ["main"]
     workflow_dispatch:
         inputs:
             logLevel:
@@ -24,12 +24,18 @@ on:
 
 jobs:
   test:
-    runs-on: [self-hosted, Ubuntu]
+    runs-on: [self-hosted, Linux-wheels]
     permissions:
         contents: read
         packages: write
 
     steps:
+      - name: Set up Xvfb
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y xvfb libxrender1
+          Xvfb :99 -screen 0 1024x768x24 &
+          export DISPLAY=:99
       - uses: actions/checkout@v4
       - name: Set up Java
         uses: actions/setup-java@v4
@@ -39,7 +45,9 @@ jobs:
           cache: 'maven'
 
       - name: Install Maven
-        run: apt-get update; apt-get install maven -y
+        run: sudo apt-get update; sudo apt-get install maven -y
 
       - name: Build with Maven
-        run: mvn clean validate compile test test-compile --file pom.xml
+        run: mvn clean validate compile test test-compile --file pom.xml
+        env:
+          DISPLAY: :99
diff --git a/pom.xml b/pom.xml
@@ -85,31 +85,47 @@
         <dependency>
             <groupId>net.imagej</groupId>
             <artifactId>ij</artifactId>
+            <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>net.imagej</groupId>
             <artifactId>imagej-common</artifactId>
+            <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.jogamp.jocl</groupId>
             <artifactId>jocl-main</artifactId>
-            <version>2.3.2</version>
+            <version>2.5.0</version>
+            <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.jogamp.gluegen</groupId>
             <artifactId>gluegen-rt-main</artifactId>
-            <version>2.3.2</version>
+            <version>2.5.0</version>
+            <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-math3</artifactId>
             <version>3.6.1</version>
+            <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-api</artifactId>
-            <version>5.10.0</version> <!-- Or the latest stable version -->
-            <scope>test</scope>
+            <version>5.10.0</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.10.0</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-math3</artifactId>
+            <version>3.6.1</version>
         </dependency>
     </dependencies>