Merge branch 'development' into iss269-htccClusterPass2

JeffersonLab · Dec 5, 2024 · 9064c5d · 9064c5d
2 parents 580229e + 8e265ae
commit 9064c5d
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diff --git a/.containers/coatjava.Dockerfile b/.containers/coatjava.Dockerfile
@@ -0,0 +1,25 @@
+#syntax=docker/dockerfile:1
+
+FROM ubuntu:noble
+
+LABEL name="coatjava"
+LABEL maintainer="Whitney Armstrong <[email protected]>"
+LABEL architecture="amd64"
+
+USER root
+
+
+RUN apt update && apt upgrade -y
+RUN apt install cmake vim maven groovy git ca-certificates wget curl python-is-python3 \
+                openjdk-17-jdk openjdk-17-jre openjdk-17-jdk-headless openjdk-17-jre-headless \
+                python3-sqlalchemy -y && update-ca-certificates
+
+# CA certificates
+ADD https://pki.jlab.org/JLabCA.crt /etc/ssl/certs/JLabCA.crt 
+#RUN trust anchor --store /image/JLabCA.crt
+
+ARG REF_NAME=development 
+# build coatjava 
+RUN java --version && cd /opt && \
+    git clone https://code.jlab.org/hallb/alert/coatjava.git && cd coatjava && \
+    git fetch origin && git checkout ${REF_NAME} && ./build-coatjava.sh --nomaps
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: "maven"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "org.jlab:groot" # since version numbers are not in order
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -16,6 +16,15 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    shell: bash
+
+env:
+  java_version: 17
+  java_distribution: zulu
+  groovy_version: 4.0.3
+
 jobs:
 
   # build
@@ -28,16 +37,14 @@ jobs:
         runner:
           - ubuntu-latest
           - macos-latest
-    outputs:
-      default_runner: ubuntu-latest
     runs-on: ${{ matrix.runner }}
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 11
-          distribution: zulu
+          java-version: ${{ env.java_version }}
+          distribution: ${{ env.java_distribution }}
       - name: build
         run: ./build-coatjava.sh --spotbugs --unittests --quiet -T4
       - name: tar # tarball to preserve permissions
@@ -52,8 +59,9 @@ jobs:
         run: validation/jacoco-aggregate.sh
       - name: publish jacoco report
         if: ${{ matrix.runner == 'ubuntu-latest' }}
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
+          name: jacoco_report
           path: publish/
           retention-days: 1
 
@@ -90,8 +98,8 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 11
-          distribution: zulu
+          java-version: ${{ env.java_version }}
+          distribution: ${{ env.java_distribution }}
       - uses: actions/download-artifact@v4
         with:
           name: build_${{ matrix.runner }}
@@ -105,21 +113,21 @@ jobs:
 
   test_run-groovy:
     needs: [ build ]
-    runs-on: ${{ needs.build.outputs.default_runner }}
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: 11
-          distribution: zulu
+          java-version: ${{ env.java_version }}
+          distribution: ${{ env.java_distribution }}
       - name: setup groovy
         uses: wtfjoke/setup-groovy@v2
         with:
-          groovy-version: 4.x
+          groovy-version: ${{ env.groovy_version }}
       - uses: actions/download-artifact@v4
         with:
-          name: build_${{ needs.build.outputs.default_runner }}
+          name: build_ubuntu-latest
       - name: untar build
         run: tar xzvf coatjava.tar.gz
       - name: test run-groovy
@@ -130,17 +138,60 @@ jobs:
       - build
       - test_coatjava
       - test_run-groovy
-    runs-on: ${{ needs.build.outputs.default_runner }}
+    runs-on: ubuntu-latest
     steps:
       - name: pass
         run: exit 0
 
+  # generate documentation
+  #############################################################################
+
+  generate_documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{ env.java_version }}
+          distribution: ${{ env.java_distribution }}
+      - name: build
+        run: ./build-coatjava.sh
+      - name: generate documentation
+        run: ./build-javadocs.sh
+      - uses: actions/upload-artifact@v4
+        with:
+          name: javadoc
+          path: docs/javadoc/
+          retention-days: 1
+
   # deploy web pages
   #############################################################################
 
+  collect_webpages:
+    if: ${{ github.ref == 'refs/heads/development' }}
+    needs: [ build, generate_documentation ]
+    runs-on: ubuntu-latest
+    steps:
+      - name: download jacoco report
+        uses: actions/download-artifact@v4
+        with:
+          name: jacoco_report
+          path: pages/jacoco
+      - name: download javadoc documentation
+        uses: actions/download-artifact@v4
+        with:
+          name: javadoc
+          path: pages/javadoc
+      - run: tree pages
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          retention-days: 1
+          path: pages/
+
   deploy_web_pages:
-    if: ${{ github.event_name == 'push' }}
-    needs: build
+    if: ${{ github.ref == 'refs/heads/development' }}
+    needs: collect_webpages
     permissions:
       pages: write
       id-token: write

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,31 @@
+workflow:
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+    - if: '$CI_PIPELINE_SOURCE == "web"'
+    - if: '$CI_PIPELINE_SOURCE == "webide"'
+    - if: '$CI_COMMIT_BRANCH == "master"'
+    - if: '$CI_COMMIT_BRANCH == "development"'
+    - if: '$CI_COMMIT_TAG'
+
+default:
+  image: ubuntu:noble
+  retry: 2
+
+coatjava_build:
+  image: gcr.io/kaniko-project/executor:debug
+  script:
+    - echo "${CI_COMMIT_REF_NAME}"
+    - >-
+      /kaniko/executor
+      --context     $CI_PROJECT_DIR/docker
+      --dockerfile  $CI_PROJECT_DIR/.containers/coatjava.Dockerfile
+      --destination $CI_REGISTRY_IMAGE/coatjava:${CI_COMMIT_REF_NAME}
+      --build-arg REF_NAME=${CI_COMMIT_REF_NAME}
+    
+alert_testing:
+  needs: ["coatjava_build"]
+  variables:
+    REF_NAME: "$CI_COMMIT_REF_NAME"
+  trigger:
+    project: hallb/alert/c12
+    strategy: depend
diff --git a/README.md b/README.md
@@ -1,7 +1,11 @@
 # COATJAVA
 [![Build Status](https://github.com/jeffersonlab/coatjava/workflows/Coatjava-CI/badge.svg)](https://github.com/jeffersonlab/coatjava/actions)
 [![Validation Status](https://github.com/JeffersonLab/coatjava/actions/workflows/validation.yml/badge.svg)](https://github.com/JeffersonLab/coatjava/actions/workflows/validation.yml)
-[![Coverage](https://badgen.net/static/JaCoCo/coverage/purple)](https://jeffersonlab.github.io/coatjava)
+[![Coverage](https://badgen.net/static/JaCoCo/coverage/purple)](https://jeffersonlab.github.io/coatjava/jacoco)
+
+- [API Documentation (Javadoc)](https://jeffersonlab.github.io/coatjava/javadoc)
+
+----
 
 The original repository for COATJAVA was named "clas12-offline-software" and is [now archived and read-only](https://github.com/JeffersonLab/clas12-offline-software).  On May 17, 2023, this new repository was created by running BFG Repo Cleaner to get rid of old, large data files and things that should never have been in the repository, giving 10x reduction in repository size, clone time, etc, and renamed `coatjava`.  The most critical, GitHub-specific aspects have been transferred to this new repository:
 
@@ -27,8 +31,6 @@ For anything more, see the "General Developer Documentation" link on that softwa
 
 The [troubleshooting](https://github.com/JeffersonLab/clas12-offline-software/wiki/Troubleshooting) wiki page may also still be useful but likely outdated.
 
-<!--Javadocs can be found at the repository's [gh-page](https://jeffersonlab.github.io/clas12-offline-software/). A build history can be found at [Travis CI](https://travis-ci.org/JeffersonLab/clas12-offline-software).-->
-
 <!--
 ## Repository Structure and Dependency Management
 ### Common Tools

diff --git a/bin/bg-merger b/bin/bg-merger
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/bos2hipo b/bin/bos2hipo
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -Xms1024m -XX:+UseSerialGC \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" \

diff --git a/bin/cvt-compare b/bin/cvt-compare
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/daqEventViewer b/bin/daqEventViewer
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -Xms1024m \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/services/*:$CLAS12DIR/lib/utils/*" \

diff --git a/bin/dclayereffs-ana b/bin/dclayereffs-ana
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -Dsun.java2d.pmoffscreen=false -Xmx2048m -Xms1024m \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/utils/*:$CLAS12DIR/lib/services/*" \

diff --git a/bin/decoder b/bin/decoder
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/dict-generator b/bin/dict-generator
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/dict-maker b/bin/dict-maker
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/dict-merger b/bin/dict-merger
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/dict-validator b/bin/dict-validator
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/evio-viewer b/bin/evio-viewer
@@ -1,5 +1,5 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -cp "$CLAS12DIR/lib/clas/*" org.jlab.coda.eventViewer.EventTreeFrame $*
diff --git a/bin/evio2hipo b/bin/evio2hipo
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/eviocure b/bin/eviocure
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/eviodump b/bin/eviodump
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -Xms1024m \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" \

diff --git a/bin/hipo-add b/bin/hipo-add
diff --git a/bin/hipo-browser b/bin/hipo-browser
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -Xms1024m \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" \

diff --git a/bin/hipo-diff b/bin/hipo-diff
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 export MALLOC_ARENA_MAX=1
 

diff --git a/bin/hipo-json b/bin/hipo-json
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-. `dirname $0`/env.sh 
+. `dirname $0`/../libexec/env.sh
 
 java -Xms1024m \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" \