pipeline {
    agent {
        kubernetes {
            cloud 'rsys-devel'
            defaultContainer 'miniforge3'
            inheritFrom 'miniforge'
        }
    }
    stages {
        stage("prepare") {
            parallel {
                stage("recipes repo") {
                    steps {
                        sh 'git clone https://github.com/RealYHD/bioconda-recipes.git'
                        dir('bioconda-recipes') {
                            sh 'git pull'
                            sh 'git pull origin update-autobigs-engine'
                            sh 'git pull origin update-autobigs-engine'
                        }
                    }
                }
                stage("conda") {
                    steps {
                        sh 'conda env update -n base --file environment.yml'
                    }
                }
            }
        }
        stage("update recipes") {
            parallel {
                stage("autoBIGS.cli") {
                    steps {
                        sh 'grayskull pypi autobigs.cli --maintainers "Harrison Deng"'
                        sh 'python scripts/adapt_names.py autobigs.cli'
                    }
                }
                stage("autoBIGS.engine") {
                    steps {
                        sh 'grayskull pypi autobigs.cli --maintainers "Harrison Deng"'
                        sh 'python scripts/adapt_names.py autobigs.engine'
                    }
                }
            }
            stage("overwrite") {
                steps {
                    dir('bioconda-recipes') {
                        sh 'checkout '
                        sh 'cp autobigs-engine/* '
                    }
                }
            }
        }
    }
}