pipeline {
    agent {
        kubernetes {
            cloud 'rsys-devel'
            defaultContainer 'miniforge3'
            inheritFrom 'miniforge'
        }
    }
    stages {
        stage("prepare") {
            parallel {
                stage("recipes repo") {
                    steps {
                        sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
                        dir('auto-updated-bioconda-recipes') {
                            sh 'git checkout update-autobigs-engine'
                        }
                    }
                }
                stage("conda") {
                    steps {
                        sh 'conda env update -n base --file environment.yml'
                    }
                }
            }
        }
        stage("generate recipe") {
            steps {
                sh 'grayskull pypi autoBIGS.engine --maintainers "Harrison Deng"'
                sh 'python patch_recipe.py'
                sh 'cp -r autobigs-engine/* auto-updated-bioconda-recipes/recipes/autobigs-engine/.'
            }
        }
        stage("build") {
            steps {
                dir('auto-updated-bioconda-recipes') {
                    sh 'conda build recipes/autobigs-engine --output-folder ./conda-dist'
                }
            }
        }
        stage('publish') {
            parallel {
                stage("archive") {
                    steps {
                        archiveArtifacts artifacts: './conda-dist/**/*.conda', followSymlinks: false
                    }
                }
                stage("bioconda") {
                    stages {
                        stage('lint') {
                            sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
                        }
                        stage('commit') {
                            environment {
                                TOKEN = credentials('github.com')
                            }
                            steps {
                                dir('auto-updated-bioconda-recipes') {
                                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
                                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
                                }
                            }
                        }
                    }
                }
                stage('git.reslate.systems') {
                    environment {
                        AUTH = credentials('git.reslate.systems')
                    }
                    steps {
                        sh 'curl --user AUTH_USR:AUTH_PSW --upload-file ./conda-dist/**/*.conda https://git.reslate.systems/api/packages/${AUTH_USR}/conda/package-1.0.conda'
                    }
                }
            }
        }
    }
}