resolve merge conflicts

Author: baltzell

.codecov.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"

.github/dependabot.yml

@@ -16,34 +16,57 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    shell: bash
+
+env:
+  java_version: 11
+  java_distribution: zulu
+  groovy_version: 4.0.3
+
 jobs:
 
+  # build
+  #############################################################################
+
   build:
     strategy:
       fail-fast: true
       matrix:
         runner:
           - ubuntu-latest
           - macos-latest
-    outputs:
-      default_runner: ubuntu-latest
     runs-on: ${{ matrix.runner }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
-          java-version: 11
-          distribution: zulu
+          java-version: ${{ env.java_version }}
+          distribution: ${{ env.java_distribution }}
       - name: build
-        run: ./build-coatjava.sh --spotbugs --unittests --quiet
+        run: ./build-coatjava.sh --spotbugs --unittests --quiet -T4
       - name: tar # tarball to preserve permissions
         run: tar czvf coatjava.tar.gz coatjava
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: build_${{ matrix.runner }}
           retention-days: 1
           path: coatjava.tar.gz
+      - name: collect jacoco report
+        if: ${{ matrix.runner == 'ubuntu-latest' }}
+        run: validation/jacoco-aggregate.sh
+      - name: publish jacoco report
+        if: ${{ matrix.runner == 'ubuntu-latest' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: jacoco_report
+          path: publish/
+          retention-days: 1
+
+  # tests
+  #############################################################################
 
   test_coatjava:
     needs: [ build ]
@@ -71,13 +94,13 @@ jobs:
           - { runner: macos-latest, id: eb-ep, cmd: ./run-eb-tests.sh -100 electronproton }
     runs-on: ${{ matrix.runner }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
-          java-version: 11
-          distribution: zulu
-      - uses: actions/download-artifact@v3
+          java-version: ${{ env.java_version }}
+          distribution: ${{ env.java_distribution }}
+      - uses: actions/download-artifact@v4
         with:
           name: build_${{ matrix.runner }}
       - name: untar build
@@ -90,21 +113,21 @@ jobs:
 
   test_run-groovy:
     needs: [ build ]
-    runs-on: ${{ needs.build.outputs.default_runner }}
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up JDK
-        uses: actions/setup-java@v3
+        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@v1
+        uses: wtfjoke/setup-groovy@v2
         with:
-          groovy-version: 4.x
-      - uses: actions/download-artifact@v3
+          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
@@ -115,7 +138,68 @@ 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.ref == 'refs/heads/development' }}
+    needs: collect_webpages
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: deployment
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/maven.yml

@@ -7,10 +7,6 @@ on:
     tags: [ '*' ]
   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
-  cancel-in-progress: true
-
 jobs:
   validation:
     uses: JeffersonLab/clas12-validation/.github/workflows/ci.yml@main

.github/workflows/validation.yml

@@ -2,6 +2,7 @@
 /coatjava
 /myLocalMvnRepo
 target
+/publish
 
 *.class
 *lundfiles*.dat
@@ -36,4 +37,4 @@ hs_err_pid*
 *.evio 
 
 bin/evio2hipotest
-export.sh
+export.sh

.gitignore

@@ -43,6 +43,7 @@ Nathan Baltzell <[email protected]> <[email protected]>
 Nathan Baltzell <[email protected]> <[email protected]>
 Nathan Baltzell <[email protected]> <[email protected]>
 Nathan Baltzell <[email protected]> <[email protected]>
+Nathan Baltzell <[email protected]> <[email protected]>
 Nathan Harrison <[email protected]> <[email protected]>
 Nathan Harrison <[email protected]> <[email protected]>
 Nick Markov <[email protected]>

.mailmap

@@ -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)
-[![codecov](https://codecov.io/gh/JeffersonLab/coatjava/branch/development/graph/badge.svg?precision=2)](https://codecov.io/gh/JeffersonLab/coatjava/branch/development)
+[![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

README.md

@@ -1,7 +1,6 @@
 #!/bin/bash
 
-thisEnv=${BASH_SOURCE[0]:-$0}
-CLAS12DIR=$(cd $(dirname $thisEnv)/.. && pwd -P)
+CLAS12DIR=$(cd $(dirname ${BASH_SOURCE[0]:-$0})/.. && pwd -P)
 export CLAS12DIR
 
 # Set default field maps (but do not override user's env):
@@ -26,6 +25,7 @@ if [ $# -ge 1 ]; then
         JYPATH="${JYPATH:+${JYPATH}:}${jars}"
       done
     done
+    unset lib jars
 
     # additional variables and settings for groovy
     if [ "$1" = "groovy" ]; then

bin/env.sh

@@ -4,33 +4,28 @@ set -e
 set -u
 set -o pipefail
 
-usage='build-coatjava.sh [-h] [--quiet] [--spotbugs] [--nomaps] [--unittests]'
+usage='''build-coatjava.sh [-h] [--help] [--quiet] [--spotbugs] [--nomaps] [--unittests]
+ - all other arguments will be passed to `mvn`, e.g., -T4 will build with 4 parallel threads'''
 
 quiet="no"
 runSpotBugs="no"
 downloadMaps="yes"
 runUnitTests="no"
+mvnArgs=()
 for xx in $@
 do
-    if [ "$xx" == "--spotbugs" ]
-    then
-        runSpotBugs="yes"
-    elif [ "$xx" == "-n" ]
-    then
-        runSpotBugs="no"
-    elif [ "$xx" == "--nomaps" ]
-    then
-        downloadMaps="no"
-    elif [ "$xx" == "--unittests" ]
-    then
-        runUnitTests="yes"
-    elif [ "$xx" == "--quiet" ]
-    then
-        quiet="yes"
-    else
-        echo "$usage"
-        exit 2
-    fi
+  case $xx in
+    --spotbugs)  runSpotBugs="yes"  ;;
+    -n)          runSpotBugs="no"   ;;
+    --nomaps)    downloadMaps="no"  ;;
+    --unittests) runUnitTests="yes" ;;
+    --quiet)     quiet="yes"        ;;
+    -h|--help)
+      echo "$usage"
+      exit 2
+      ;;
+    *) mvnArgs+=($xx) ;;
+  esac
 done
 
 top="$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)"
@@ -42,6 +37,7 @@ then
     wget='wget --progress=dot:mega'
     mvn="mvn -q -B --settings $top/maven-settings.xml"
 fi
+mvn+=" ${mvnArgs[*]:-}"
 
 command_exists () {
     type "$1" &> /dev/null
@@ -96,13 +92,12 @@ cp -r etc coatjava/
 which python3 >& /dev/null && python=python3 || python=python
 $python etc/bankdefs/util/bankSplit.py coatjava/etc/bankdefs/hipo4 || exit 1
 mkdir -p coatjava/lib/clas
-#cp external-dependencies/JEventViewer-1.1.jar coatjava/lib/clas/
-#cp external-dependencies/vecmath-1.3.1-2.jar coatjava/lib/clas/
 mkdir -p coatjava/lib/utils
-cp external-dependencies/jclara-4.3-SNAPSHOT.jar coatjava/lib/utils
-#cp external-dependencies/jaw-1.0.jar coatjava/lib/utils
 mkdir -p coatjava/lib/services
 
+# FIXME:  this is still needed by one of the tests
+cp external-dependencies/jclara-4.3-SNAPSHOT.jar coatjava/lib/utils
+
 ### clean up any cache copies ###
 cd common-tools/coat-lib; $mvn clean; cd -