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khadijeh.alibabaei
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update jenkins
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‎.sqa/config.yml‎

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# .sqa/config.yml - jenkins-pipeline-library configuration file
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sqa_criteria:
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qc_style:
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repos:
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posenet-tf:
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container: testing
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tox:
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tox_file: tox.ini
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testenv:
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- qc.sty
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qc_coverage:
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repos:
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posenet-tf:
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container: testing
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tox:
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tox_file: tox.ini
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testenv:
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- qc.cov
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qc_security:
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repos:
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posenet-tf:
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container: testing
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tox:
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tox_file: tox.ini
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testenv:
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- qc.sec
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environment:
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GIT_COMMITTER_NAME: "Lara Lloret (CSIC)"
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GIT_COMMITTER_EMAIL: "lloret@ifca.unican.es"
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LANG: C.UTF-8
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timeout: 600

‎.sqa/docker-compose.yml‎

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version: "3.6"
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services:
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testing:
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container_name: testing
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working_dir: /srv
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build:
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context: ./.sqa
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volumes:
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- type: bind
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source: ./
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target: /srv

‎.sqa/dockerfile‎

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# Docker image for CI testing of the DEEPaaS API
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# Note there is probably no gpu in the CI server
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ARG tag=1.14.0-py3
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FROM tensorflow/tensorflow:${tag}
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RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel
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RUN pip3 install --no-cache-dir tox
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CMD ["sleep", "infinity"]

‎Jenkinsfile‎

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#!/usr/bin/groovy
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@Library(['github.com/indigo-dc/jenkins-pipeline-library@release/2.1.1']) _
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@Library(['github.com/indigo-dc/jenkins-pipeline-library@release/1.4.0']) _
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def job_result_url = ''
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def projectConfig
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pipeline {
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agent {
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label 'python3.6'
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}
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environment {
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author_name = "Ignacio Heredia (CSIC)"
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author_email = "iheredia@ifca.unican.es"
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app_name = "image-classification-tf-dicom"
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job_location = "Pipeline-as-code/DEEP-OC-org/DEEP-OC-image-classification-tf-dicom/${env.BRANCH_NAME}"
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}
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agent any
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stages {
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stage('Code fetching') {
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steps {
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checkout scm
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}
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}
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stage('Style analysis') {
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stage('Application testing') {
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steps {
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ToxEnvRun('pep8')
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}
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post {
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always {
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WarningsReport('Pep8')
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}
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}
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}
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stage('Security scanner') {
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steps {
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ToxEnvRun('bandit-report')
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script {
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if (currentBuild.result == 'FAILURE') {
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currentBuild.result = 'UNSTABLE'
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}
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}
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}
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post {
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always {
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HTMLReport("/tmp/bandit", 'index.html', 'Bandit report')
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}
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}
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}
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stage("Re-build Docker image") {
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when {
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anyOf {
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branch 'master'
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branch 'test'
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buildingTag()
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}
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}
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steps {
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script {
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def job_result = JenkinsBuildJob("${env.job_location}")
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job_result_url = job_result.absoluteUrl
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projectConfig = pipelineConfig()
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buildStages(projectConfig)
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}
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}
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}
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}
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post {
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failure {
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// publish results and clean-up
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always {
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script {
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currentBuild.result = 'FAILURE'
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}
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}
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always {
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script { //stage("Email notification")
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def build_status = currentBuild.result
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build_status = build_status ?: 'SUCCESS'
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def subject = """
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New ${app_name} build in Jenkins@DEEP:\
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${build_status}: Job '${env.JOB_NAME}\
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[${env.BUILD_NUMBER}]'"""
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def body = """
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Dear ${author_name},\n\n
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A new build of '${app_name} DEEP application is available in Jenkins at:\n\n
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* ${env.BUILD_URL}\n\n
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terminated with '${build_status}' status.\n\n
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Check console output at:\n\n
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* ${env.BUILD_URL}/console\n\n
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and resultant Docker image rebuilding job at (may be empty in case of FAILURE):\n\n
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* ${job_result_url}\n\n
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DEEP Jenkins CI service"""
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EmailSend(subject, body, "${author_email}")
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if (fileExists("flake8.log")) {
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// file locations are defined in tox.ini
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// publish results of the style analysis
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recordIssues(tools: [flake8(pattern: 'flake8.log',
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name: 'PEP8 report',
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id: "flake8_pylint")])
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}
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if (fileExists("htmlcov/index.html")) {
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// publish results of the coverage test
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publishHTML([allowMissing: false,
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alwaysLinkToLastBuild: false,
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keepAll: true,
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reportDir: "htmlcov",
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reportFiles: 'index.html',
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reportName: 'Coverage report',
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reportTitles: ''])
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}
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if (fileExists("bandit/index.html")) {
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// publish results of the security check
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publishHTML([allowMissing: false,
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alwaysLinkToLastBuild: false,
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keepAll: true,
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reportDir: "bandit",
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reportFiles: 'index.html',
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reportName: 'Bandit report',
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reportTitles: ''])
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}
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}
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// Clean after build
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cleanWs()
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}
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}
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}

‎tox.ini‎

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[tox]
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minversion = 1.6
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envlist = py{35,36,27},pep8
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skipsdist = True
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minversion = 2.5.0
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isolated_build = True
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envlist = qc.sty,qc.cov,qc.sec,py37,py38,py36
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[testenv]
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usedevelop = True
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basepython = python3
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whitelist_externals =
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find
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install_command = pip install -U {opts} {packages}
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# envdir = {toxworkdir}/shared # Comment out or remove this line
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commands = pytest --numprocesses=auto {posargs}
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allowlist_externals =
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mkdir
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passenv =
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RCLONERCLONE_CONFIG_RSHARE_VENDOR
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RCLONE_CONFIG
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RCLONE_CONFIG_RSHARE_PASS
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RCLONE_CONFIG_RSHARE_URL
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RCLONE_CONFIG_RSHARE_TYPE
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RCLONE_CONFIG_RSHARE_USER
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setenv =
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VIRTUAL_ENV={envdir}
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LC_ALL=C.UTF-8
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OS_STDOUT_CAPTURE=1
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OS_STDERR_CAPTURE=1
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OS_TEST_TIMEOUT=160
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deps = -r{toxinidir}/requirements.txt
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-r{toxinidir}/test-requirements.txt
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commands =
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find . -type f -name "*.pyc" -delete
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OS_TEST_TIMEOUT=240
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deps =
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-r{toxinidir}/requirements-test.txt
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-r{toxinidir}/test-requirements.txt
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[testenv:cover]
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# TODO(stephenfin): Remove the PYTHON hack below in favour of a [coverage]
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# section once we rely on coverage 4.3+
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#
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# https://bitbucket.org/ned/coveragepy/issues/519/
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envdir = {toxworkdir}/shared
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setenv =
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{[testenv]setenv}
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PYTHON=coverage run --source image-classification-tf-dicom --parallel-mode
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[testenv:qc.sty]
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commands =
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{[testenv]commands}
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coverage erase
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stestr run {posargs}
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coverage combine
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coverage html -d cover
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coverage xml -o cover/coverage.xml
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coverage report
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[testenv:py27]
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# TODO(efried): Remove this once https://github.com/tox-dev/tox/issues/425 is fixed.
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basepython = python2.7
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- flake8 --statistics --tee --output-file={toxinidir}/flake8.log \
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--format=pylint image-classification-tf-dicom
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[testenv:qc.cov]
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commands =
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{[testenv]commands}
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stestr run {posargs}
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pytest --cov=image-classification-tf-dicom --cov-report=html:{toxinidir}/htmlcov --cov-report=term-missing tests
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[testenv:py35]
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# TODO(efried): Remove this once https://github.com/tox-dev/tox/issues/425 is fixed.
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basepython = python3.5
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[testenv:qc.sec]
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commands =
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{[testenv]commands}
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stestr run {posargs}
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[testenv:py36]
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# TODO(efried): Remove this once https://github.com/tox-dev/tox/issues/425 is fixed.
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basepython = python3.6
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commands =
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{[testenv:py35]commands}
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[testenv:pep8]
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envdir = {toxworkdir}/shared
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commands =
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- flake8 --format=pylint --output-file=flake8.log
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[testenv:bandit]
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envdir = {toxworkdir}/shared
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commands = bandit -r image-classification-tf-dicom -x tests -s B110,B410
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[flake8]
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# H803 skipped on purpose per list discussion.
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# E123, E125 skipped as they are invalid PEP-8.
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show-source = True
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ignore = E123,E125,H803,H405
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builtins = _
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exclude=.venv,.git,.tox,dist,doc,*lib/python*,*egg,build
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[testenv:cobertura]
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commands = py.test --cov=image-classification-tf-dicom --cov-report=xml --cov-report=term-missing image-classification-tf-dicom/tests
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[testenv:bandit-report]
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#basepython = python2.7
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commands =
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- mkdir /tmp/bandit
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- bandit -r image-classification-tf-dicom -x tests -s B110,B410 -f html -o /tmp/bandit/index.html
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mkdir -p {toxinidir}/bandit
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bandit -r image-classification-tf-dicom -x tests -s B101,B607,B602,B603,B404,B310 -f html -o {toxinidir}/bandit/index.html

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