Harrison Deng
41c05cc521
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Added default MLST scheme Added multiple ways of defining a MLST scheme CSV output now shows database name for each scheme ID Now uses native argparse library for ensuring mutual exclusivity of arguments and whether or not one is required. Updated to use 0.13.* of engine
64 lines
2.5 KiB
Groovy
64 lines
2.5 KiB
Groovy
pipeline {
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agent {
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kubernetes {
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cloud 'rsys-devel'
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defaultContainer 'miniforge3'
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inheritFrom 'miniforge'
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}
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}
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stages {
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stage("install") {
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steps {
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sh 'conda env update -n base -f environment.yml'
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}
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}
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stage("unit tests") {
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steps {
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sh returnStatus: true, script: "python -m pytest --junitxml=test_results.xml --cov=src --cov-report xml:coverage.xml"
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xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
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recordCoverage(tools: [[parser: 'COBERTURA', pattern: 'coverage.xml']])
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}
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}
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stage("build") {
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steps {
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sh "python -m build"
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sh "grayskull pypi dist/*.tar.gz --maintainers 'Harrison Deng'"
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sh "python scripts/patch_recipe.py"
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sh 'conda build autobigs-cli -c bioconda --output-folder conda-bld --verify'
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}
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}
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stage("archive") {
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steps {
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archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl, conda-bld/**/*.conda', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
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}
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}
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stage("publish") {
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parallel {
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stage ("git.reslate.systems") {
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when {
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branch '**/main'
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}
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environment {
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CREDS = credentials('username-password-rs-git')
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}
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steps {
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sh script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
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sh 'curl --user ${CREDS_USR}:${CREDS_PSW} --upload-file conda-bld/**/*.conda https://git.reslate.systems/api/packages/${CREDS_USR}/conda/$(basename conda-bld/**/*.conda)'
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}
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}
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stage ("pypi.org") {
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when {
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tag '*.*.*'
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}
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environment {
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TOKEN = credentials('pypi.org')
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}
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steps {
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sh script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
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}
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}
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}
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}
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}
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} |