Jenkinsfile

#!/usr/bin/env groovy

// Continuous Integration script for Clinica
// www.clinica.run
// Author: mauricio.diaz@inria.fr

pipeline {
  agent none
    stages {
      stage('Build Env') {
        parallel {
          stage('Build in Linux') {
            agent { label 'ubuntu' }
            environment {
              PATH = "$HOME/miniconda/bin:$PATH"
              }
            when { changeset "environment.yml" }
            steps {
              echo 'Building Conda environment... ${BRANCH_NAME}'
              sh 'ls'
              sh 'conda env create --force --file environment.yml -n clinica_env_${BRANCH_NAME}'
            }
          }
          stage('Build in Mac') {
            agent { label 'macos' }
            environment {
              PATH = "$HOME/miniconda3/bin:$PATH"
              }
            when { changeset "environment.yml" }
            steps {
              echo 'Building Conda environment...' + 'env.BRANCH_NAME'
              sh 'ls'
              sh 'conda env create --force --file environment.yml -n clinica_env_${BRANCH_NAME}'
            }
          }
        }
      }
      stage('Install') {
        parallel {
          stage('Launch in Linux') {
            agent { label 'ubuntu' }
            environment {
              PATH = "$HOME/miniconda/bin:$PATH"
              }
            steps {
            echo 'Installing Clinica sources in Linux...'
            echo 'My branch name is ${BRANCH_NAME}'
            sh 'echo "My branch name is ${BRANCH_NAME}"'
            sh 'printenv'
            sh 'echo "Agent name: ${NODE_NAME}"'
            script {
              echo "My conda env name is clinica_env_${BRANCH_NAME}"
              }
            sh '''
               set +x
               ./.jenkins/scripts/find_env.sh
               conda info --envs
               eval "$(conda shell.bash hook)"
               conda activate clinica_env_$BRANCH_NAME
               echo "Install clinica using pip..."
               pip install --ignore-installed .
               eval "$(register-python-argcomplete clinica)"
               # Show clinica help message
               echo "Display clinica help message"
               clinica --help
               conda deactivate
               '''
            }
          }
          stage('Launch in MacOS') {
            agent { label 'macos' }
            environment {
              PATH = "$HOME/miniconda3/bin:$PATH"
              }
            steps {
            echo 'Installing Clinica sources in MacOS...'
            sh 'echo "Agent name: ${NODE_NAME}"'
            sh '''
               set +x
               ./.jenkins/scripts/find_env.sh
               eval "$(conda shell.bash hook)"
               conda activate clinica_env_$BRANCH_NAME
               echo "Install clinica using pip..."
               pip install --ignore-installed .
               eval "$(register-python-argcomplete clinica)"
               # Show clinica help message
               echo "Display clinica help message"
               clinica --help
               conda deactivate
            '''
            }
          }
        }
      }
      stage('Short Tests') {
        parallel {
          stage('Instantiate Linux') {
            agent { label 'ubuntu' }
            environment {
              PATH = "$HOME/miniconda/bin:/usr/local/Modules/bin:$PATH"
              CLINICA_ENV_BRANCH = "clinica_env_$BRANCH_NAME"
              WORK_DIR_LINUX = "/mnt/data/ci/working_dir_linux"
              }
            steps {
              echo 'Testing pipeline instantation...'
              sh 'echo "Agent name: ${NODE_NAME}"'
              sh '''
                 set +x
                 ./.jenkins/scripts/find_env.sh
                 eval "$(conda shell.bash hook)"
                 conda activate clinica_env_$BRANCH_NAME
                 source /usr/local/Modules/init/profile.sh
                 module load clinica.all
                 cd test
                 ln -s /mnt/data/ci/data_ci_linux ./data
                 taskset -c 0-21 pytest \
                    --verbose \
                    --working_directory=$WORK_DIR_LINUX \
                    --disable-warnings \
                    --timeout=0 \
                    -n 6 \
                    -k 'test_instantiate'
                 module purge
                 conda deactivate
                 '''
            }
          }
          stage('Instantiate Mac') {
            agent { label 'macos' }
            environment {
              PATH = "$HOME/miniconda3/bin:/usr/local/Cellar/modules/4.1.2/bin:$PATH"
              CLINICA_ENV_BRANCH = "clinica_env_$BRANCH_NAME"
              }
            steps {
              echo 'Testing pipeline instantation...'
              sh 'echo "Agent name: ${NODE_NAME}"'
              sh '''
                 set +x
                 ./.jenkins/scripts/find_env.sh
                 eval "$(conda shell.bash hook)"
                 conda activate clinica_env_$BRANCH_NAME
                 source /usr/local/opt/modules/init/bash
                 module load clinica.all
                 cd test
                 ln -s /Volumes/data/data_ci ./data
                 pytest --verbose --disable-warnings -k 'test_instantiate'
                 module purge
                 conda deactivate
                 '''
            }
          }
        }
      }
    }
    post {
      failure {
        mail to: 'clinica-ci@inria.fr',
          subject: "Failed Pipeline: ${currentBuild.fullDisplayName}",
          body: "Something is wrong with ${env.BUILD_URL}"
      }
    }
  }