Merge branch 'development' into recoil_detector

.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 

.github/dependabot.yml

@@ -1,9 +1,21 @@
 version: 2
+
+registries:
+  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
   - package-ecosystem: "github-actions"

.github/workflows/maven.yml

@@ -23,7 +23,7 @@ defaults:
 env:
   java_version: 17
   java_distribution: zulu
-  groovy_version: 4.0.3
+  groovy_version: 4.x
 
 jobs:
 
@@ -133,11 +133,28 @@ jobs:
       - name: test run-groovy
         run: coatjava/bin/run-groovy validation/advanced-tests/test-run-groovy.groovy
 
+  release:
+    needs: [ build ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: build_ubuntu-latest
+      - name: Release
+        uses: softprops/action-gh-release@v2
+        if: startsWith(github.ref, 'refs/tags/')
+        with:
+          files: coatjava.tar.gz
+        env:
+          GITHUB_TOKEN:  ${{ secrets.GITHUB_TOKEN }}
+
   final:
     needs:
       - build
       - test_coatjava
       - test_run-groovy
+      - release
     runs-on: ubuntu-latest
     steps:
       - name: pass

.github/workflows/validation.yml

@@ -10,3 +10,17 @@ on:
 jobs:
   validation:
     uses: JeffersonLab/clas12-validation/.github/workflows/ci.yml@main
+    with:
+      matrix_evgen: >-
+        [
+          "e_p",
+          "e_n",
+          "e_g",
+          "e_pC",
+          "eFT_K",
+          "e_gFT"
+        ]
+      matrix_config: >-
+        [
+          "rgb_fall2019"
+        ]

.gitlab-ci.yml

@@ -0,0 +1,40 @@
+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
+
+shared_for_alert_tests:
+  needs: ["coatjava_build"]
+  variables:
+    REF_NAME: "$CI_COMMIT_REF_NAME"
+  trigger:
+    project: hallb/alert/atof/shared_for_alert
+    strategy: depend
+

bin/hipo-multi-merge

@@ -0,0 +1,107 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'ostruct'
+require 'fileutils'
+
+def print_log(name, val)
+  puts name.rjust(30) + " = #{val}"
+end
+
+# user options
+@args = OpenStruct.new
+@args.inputs     = nil
+@args.output_dir = nil
+@args.prefix     = nil
+@args.num_merge  = nil
+@args.use_batch  = false
+@args.dry_run    = false
+OptionParser.new do |o|
+  o.banner = '''
+  This tool merges a set of input HIPO files to a set of output HIPO files,
+  where you may control the number of input files per output file; for example,
+  use this tool if you have 1000 small HIPO files but would rather have 10
+  large HIPO files.
+  '''
+  o.separator "USAGE: #{$0} [OPTIONS]..."
+  o.separator ''
+  o.separator 'REQUIRED OPTIONS:'
+  o.on('-i', '--input INPUTS', 'input directory or file glob;', 'surround file glob in quotes') { |a| @args.inputs = a }
+  o.on('-o', '--output OUTPUT_DIR', 'output directory') { |a| @args.output_dir = a }
+  o.on('-p', '--prefix OUTPUT_PREFIX', 'output filename prefix; names will be:', ' [OUTPUT_DIR]/[OUTPUT_PREFIX]_#####.hipo') { |a| @args.prefix = a }
+  o.on('-n', '--num NUM_FILES', 'number of files per output merged file') { |a| @args.num_merge = a.to_i }
+  o.separator ''
+  o.separator 'OPTIONAL OPTIONS:'
+  o.on('-b', '--batch', 'submit jobs to Slurm', '(default is sequential jobs)') { |a| @args.use_batch = true }
+  o.on('-d', '--dry-run', 'just print what would be done') { |a| @args.dry_run = true }
+  o.on_tail('-h', '--help', 'show this message') do
+    puts o
+    exit
+  end
+end.parse! ARGV.empty? ? ['--help'] : ARGV
+
+# check required options
+if [@args.inputs, @args.output_dir, @args.prefix, @args.num_merge].include? nil
+  raise 'missing required option(s;) re-run with "--help" for guidance.'
+end
+raise 'option "--num" must be greater than zero' unless @args.num_merge > 0
+
+# glob inputs
+input_glob = File.expand_path @args.inputs
+input_glob = File.join input_glob, "*.hipo" if File.directory? input_glob
+print_log 'input glob', input_glob
+print_log 'output dir', @args.output_dir
+print_log 'output prefix', @args.prefix
+print_log 'num files per output', @args.num_merge
+
+# chunks
+input_files = Dir.glob input_glob
+raise "no input files found with glob '#{input_glob}'" if input_files.empty?
+input_chunks = input_files.each_slice(@args.num_merge).to_a
+print_log 'num input files', input_files.size
+print_log 'num output files', input_chunks.size
+raise 'option "--num" >= num input files, therefore there is nothing to do' if input_chunks.size == 1
+
+# build commands
+puts "="*82
+merge_cmds = input_chunks.each_with_index.map do |input_chunk, chunk_num|
+  out_name = File.join @args.output_dir, "#{@args.prefix}_#{chunk_num.to_s.rjust(5, '0')}.hipo"
+  raise "output file #{out_name} already exists; cannot overwrite! delete it or choose another path/name" if File.exist? out_name
+  [ 'hipo-utils', '-merge', '-o', out_name, *input_chunk ].join ' '
+end
+
+# sbatch commands
+if @args.use_batch
+  sbatch_args = {
+    'job-name'      => "hipo_multi_merge___#{@args.prefix}",
+    'account'       => 'clas12',
+    'partition'     => 'production',
+    'mem-per-cpu'   => 500,
+    'time'          => '1:00:00',
+    'ntasks'        => 1,
+    'cpus-per-task' => 1,
+  }.map{ |opt, val| "--#{opt}=#{val.to_s}" }
+  exe_cmds = merge_cmds.each_with_index.map do |merge_cmd, job_num|
+    log_name = "/farm_out/%u/%x_#{job_num.to_s.rjust(5, '0')}"
+    [
+      'sbatch',
+      *sbatch_args,
+      "--output=#{log_name}.out",
+      "--error=#{log_name}.err",
+      "--wrap='#{merge_cmd}'",
+    ].join ' '
+  end
+else
+  exe_cmds = merge_cmds
+end
+
+# execute
+if @args.dry_run
+  puts 'THIS IS JUST A DRY RUN. Here are the commands which would be executed:'
+  puts "="*82
+  puts "mkdir -p #{@args.output_dir}"
+  exe_cmds.each do |cmd| puts cmd end
+else
+  FileUtils.mkdir_p @args.output_dir
+  exe_cmds.each do |cmd| system cmd end
+end