Sync fork on november 24, 2025

.github/dependabot.yml

@@ -1,21 +1,18 @@
 version: 2
 
-registries:
-  clas12maven:
-    type: maven-repository
-    url: https://clasweb.jlab.org/clas12maven
-  jhep:
-    type: maven-repository
-    url: https://clasweb.jlab.org/jhep/maven
+# registries: FIXME: disabled, see <https://github.com/JeffersonLab/coatjava/issues/915>
+#   clas12maven:
+#     type: maven-repository
+#     url: https://clasweb.jlab.org/.clas12maven
+#   jhep:
+#     type: maven-repository
+#     url: https://clasweb.jlab.org/.jhep/maven
 
 updates:
   - package-ecosystem: "maven"
     directory: "/"
     schedule:
       interval: "weekly"
-    registries:
-      - clas12maven
-      - jhep
     ignore:
       - dependency-name: "org.jlab:groot" # since version numbers are not in order
       - dependency-name: "org.ejml:ejml-simple" # keep version the same as `j4ml:j4ml-clas12:jar:0.9-SNAPSHOT`; see pull requests #636 and #632

.github/workflows/ci.yml

@@ -21,8 +21,10 @@ defaults:
     shell: bash
 
 env:
-  java_version: 25
+  JAVA_VERSION: 21 # must be consistent with POM; see also dependabot config for any version limits
+  JAVA_VERSION_LATEST: 25 # the latest `JAVA_VERSION` that we test with CI
   java_distribution: zulu
+  javadoc_version: 25 # newer than `JAVA_VERSION` for better javadoc
   groovy_version: 4.x
   CCDB_CONNECTION: 'sqlite:////cvmfs/oasis.opensciencegrid.org/jlab/hallb/clas12/sw/noarch/data/ccdb/ccdb_latest.sqlite'
   nthreads: 1
@@ -40,8 +42,6 @@ jobs:
         with:
           key: raw_test_data # fixed key will always hit; clear cache to trigger cache miss
           path: |
-            clas_005038.evio.00000
-            clas_021559.evio.00001
             clas_018779.evio.00001
           lookup-only: true
       - name: install xrootd-client
@@ -51,10 +51,12 @@ jobs:
           sudo apt -y install xrootd-client
       - name: download
         if: ${{ steps.cache.outputs.cache-hit != 'true' }}
+#        run: |
+#          xrdcp xroot://sci-xrootd.jlab.org///osgpool/hallb/clas12/validation/raw/rg-d/clas_018779.evio.00001 ./
         run: |
-          xrdcp xroot://sci-xrootd.jlab.org///osgpool/hallb/clas12/validation/clas_005038.evio.00000 ./
-          xrdcp xroot://sci-xrootd.jlab.org///osgpool/hallb/clas12/validation/raw/rg-l/clas_021559.evio.00001 ./
-          xrdcp xroot://sci-xrootd.jlab.org///osgpool/hallb/clas12/validation/raw/rg-d/clas_018779.evio.00001 ./
+          git lfs install
+          git clone --depth 1 https://code.jlab.org/hallb/clas12/validation-data
+          cp validation-data/raw/rg-d/clas_018779.evio.00001 .
 
   # build
   #############################################################################
@@ -71,17 +73,9 @@ jobs:
       - uses: actions/checkout@v5
       - uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
-      - name: install xrootd-client (linux)
-        if: ${{ matrix.runner == 'ubuntu-latest' }}
-        run: |
-          sudo apt -y update
-          sudo apt -y install xrootd-client
-      - name: install xrootd-client (macos)
-        if: ${{ matrix.runner == 'macos-latest' }}
-        run: brew install xrootd
       - name: setup cvmfs
         uses: cvmfs-contrib/github-action-cvmfs@v5
         with:
@@ -92,7 +86,11 @@ jobs:
         if: ${{ github.ref_type == 'tag' }}
         run: libexec/version-bump.sh ${{ github.ref_name }}
       - name: build
-        run: ./build-coatjava.sh --clara --xrootd --no-progress -T${{ env.nthreads }}
+        run: |
+          git lfs install
+          git submodule update --init ./etc/data/magfield
+          ./build-coatjava.sh --cvmfs --no-progress -T${{ env.nthreads }}
+          ./install-clara -b -c ./coatjava ./clara  
       - name: tar # tarball to preserve permissions
         run: |
           tar czvf coatjava.tar.gz coatjava
@@ -108,27 +106,40 @@ jobs:
   # tests
   #############################################################################
 
+  java_matrix: # make JSON job matrix, to workaround GitHub's lack of `env` var support in job matrix params
+    runs-on: ubuntu-latest
+    outputs:
+      versions: ${{ steps.matrix.outputs.versions }}
+    steps:
+      - name: matrix
+        id: matrix
+        run: echo versions="[\"${{ env.JAVA_VERSION }}\",\"${{ env.JAVA_VERSION_LATEST }}\"]" | tee -a $GITHUB_OUTPUT
+
   unit_tests:
+    needs:
+      - java_matrix
+    strategy:
+      fail-fast: false
+      matrix:
+        JAVA_VERSION: ${{ fromJson(needs.java_matrix.outputs.versions) }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
       - uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ matrix.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
-      - name: install xrootd-client
-        run: |
-          sudo apt -y update
-          sudo apt -y install xrootd-client
       - uses: cvmfs-contrib/github-action-cvmfs@v5
         with:
           cvmfs_repositories: 'oasis.opensciencegrid.org'
       - name: unit tests
-        run: ./build-coatjava.sh --xrootd --unittests --no-progress -T${{ env.nthreads }}
+        run: ./build-coatjava.sh --cvmfs --unittests --no-progress -T${{ env.nthreads }}
       - name: collect jacoco report
+        if: ${{ matrix.JAVA_VERSION == env.JAVA_VERSION }}
         run: validation/jacoco-aggregate.sh
       - name: publish jacoco report
+        if: ${{ matrix.JAVA_VERSION == env.JAVA_VERSION }}
         uses: actions/upload-artifact@v5
         with:
           name: jacoco_report
@@ -143,7 +154,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - uses: cvmfs-contrib/github-action-cvmfs@v5
@@ -165,32 +176,26 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - uses: cvmfs-contrib/github-action-cvmfs@v5
         with:
           cvmfs_repositories: 'oasis.opensciencegrid.org'
-      - name: install xrootd-client
-        run: |
-          sudo apt -y update
-          sudo apt -y install xrootd-client
       - uses: actions/download-artifact@v6
         with:
           name: build_ubuntu-latest
       - uses: actions/cache/restore@v4
         with:
           key: raw_test_data
           path: |
-            clas_005038.evio.00000
-            clas_021559.evio.00001
             clas_018779.evio.00001
       - name: untar build
         run: tar xzvf coatjava.tar.gz
       - name: run test
         run: |
           ls -lhtr
-          ./coatjava/bin/decoder -n 10000 -o dog.hipo ./clas_005038.evio.00000
+          ./coatjava/bin/decoder -n 10000 -o dog.hipo ./clas_018779.evio.00001
 
   test_clara:
     needs: [ build, download_test_data ]
@@ -202,7 +207,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - name: setup cvmfs
@@ -216,8 +221,6 @@ jobs:
         with:
           key: raw_test_data
           path: |
-            clas_005038.evio.00000
-            clas_021559.evio.00001
             clas_018779.evio.00001
       - name: untar build
         run: |
@@ -258,7 +261,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - uses: actions/download-artifact@v6
@@ -268,9 +271,13 @@ jobs:
         with:
           cvmfs_repositories: 'oasis.opensciencegrid.org'
       - name: untar build
-        run: tar xzvf coatjava.tar.gz
+        run: |
+          tar xzvf coatjava.tar.gz
+          tar xzvf clara.tar.gz
       - name: run test
         run: |
+          git lfs install
+          git submodule update --init validation/advanced-tests/data
           cd validation/advanced-tests
           echo "COMMAND: ${{ matrix.cmd }}"
           ${{ matrix.cmd }}
@@ -283,7 +290,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - name: setup groovy
@@ -306,7 +313,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.JAVA_VERSION }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - uses: actions/download-artifact@v6
@@ -342,7 +349,7 @@ jobs:
       - name: set up JDK
         uses: actions/setup-java@v5
         with:
-          java-version: ${{ env.java_version }}
+          java-version: ${{ env.javadoc_version }}
           distribution: ${{ env.java_distribution }}
           cache: maven
       - name: build coatjava javadocs # javadoc:aggregate output dir cannot be controlled, so assume the latest "standard" path and `mv` it