49 lines
2.1 KiB
Groovy
49 lines
2.1 KiB
Groovy
pipeline {
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agent any
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stages {
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stage("install") {
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steps {
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sh 'mamba env update --file environment.yml || mamba env create --force --file environment.yml'
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sh 'echo "mamba activate bmlsa" >> ~/.bashrc'
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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 "python -m pytest --junitxml=test_results.xml"
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xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
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}
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}
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stage("build") {
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steps {
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sh 'rm -rf ./dist/*'
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sh 'rm -rf ./docs/build/*'
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sh "python -m build"
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sh 'sphinx-apidoc -o docs/source/ src/bmlsa --force'
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sh 'make -C docs html'
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publishHTML([allowMissing: false, alwaysLinkToLastBuild: false, keepAll: false, reportDir: 'docs/build/html', reportFiles: 'index.html', reportName: 'Documentation', reportTitles: ''])
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}
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}
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stage("test installation") {
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steps {
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sh "pip install dist/*.whl --force-reinstall"
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sh "bmlsa -h"
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sh "bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/"
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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', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
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}
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}
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stage("publish") {
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when {
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branch '**/master'
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}
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steps {
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withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
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sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --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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} |