dc1 redux

.containers/coatjava.Dockerfile

@@ -22,4 +22,5 @@ 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 --quiet
+    git fetch origin && git checkout ${REF_NAME} && ./build-coatjava.sh --quiet && \
+    ./install-clara /opt/clara

.containers/coatjava.def

@@ -0,0 +1,14 @@
+Bootstrap: docker
+From: codecr.jlab.org/hallb/alert/coatjava/coatjava:{{ REF_NAME }}
+
+
+%environment
+    export CLAS12DIR=/opt/coatjava/coatjava
+
+%help
+    This is a clas12 coatjava container used to run coatjava on HPC systems
+    and do rapid development.
+
+%labels
+    Author Whitney Armstrong warmstrong@anl.gov
+    REF_NAME {{ REF_NAME }}

.github/workflows/maven.yml → .github/workflows/ci.yml

@@ -23,7 +23,9 @@ defaults:
 env:
   java_version: 17
   java_distribution: zulu
+  javadoc_version: 24 # 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'
 
 jobs:
 
@@ -40,11 +42,17 @@ jobs:
     runs-on: ${{ matrix.runner }}
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK
-        uses: actions/setup-java@v4
+      - uses: actions/setup-java@v4
         with:
           java-version: ${{ env.java_version }}
           distribution: ${{ env.java_distribution }}
+      - uses: cvmfs-contrib/github-action-cvmfs@v5
+        with:
+          cvmfs_repositories: 'oasis.opensciencegrid.org'
+      - name: cvmfs
+        run: ls /cvmfs/oasis.opensciencegrid.org/jlab/hallb/clas12/sw/noarch/data/ccdb/ccdb_latest.sqlite
+      - name: echo CCDB_CONNECTION
+        run: echo $CCDB_CONNECTION
       - name: build
         run: ./build-coatjava.sh --spotbugs --unittests --quiet -T4
       - name: tar # tarball to preserve permissions
@@ -103,8 +111,13 @@ jobs:
       - uses: actions/download-artifact@v4
         with:
           name: build_${{ matrix.runner }}
+      - uses: cvmfs-contrib/github-action-cvmfs@v5
+        with:
+          cvmfs_repositories: 'oasis.opensciencegrid.org'
       - name: untar build
         run: tar xzvf coatjava.tar.gz
+      - name: echo CCDB_CONNECTION
+        run: echo $CCDB_CONNECTION
       - name: run test
         run: |
           cd validation/advanced-tests
@@ -160,55 +173,46 @@ jobs:
       - name: pass
         run: exit 0
 
-  # generate documentation
+  # documentation
   #############################################################################
 
   generate_documentation:
     runs-on: ubuntu-latest
+    needs: [ build ]
     steps:
+      ### mkdocs
       - 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
+      - name: install mkdocs dependencies
+        run: python -m pip install -r docs/mkdocs/requirements.txt
+      - name: generate mkdocs
+        run: docs/mkdocs/generate.sh pages
+      ### jacoco
+      - name: download jacoco report artifact
         uses: actions/download-artifact@v4
         with:
           name: jacoco_report
           path: pages/jacoco
-      - name: download javadoc documentation
-        uses: actions/download-artifact@v4
+      ### javadoc
+      - name: set up JDK
+        uses: actions/setup-java@v4
         with:
-          name: javadoc
-          path: pages/javadoc
-      - run: tree pages
+          java-version: ${{ env.javadoc_version }}
+          distribution: ${{ env.java_distribution }}
+      - name: build coatjava
+        run: ./build-coatjava.sh
+      - name: generate javadoc documentation
+        run: |
+          ./build-javadocs.sh
+          mv docs/javadoc pages/
+      ### upload artifacts
       - uses: actions/upload-pages-artifact@v3
         with:
-          retention-days: 1
+          retention-days: 7
           path: pages/
 
   deploy_web_pages:
     if: ${{ github.ref == 'refs/heads/development' }}
-    needs: collect_webpages
+    needs: [ generate_documentation ]
     permissions:
       pages: write
       id-token: write

.gitignore

@@ -32,6 +32,12 @@ hs_err_pid*
 *.iml
 .idea
 
+# eclipse JDT language server
+.classpath
+.factorypath
+.project
+.settings
+
 # no log files:
 *.log
 *.evio 

.gitlab-ci.yml

@@ -9,6 +9,7 @@ workflow:
 
 variables:
   KUBERNETES_MEMORY_LIMIT: "8Gi"
+  REF_NAME: ${CI_COMMIT_REF_NAME}
 
 default:
   image: ubuntu:noble
@@ -69,3 +70,34 @@ shared_for_alert_tests:
     project: hallb/alert/atof/shared_for_alert
     strategy: depend
 
+coatjava:singularity:
+  image: eicweb.phy.anl.gov:4567/containers/image_recipes/ubuntu_dind:latest
+  needs: ["coatjava_build"]
+  tags:
+     - silicon
+  allow_failure: true
+  script:
+    - apptainer build  --build-arg REF_NAME=${REF_NAME} coatjava.sif .containers/coatjava.def
+    - ls -lrth
+  artifacts:
+      paths:
+        - coatjava.sif
+
+create-pages:
+  image: codecr.jlab.org/hallb/alert/coatjava/coatjava:development
+  script:
+    - export MAVEN_OPTS=" -Dfile.encoding=UTF-8"
+    - echo "${CI_COMMIT_REF_NAME}"
+    - ls -lrth
+    - mvn --version
+    - java --version 
+    - ls -lrth
+    - pwd
+    - ls -lrth docs/javadoc
+    - ./build-javadocs.sh 
+    - ls -lrth
+    - ls -lrth docs/
+    - ls -lrth docs/javadoc
+    - mv docs/javadoc public
+  pages: true  # specifies that this is a Pages job and publishes the default public directory
+

README.md

@@ -3,6 +3,7 @@
 [![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/jacoco)
 
+- [**Documentation Homepage**](https://jeffersonlab.github.io/coatjava)
 - [API Documentation (Javadoc)](https://jeffersonlab.github.io/coatjava/javadoc)
 
 ----
@@ -58,3 +59,6 @@ http://stackoverflow.com/questions/600079/how-do-i-clone-a-subdirectory-only-of-
 
 -->
 
+
+[Coatjava Apptainer](https://code.jlab.org/hallb/alert/coatjava/-/jobs/artifacts/development/raw/coatjava.sif?job=coatjava%3Asingularity)
+

bin/hipo-multi-merge

@@ -8,6 +8,8 @@ def print_log(name, val)
   puts name.rjust(30) + " = #{val}"
 end
 
+SlurmMemReq = 2048 + 200 # `-Xmx` argument from `hipo-utils`, plus extra padding
+
 # user options
 @args = OpenStruct.new
 @args.inputs     = nil
@@ -76,7 +78,7 @@ if @args.use_batch
     'job-name'      => "hipo_multi_merge___#{@args.prefix}",
     'account'       => 'clas12',
     'partition'     => 'production',
-    'mem-per-cpu'   => 500,
+    'mem-per-cpu'   => SlurmMemReq,
     'time'          => '1:00:00',
     'ntasks'        => 1,
     'cpus-per-task' => 1,

bin/recon-util

@@ -2,9 +2,12 @@
 
 . `dirname $0`/../libexec/env.sh
 
+split_cli $@
+
 export MALLOC_ARENA_MAX=1
 
-java -Xmx1536m -Xms1024m -XX:+UseSerialGC \
+java -Xmx1536m -Xms1024m -XX:+UseSerialGC ${jvm_options[@]} \
     -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/services/*:$CLAS12DIR/lib/utils/*" \
     org.jlab.clas.reco.EngineProcessor \
-    $*
+    ${class_options[@]}
+

build-javadocs.sh

@@ -5,8 +5,10 @@
 
 set -e
 
+export MAVEN_OPTS=" -Dfile.encoding=UTF-8"
+
 ##### generate documentation
-mvn javadoc:javadoc -Ddoclint=none
+mvn javadoc:javadoc -Ddoclint=none 
 
 
 ##### collect documentation

common-tools/clara-io/pom.xml

@@ -3,14 +3,14 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clara-io</artifactId>
-  <version>11.1.2-SNAPSHOT</version>
+  <version>12.0.6t-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.1.2-SNAPSHOT</version>
+    <version>12.0.6t-SNAPSHOT</version>
   </parent>
 
   <dependencies>
@@ -61,7 +61,7 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-text</artifactId>
-      <version>1.13.0</version>
+      <version>1.13.1</version>
     </dependency>
 
   </dependencies>

common-tools/clas-analysis/pom.xml

@@ -3,63 +3,63 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-analysis</artifactId>
-  <version>11.1.2-SNAPSHOT</version>
+  <version>12.0.6t-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.1.2-SNAPSHOT</version>
+    <version>12.0.6t-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-physics</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-jcsg</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>swim-tools</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-detector</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-reco</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.6t-SNAPSHOT</version>
     </dependency>
   </dependencies>