pyannotators-patterns 1.6.25__tar.gz → 1.6.29__tar.gz

{pyannotators_patterns-1.6.25 → pyannotators_patterns-1.6.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyannotators-patterns
-Version: 1.6.25
+Version: 1.6.29
 Summary: Annotator based on Presidio pattern recognizer
 Project-URL: Homepage, https://github.com/oterrier/pyannotators_patterns/
 Author-email: Olivier Terrier <olivier.terrier@kairntech.com>

{pyannotators_patterns-1.6.25 → pyannotators_patterns-1.6.29}/pyproject.toml

@@ -71,6 +71,21 @@ path = "src/pyannotators_patterns/__init__.py"
 [tool.hatch.build.targets.wheel]
 packages = ["src/pyannotators_patterns"]
 
+[tool.hatch.build]
+exclude = [
+  "/tests",
+  "/docs",
+  "Jenkinsfile",
+  "Dockerfile",
+  "bumpversion.py",
+  "mypy.ini",
+  "hgnc_cache.sqlite",
+  "trivy-html-template.tpl",
+  "MIGRATION.md",
+  ".gitignore",
+  ".dockerignore"
+]
+
 [tool.pytest.ini_options]
 addopts = "--durations=5"
 norecursedirs = ["docs"]

{pyannotators_patterns-1.6.25 → pyannotators_patterns-1.6.29}/src/pyannotators_patterns/__init__.py

@@ -1,3 +1,3 @@
 """Annotator based on Presidio pattern recognizer"""
 
-__version__ = "1.6.25"
+__version__ = "1.6.29"

pyannotators_patterns-1.6.25/Dockerfile

@@ -1,19 +0,0 @@
-FROM python:3.12-slim-bookworm
-# Install prerequisites
-RUN apt-get update -y && \
-    apt-get install -y \
-    patch \
-    gcc && \
-    apt-get install -y --no-install-recommends \
-    g++ \
-    git && \
-# Final upgrade + clean
-    apt-get update -y && \
-    apt-get clean all -y
-
-# Install uv
-RUN pip install uv
-
-# Add pyproject.toml + README.md for uv install
-ADD pyproject.toml pyproject.toml
-ADD README.md README.md

pyannotators_patterns-1.6.25/Jenkinsfile

@@ -1,496 +0,0 @@
-#!groovy
-// to test groovy snippets online:
-//    https://www.jdoodle.com/execute-groovy-online
-
-pipeline {
-
-  agent none
-
-  options {
-    throttleJobProperty(
-      categories: ['pyannotators'],
-      throttleEnabled: true,
-      throttleOption: 'category'
-    )
-  }
-
-  triggers {
-    upstream(upstreamProjects: 'pymultirole_plugins/' + BRANCH_NAME.replaceAll('/', '%2F'),\
-                                threshold: hudson.model.Result.SUCCESS)
-  }
-
-  // variables declared in environment block can not be changed in any steps/stages
-  environment {
-    PATH_HOME = '/home/jenkins'
-    TEST_REPORT_DIR = '/root/test-reports'
-    PYTHONPYCACHEPREFIX = '/tmp/.pytest_cache'
-    PYTHONDONTWRITEBYTECODE = '1'
-    JENKINS_UIDGID = '1004:1004'
-    SBOM_PROJECT_NAME = "sbom-${JOB_NAME.replaceAll('[^a-zA-Z0-9_.-]', '_')}"
-
-    MAJOR_VERSION = "${MAJOR_VERSION_PY312}"
-    MINOR_VERSION = "${MINOR_VERSION_PY312}"
-  }
-
-  stages {
-    stage('Catch build termination') {
-      agent {
-        node {
-          label 'pre-build'
-          customWorkspace "${PATH_HOME}/${JOB_NAME}"
-        }
-      }
-      stages {
-        stage('Analyse build cause') {
-          steps {
-            script {
-              analyseBuildCause()
-            }
-          }
-        }
-      }
-    }
-
-    stage('Generate new version') {
-      when {
-        environment name: 'SKIP_JOB', value: '0'
-      }
-
-      agent {
-        node {
-          label 'built-in'
-          customWorkspace "${PATH_HOME}/${JOB_NAME}"
-        }
-      }
-
-      stages {
-        stage('Add credentials') {
-          steps {
-            script {
-              // Add password file for uv publishing
-              sh "cp ${PATH_HOME}/.passwd-pypi .env"
-            }
-          }
-        }
-
-        stage('Commit new version') {
-          steps {
-            script {
-              println("attempt to publish ${JOB_NAME} with version: ${MAJOR_VERSION}.${MINOR_VERSION}.${BUILD_ID}")
-
-              // push updates of file __init__.py
-              withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
-                sh 'git pull'
-                sh "echo '\"\"\"Annotator based on Presidio pattern recognizer\"\"\"' > src/pyannotators_patterns/__init__.py"
-                sh "echo '' >> src/pyannotators_patterns/__init__.py"
-                sh "echo '__version__ = \"${MAJOR_VERSION}.${MINOR_VERSION}.${BUILD_ID}\"' >> src/pyannotators_patterns/__init__.py"
-                sh 'git commit src/pyannotators_patterns/__init__.py -m "[Jenkins CI] Commit on version files" || echo "No changes to commit"'
-                sh 'git push'
-              }
-            }
-          }
-        }
-      }
-    }
-
-    stage('Build, test and publish') {
-      when {
-        beforeAgent true
-        environment name: 'SKIP_JOB', value: '0'
-      }
-
-      agent {
-        // dockerfile agent
-        // Mounted volume for Junit reports
-        //   - docker: /root/test-reports
-        //   - host  : /tmp/_${JOB_NAME}/test-reports
-        dockerfile {
-          label 'docker-build'
-          customWorkspace "${PATH_HOME}/${JOB_NAME}"
-          filename 'Dockerfile'
-          args "-u root --privileged -v /tmp/_${JOB_NAME}/test-reports:${TEST_REPORT_DIR}"
-        }
-      }
-
-      stages {
-        stage('Install dependencies') {
-          steps {
-            sh 'rm -f uv.lock'
-            sh 'pip install uv'
-            sh 'uv sync --no-cache --extra test'
-          }
-        }
-
-        stage('Test & lint python code') {
-          steps {
-            // remove any previous results.xml file
-            sh "rm -f ${TEST_REPORT_DIR}/results.xml"
-            sh 'uv run ruff check .'
-            sh 'uv run ruff format --check .'
-            sh "uv run pytest --junit-xml=${TEST_REPORT_DIR}/results.xml"
-          }
-        }
-
-        stage('Publish on PyPI') {
-          environment {
-            UV_PUBLISH_USERNAME = getUserName '.env'
-            UV_PUBLISH_PASSWORD = getUserPass '.env'
-          }
-          steps {
-            // remove any previous folder dist
-            sh 'rm -rf dist'
-            // remove any previous files used for sbom
-            sh 'rm -f sbom*.json trivy*.html syft trivy'
-            // pull recent updates of file __init__.py
-            withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
-              sh 'git config --global pull.rebase false'
-              sh "git config --global --add safe.directory ${WORKSPACE}"
-              sh 'git pull'
-            }
-            // put back owner of .git folder
-            sh "chown -R ${JENKINS_UIDGID} ${WORKSPACE}/.git"
-            // put back owner of pulled file
-            sh "chown ${JENKINS_UIDGID} src/pyannotators_patterns/__init__.py"
-            // get git status
-            sh 'git status'
-            // build and publish on PyPI
-            sh '''
-               export COMMIT_VERSION=$( cat src/pyannotators_patterns/__init__.py|grep version|cut -d '"' -f2|tr -s '[:blank:]' )
-               export BUILD_VERSION="${MAJOR_VERSION}"."${MINOR_VERSION}"."${BUILD_ID}"
-               if [ "${COMMIT_VERSION}" = "${BUILD_VERSION}" ] ; then uv build && uv publish ; fi
-               '''
-            // remove current folder dist
-            sh 'rm -rf dist'
-            // remove current folder .hypothesis
-            sh 'rm -rf .hypothesis'
-          }
-        }
-      }
-    }
-
-    stage('Prepare SBOM') {
-      when {
-        beforeAgent true
-        environment name: 'SKIP_JOB', value: '0'
-      }
-      options {
-        timeout(time: 120, unit: 'SECONDS')
-      }
-
-      agent {
-        docker {
-          image 'alpine:3.19'
-          label 'docker-build'
-          customWorkspace "${PATH_HOME}/${JOB_NAME}"
-          args "-u 0 -v ${PATH_HOME}/.cache/trivy:/root/.cache/trivy"
-        }
-      }
-
-      stages {
-        stage('Generate SBOM') {
-          steps {
-            sh """
-               apk add --no-cache curl
-
-               curl -sSfL https://raw.githubusercontent.com/anchore/syft/main/install.sh | sh -s -- -b . v${SYFT_VERSION}
-
-               ./syft . \
-                --exclude '**/syft' \
-                --exclude '**/.pytest_cache' \
-                --exclude '**/.ruff_cache' \
-                --exclude '**/sbom.cdx.json' \
-                --exclude '**/sbom.spdx.json' \
-                --source-name "${JOB_NAME}" \
-                --source-version "${BUILD_NUMBER}" \
-                -o cyclonedx-json=${SBOM_PROJECT_NAME}.cdx.json \
-                -o spdx-json=${SBOM_PROJECT_NAME}.spdx.json
-
-               rm -f ./syft
-               """
-          }
-        }
-
-        stage('Analyse SBOM') {
-          steps {
-            sh """
-               curl -sfL https://raw.githubusercontent.com/aquasecurity/trivy/main/contrib/install.sh | sh -s -- -b . v${TRIVY_VERSION}
-               if [ ! -f trivy-html-template.tpl ]; then
-                 curl -L https://raw.githubusercontent.com/aquasecurity/trivy/main/contrib/html.tpl -o trivy-html-template.tpl
-               fi
-
-               ./trivy sbom ${SBOM_PROJECT_NAME}.cdx.json \
-                --cache-dir "/root/.cache/trivy" \
-                --severity HIGH,CRITICAL \
-                --exit-code 1 \
-                --no-progress \
-                --format template \
-                --template "@trivy-html-template.tpl" \
-                -o trivy-report-${SBOM_PROJECT_NAME}.html || EXIT_CODE=\$?
-
-               rm -f ./trivy
-
-               exit \${EXIT_CODE:-0}
-               """
-          }
-        }
-
-        stage('Archive SBOM & analysis') {
-          steps {
-            archiveArtifacts artifacts: 'sbom*.json, trivy*.html', excludes: 'sbom.cdx.json, sbom.spdx.json', fingerprint: true
-          }
-        }
-      }
-    }
-  }
-
-  post {
-    // only triggered when blue or green sign
-    success {
-      // node is specified here to get an agent
-      node('built-in') {
-        // keep using customWorkspace to store Junit report
-        ws("${PATH_HOME}/${JOB_NAME}") {
-          script {
-            try {
-              sh 'rm -f results.xml'
-              sh "cp /tmp/_${JOB_NAME}/test-reports/results.xml results.xml"
-            } catch (Exception e) {
-              println 'Exception occurred: ' + e.toString()
-            }
-            try {
-              junit 'results.xml'
-            } catch (Exception e) {
-              println 'Exception occurred: ' + e.toString()
-            }
-            if (sendEmailNotif("${PATH_HOME}/${JOB_NAME}", "${BUILD_NUMBER}")) {
-              println 'sending Success Build notification'
-              def CUSTOM_SUBJECT = '[CI - Jenkinzz SUCCESS] ' + CUSTOM_SUBJECT
-              emailext(
-                  mimeType: 'text/html',
-                  subject: CUSTOM_SUBJECT,
-                  body: '${DEFAULT_CONTENT}',
-                  replyTo: '${DEFAULT_REPLYTO}',
-                  to: '${ADMIN_RECIPIENTS}' + ';' + CUSTOM_RECIPIENTS
-              )
-              switchEmailNotif(false, BUILD_NUMBER)
-            } else {
-              println 'preventing Success Build notification'
-            }
-          }
-        }
-      }
-    }
-    // triggered when red sign
-    failure {
-      // node is specified here to get an agent
-      node('built-in') {
-        // keep using customWorkspace to store Junit report
-        ws("${PATH_HOME}/${JOB_NAME}") {
-          script {
-            try {
-              sh 'rm -f results.xml'
-              sh "cp /tmp/_${JOB_NAME}/test-reports/results.xml results.xml"
-            } catch (Exception e) {
-              println 'Exception occurred: ' + e.toString()
-            }
-            try {
-              junit 'results.xml'
-            } catch (Exception e) {
-              println 'Exception occurred: ' + e.toString()
-            }
-            println 'sending Failure Build notification'
-            def CUSTOM_SUBJECT = '[CI - Jenkinzz FAILURE] ' + CUSTOM_SUBJECT
-            emailext(
-                mimeType: 'text/html',
-                subject: CUSTOM_SUBJECT,
-                body: '${DEFAULT_CONTENT}',
-                replyTo: '${DEFAULT_REPLYTO}',
-                to: '${ADMIN_RECIPIENTS}' + ';' + CUSTOM_RECIPIENTS
-            )
-          }
-        }
-      }
-    }
-    // triggered when black sign
-    aborted {
-      println 'post-declarative message: abort job'
-    }
-    // trigger every-works
-    //always {
-    //}
-  }
-}
-
-// return UV_PUBLISH_USERNAME from given file (reads FLIT_USERNAME key)
-def getUserName(path) {
-  def USERNAME = sh(
-                 script: "grep FLIT_USERNAME ${path}|cut -d '=' -f2",
-                 returnStdout: true
-               ).trim()
-  return USERNAME
-}
-
-// return UV_PUBLISH_PASSWORD from given file (reads FLIT_PASSWORD key)
-def getUserPass(path) {
-  def USERPASS = sh(
-                 script: "grep FLIT_PASSWORD ${path}|cut -d '=' -f2",
-                 returnStdout: true
-               ).trim()
-  return USERPASS
-}
-
-// create/remove emailNotif file to trigger email notification
-def switchEmailNotif(toggle, build) {
-  if (toggle) {
-    sh 'echo ' + build + ' > .emailNotif'
-  } else {
-    if (build == BUILD_NUMBER) {
-      sh 'rm -f .emailNotif'
-    }
-  }
-}
-
-// return true if emailNotif file present
-boolean sendEmailNotif(path, build) {
-  def emailNotif = sh(
-                 script: "find ${path} -name '.emailNotif'|wc -l",
-                 returnStdout: true
-               ).trim()
-  def emailContent = ''
-  if (emailNotif == '1') {
-    emailContent = sh(
-                     script: "cat ${path}/.emailNotif",
-                     returnStdout: true
-                   ).trim()
-  }
-  return (emailContent == build)
-}
-
-def analyseBuildCause() {
-  String[] upstreamProjects = ['pymultirole_plugins']
-  boolean upstreamRunning = false
-  String jobName
-  // iterate over upstreamProjects
-  for (upstream_project in upstreamProjects) {
-    Jenkins.instance.getItemByFullName(upstream_project).items.each { repository ->
-      boolean isRunning = false
-      //repository.parent.name: project
-      //repository.name: branch
-      if ( repository.name == BRANCH_NAME ) {
-        // iterate over all jobs of current repository
-        repository.allJobs.each { job ->
-          // iterate over all builds of current job
-          job.builds.each { build ->
-            // determine if a build is running or not
-            if ( build.result == (null) ) {
-              jobName = build.parent.parent.name
-              isRunning = true
-            }
-          }
-          if ( isRunning ) {
-            upstreamRunning = true
-          }
-        }
-      }
-    }
-  }
-
-  // Catch if build has been triggered by CI Commit
-  // returnStatus = true  when string not found -> Team commit
-  // returnStatus = false when string is found  -> CI commit
-  boolean lastCommitIsTeam = sh(
-    script: 'git log -1 | grep "\\[Jenkins CI\\]"',
-    returnStatus: true
-  )
-
-  // Skip build when upstream detected
-  if (upstreamRunning) {
-    println 'Skipping build because upstream job detected (' + jobName + ')'
-    env.SKIP_JOB = '1'
-    switchEmailNotif(false, 0)
-    currentBuild.result = 'NOT_BUILT'
-  }
-
-  // Catch if build has been triggered by User
-  boolean isStartedByUser = currentBuild.rawBuild.getCause(hudson.model.Cause$UserIdCause) != null
-  if (isStartedByUser && !upstreamRunning) {
-    env.SKIP_JOB = '0'
-    env.CUSTOM_SUBJECT = JOB_NAME + ' - Manual Build #' + BUILD_NUMBER
-    env.CUSTOM_RECIPIENTS = emailextrecipients([[$class: 'RequesterRecipientProvider']])
-    switchEmailNotif(true, BUILD_NUMBER)
-    println 'Job started by User, proceeding'
-  }
-
-  // Catch if build has been triggered by Upstream
-  boolean isStartedByUpstream = currentBuild.rawBuild.getCause(hudson.model.Cause$UpstreamCause) != null
-  if (isStartedByUpstream && !upstreamRunning) {
-    int changeSetCount = 0
-    int ciSkipCount = 0
-    String upstreamFullJobName = ''
-    for (Run upstreamBuild : currentBuild.upstreamBuilds) {
-      upstreamFullJobName   = upstreamBuild.rawBuild.fullDisplayName
-      if (upstreamBuild.changeSets != null) {
-        def changeLogSets = upstreamBuild.changeSets
-        for (int i = 0; i < changeLogSets.size(); i++) {
-          changeSetCount++
-          def entries = changeLogSets[i].items
-          for (int j = 0; j < entries.length; j++) {
-            def entry = entries[j]
-            if (entry.msg.contains('[Jenkins CI]')) {
-              ciSkipCount++
-            }
-          }
-        }
-      }
-    }
-    if (changeSetCount > 0 && changeSetCount == ciSkipCount) {
-      env.SKIP_JOB = '1'
-      switchEmailNotif(false, 0)
-      println 'Job started by Upstream [' + upstreamFullJobName + '], with CI commit, skipping'
-      currentBuild.result = 'NOT_BUILT'
-    } else {
-      env.SKIP_JOB = '0'
-      env.CUSTOM_SUBJECT = JOB_NAME + ' - Upstream Build #' + BUILD_NUMBER
-      env.CUSTOM_RECIPIENTS = emailextrecipients([[$class:'UpstreamComitterRecipientProvider']])
-      switchEmailNotif(true, BUILD_NUMBER)
-      println 'Job started by Upstream [' + upstreamFullJobName + '], proceeding'
-    }
-  }
-
-  // Catch if build has been triggered by User Commit
-  boolean isStartedByCommit = currentBuild.rawBuild.getCause(jenkins.branch.BranchEventCause) != null
-  if (isStartedByCommit && lastCommitIsTeam && !upstreamRunning) {
-    env.SKIP_JOB = '0'
-    env.CUSTOM_SUBJECT = JOB_NAME + ' - SCM Build #' + BUILD_NUMBER
-    env.CUSTOM_RECIPIENTS = emailextrecipients([[$class: 'DevelopersRecipientProvider'], [$class:'CulpritsRecipientProvider']])
-    switchEmailNotif(true, BUILD_NUMBER)
-    println 'Job started by User Commit, proceeding'
-  }
-
-  // Catch if build has been triggered by cron
-  boolean isStartedByCron = currentBuild.rawBuild.getCause(hudson.triggers.TimerTrigger$TimerTriggerCause) != null
-  if (isStartedByCron && lastCommitIsTeam && !upstreamRunning) {
-    env.SKIP_JOB = '0'
-    env.CUSTOM_SUBJECT = JOB_NAME + ' - CRON Build #' + BUILD_NUMBER
-    env.CUSTOM_RECIPIENTS = emailextrecipients([[$class: 'DevelopersRecipientProvider'], [$class:'CulpritsRecipientProvider']])
-    switchEmailNotif(true, BUILD_NUMBER)
-    println 'Job started by Cron, proceeding'
-  }
-
-  // Catch if build has been triggered by branch discovery
-  boolean isStartedByBranchDiscovery = currentBuild.rawBuild.getCause(jenkins.branch.BranchIndexingCause) != null
-  if (isStartedByBranchDiscovery && lastCommitIsTeam && !upstreamRunning) {
-    env.SKIP_JOB = '0'
-    env.CUSTOM_SUBJECT = JOB_NAME + ' - BranchDiscovery Build #' + BUILD_NUMBER
-    env.CUSTOM_RECIPIENTS = emailextrecipients([[$class: 'DevelopersRecipientProvider'], [$class:'CulpritsRecipientProvider']])
-    switchEmailNotif(true, BUILD_NUMBER)
-    println 'Job started by Branch Discovery, proceeding'
-  }
-
-  if (!lastCommitIsTeam && !upstreamRunning && !isStartedByUser && !isStartedByUpstream) {
-    println 'Skipping build because last commit has been done by CI'
-    env.SKIP_JOB = '1'
-    switchEmailNotif(false, 0)
-    currentBuild.result = 'NOT_BUILT'
-  }
-}