pyconverters-cairn_xml 0.5.2__tar.gz

pyconverters_cairn_xml-0.5.2/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0.dev0
+commit = True
+tag = True
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<build>\d+))?
+serialize = 
+	{major}.{minor}.{patch}.{release}{build}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = prod
+first_value = dev
+values = 
+	dev
+	prod
+
+[bumpversion:part:build]
+
+[bumpversion:file:pyconverters_cairn_xml/__init__.py]
+
+[bumpversion:file:CHANGELOG.md]
+search = ## [unreleased]
+replace = ## [{new_version}]

pyconverters_cairn_xml-0.5.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.idea/
+.idea/*.*
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+/default
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

pyconverters_cairn_xml-0.5.2/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/ambv/black
+    rev: 19.3b0
+    hooks:
+    - id: black
+      language_version: python3.8
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.1.0
+    hooks:
+    - id: end-of-file-fixer
+      exclude: '.bumpversion.cfg'
+    - id: trailing-whitespace
+      exclude: '.bumpversion.cfg'
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+    - id: flake8

pyconverters_cairn_xml-0.5.2/.readthedocs.yml

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+version: 2
+
+build:
+    image: latest
+
+python:
+    version: 3.8
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - docs
+
+sphinx:
+    fail_on_warning: true

pyconverters_cairn_xml-0.5.2/AUTHORS.md

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+# Authors
+
+Contributors to pyconverters_cairn_xml include:
+
++ [Olivier Terrier](mailto:olivier.terrier@kairntech.com)

pyconverters_cairn_xml-0.5.2/CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [unreleased]

pyconverters_cairn_xml-0.5.2/Dockerfile

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+FROM python:3.8-slim-buster
+# Install prerequisites
+RUN apt-get update -y && \
+    apt-get install -y \
+    patch \
+    ffmpeg \
+    gcc && \
+    apt-get install -y --no-install-recommends \
+    g++ \
+    git && \
+# Final upgrade + clean
+    apt-get update -y && \
+    apt-get clean all -y
+
+# Enable Installing packages as root
+ENV FLIT_ROOT_INSTALL=1
+
+# Add pyproject.toml + README.md for flit install
+ADD pyproject.toml pyproject.toml
+ADD README.md README.md

pyconverters_cairn_xml-0.5.2/Jenkinsfile

@@ -0,0 +1,322 @@
+pipeline {
+
+  environment {
+    PATH_HOME = "/home/jenkins"
+    PYTHONDONTWRITEBYTECODE = "1"
+    PYTHONPYCACHEPREFIX = "/tmp/.pytest_cache"
+    TEST_REPORT_DIR="/root/test-reports"
+    MAJOR_VERSION = "0"
+    MINOR_VERSION = "5"
+    GIT_AUTH = credentials('bitbucket-user')
+  }
+
+  agent none
+
+  triggers {
+    upstream(upstreamProjects: "pymultirole_plugins/" + env.BRANCH_NAME.replaceAll("/", "%2F"),\
+                                threshold: hudson.model.Result.SUCCESS)
+  }
+
+  parameters {
+      booleanParam(defaultValue: false, description: 'if set to true (ticked), it will not skip on CI commit', name: 'forcePublishing')
+  }
+
+  stages {
+
+    stage('Catch build termination') {
+      agent {
+        node {
+          label 'built-in'
+          customWorkspace "/home/jenkins/${env.JOB_NAME}"
+        }
+      }
+      stages {
+        stage('Abort if upstream or CI_commit') {
+          steps {
+            script {
+              abortBuild()
+            }
+          }
+        }
+      }
+    }
+
+    stage('Generate new version') {
+      agent {
+        node {
+          label 'built-in'
+          customWorkspace "/home/jenkins/${env.JOB_NAME}"
+        }
+      }
+
+      stages {
+
+        stage('Add credentials') {
+          steps {
+            script {
+              // Add password file for flit publishing
+              sh "cp ${env.PATH_HOME}/.passwd-pypi .env"
+            }
+          }
+        }
+
+        stage('Skip on CI commit') {
+          steps {
+            script {
+              // returnStatus = 1 when string not found -> Team commit
+              // returnStatus = 0 when string is found  -> CI commit
+              env.LAST_COMMIT_IS_TEAM = sh(
+                      script: 'git log -1 | grep "\\[Jenkins CI\\]"',
+                      returnStatus: true
+              )
+              if (LAST_COMMIT_IS_TEAM == '0') {
+                println "Last commit has been done by CI, skipping next steps"
+              } else {
+                println "Last commit has been done by Team, processing"
+              }
+              if (params.forcePublishing) {
+                println "Try to publish, considering last commit has been done by Team"
+                env.LAST_COMMIT_IS_TEAM = "1"
+              }
+            }
+          }
+        }
+
+        stage('Commit new version') {
+          when {
+            environment name: "LAST_COMMIT_IS_TEAM", value: "1"
+          }
+          steps {
+            script {
+              println("attempt to publish ${env.JOB_NAME} with version: ${MAJOR_VERSION}.${MINOR_VERSION}.${env.BUILD_ID}")
+
+              // push updates of file __init__.py
+              withCredentials([gitUsernamePassword(credentialsId: 'bitbucket-user', gitToolName: 'git-tool')]) {
+                sh "echo '\"\"\"Cairn.info XML converter.\"\"\"' > src/pyconverters_cairn_xml/__init__.py"
+                sh "echo '__version__ = \"${MAJOR_VERSION}.${MINOR_VERSION}.${env.BUILD_ID}\"' >> src/pyconverters_cairn_xml/__init__.py"
+                sh 'git commit src/pyconverters_cairn_xml/__init__.py -m "[Jenkins CI] Commit on version files" || echo "No changes to commit"'
+                sh 'git push'
+              }
+            }
+          }
+        }
+
+      }
+    }
+
+    stage('Build, test and publish') {
+      when {
+        environment name: "LAST_COMMIT_IS_TEAM", value: "1"
+      }
+
+      agent {
+        // dockerfile agent
+        // Mounted volume for Junit reports
+        //   - docker: /root/test-reports
+        //   - host  : /tmp/_${env.JOB_NAME}/test-reports
+        dockerfile {
+          label 'built-in'
+          customWorkspace "/home/jenkins/${env.JOB_NAME}"
+          filename 'Dockerfile'
+          args "-u root --privileged -v /tmp/_${env.JOB_NAME}/test-reports:${TEST_REPORT_DIR}"
+        }
+      }
+
+      stages {
+
+        stage('Install flit & flake8') {
+          steps {
+            // remove any previous tox env
+            sh 'rm -rf .tox'
+            sh 'python -m pip install pip==22.0.3'
+            sh 'pip install --no-cache-dir flit==3.2.0 flake8==3.9.2 flakehell tox'
+            sh 'flit install'
+          }
+        }
+
+        stage('Test & lint python code') {
+          steps {
+            // remove any previous results.xml file
+            sh "rm -f ${TEST_REPORT_DIR}/results.xml"
+            sh 'tox'
+          }
+        }
+
+        stage('Publish on PyPI') {
+          environment {
+            FLIT_USERNAME = getUserName ".env"
+            FLIT_PASSWORD = getUserPass ".env"
+          }
+          steps {
+            // remove any previous folder dist
+            sh 'rm -rf dist'
+            // create (as root) folder dist
+            sh 'mkdir dist'
+            // 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 ${PATH_HOME}/${env.JOB_NAME}"
+              sh 'git pull'
+            }
+            // put back owner of pulled file
+            sh 'chown 1000:1000 src/pyconverters_cairn_xml/__init__.py'
+            // get git status
+            sh 'git status'
+            // publish on PyPI
+            sh 'flit publish'
+            // remove current folder dist
+            sh 'rm -rf dist'
+            // remove current folder .hypothesis
+            sh 'rm -rf .hypothesis'
+            // remove current folder .tox
+            sh 'rm -rf .tox'
+          }
+        }
+
+      }
+
+    }
+
+  }
+
+  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("/home/jenkins/${env.JOB_NAME}") {
+          script {
+            try {
+              sh "rm -f results.xml"
+              sh "cp /tmp/_${env.JOB_NAME}/test-reports/results.xml results.xml"
+            } catch (Exception e) {
+              echo 'Exception occurred: ' + e.toString()
+            }
+            try {
+              junit 'results.xml'
+            } catch (Exception e) {
+              echo 'Exception occurred: ' + e.toString()
+            }
+            println "sending Systematic Build notification"
+            emailext(body: '${DEFAULT_CONTENT}', mimeType: 'text/html',
+                    replyTo: '${DEFAULT_REPLYTO}', subject: '${DEFAULT_SUBJECT}',
+                    to: '${DEFAULT_RECIPIENTS}')
+          }
+        }
+      }
+    }
+    // triggered when red sign
+    failure {
+      // node is specified here to get an agent
+      node('built-in') {
+        // keep using customWorkspace to store Junit report
+        ws("/home/jenkins/${env.JOB_NAME}") {
+          script {
+            try {
+              sh "rm -f results.xml"
+              sh "cp /tmp/_${env.JOB_NAME}/test-reports/results.xml results.xml"
+            } catch (Exception e) {
+              echo 'Exception occurred: ' + e.toString()
+            }
+            try {
+              junit 'results.xml'
+            } catch (Exception e) {
+              echo 'Exception occurred: ' + e.toString()
+            }
+            println "sending Systematic Build notification"
+            emailext(body: '${DEFAULT_CONTENT}', mimeType: 'text/html',
+                    replyTo: '${DEFAULT_REPLYTO}', subject: '${DEFAULT_SUBJECT}',
+                    to: '${DEFAULT_RECIPIENTS}')
+          }
+        }
+      }
+    }
+    // trigger every-works
+    //always {
+    //}
+  }
+
+}
+
+// return FLIT_USERNAME from given file
+def getUserName(path) {
+  USERNAME = sh(
+                 script: "grep FLIT_USERNAME ${path}|cut -d '=' -f2",
+                 returnStdout: true
+               ).trim()
+  return USERNAME
+}
+
+// return FLIT_PASSWORD from given file
+def getUserPass(path) {
+  USERPASS = sh(
+                 script: "grep FLIT_PASSWORD ${path}|cut -d '=' -f2",
+                 returnStdout: true
+               ).trim()
+  return USERPASS
+}
+
+def abortBuild() {
+  def upstream_projects = ["pymultirole_plugins"]
+  def upstream_running = null
+  def jobName
+  // iterate over upstream_projects
+  for (upstream_project in upstream_projects) {
+    Jenkins.instance.getItemByFullName(upstream_project).getItems().each { repository ->
+      def isRunning = false
+      //repository.parent.name: project
+      //repository.name: branch
+      if ( repository.name == env.BRANCH_NAME ) {
+        // iterate over all jobs of current repository
+        repository.getAllJobs().each { job ->
+          // iterate over all builds of current job
+          job.builds.each { build ->
+            // determine if a build is running or not
+            if ( build.getResult().equals(null) ) {
+              jobName = build.parent.parent.name
+              isRunning = true
+            }
+          }
+          if ( isRunning ) {
+            upstream_running = true
+          }
+        }
+      }
+    }
+  }
+  // Abort build when upstream detected
+  if (upstream_running != null) {
+    println 'Aborting build because upstream job detected (' + jobName + ')'
+    currentBuild.result = 'ABORTED'
+    currentBuild.getRawBuild().getExecutor().interrupt(Result.ABORTED)
+    sleep(1)   // Interrupt is not blocking and does not take effect immediately.
+  }
+  // Abort build when last commit is CI commit
+  // returnStatus = 1 when string not found -> Team commit
+  // returnStatus = 0 when string is found  -> CI commit
+  def last_commit_is_team = sh(
+    script: 'git log -1 | grep "\\[Jenkins CI\\]"',
+    returnStatus: true
+  )
+  if (params.forcePublishing) {
+    println "Try to publish, proceeding"
+    last_commit_is_team = 1
+  }
+  def isStartedByUser = currentBuild.rawBuild.getCause(hudson.model.Cause$UserIdCause) != null
+  if (isStartedByUser) {
+    println "Job started by User, proceeding"
+    last_commit_is_team = 1
+  }
+  def isStartedByUpstream = currentBuild.rawBuild.getCause(hudson.model.Cause$UpstreamCause) != null
+  if (isStartedByUpstream) {
+    println "Job started by Upstream, proceeding"
+    last_commit_is_team = 1
+  }
+  if (last_commit_is_team == 0) {
+    println 'Aborting build because last commit has been done by CI'
+    currentBuild.result = 'ABORTED'
+    currentBuild.getRawBuild().getExecutor().interrupt(Result.ABORTED)
+    sleep(1)   // Interrupt is not blocking and does not take effect immediately.
+  }
+}

pyconverters_cairn_xml-0.5.2/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2021 Olivier Terrier
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

pyconverters_cairn_xml-0.5.2/PKG-INFO

@@ -0,0 +1,92 @@
+Metadata-Version: 2.3
+Name: pyconverters-cairn_xml
+Version: 0.5.2
+Summary: Cairn.info XML converter.
+Home-page: https://github.com/oterrier/pyconverters_cairn_xml/
+Keywords: 
+Author: Olivier Terrier
+Author-email: olivier.terrier@kairntech.com
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Classifier: Intended Audience :: Information Technology
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: System Administrators
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3.8
+Requires-Dist: pymultirole-plugins>=0.5.0,<0.6.0
+Requires-Dist: lxml
+Requires-Dist: beautifulsoup4
+Requires-Dist: inscriptis==1.2
+Requires-Dist: flit ; extra == "dev"
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: bump2version ; extra == "dev"
+Requires-Dist: sphinx ; extra == "docs"
+Requires-Dist: sphinx-rtd-theme ; extra == "docs"
+Requires-Dist: m2r2 ; extra == "docs"
+Requires-Dist: sphinxcontrib.apidoc ; extra == "docs"
+Requires-Dist: jupyter_sphinx ; extra == "docs"
+Requires-Dist: pytest>=7.1.0 ; extra == "test"
+Requires-Dist: pytest-cov ; extra == "test"
+Requires-Dist: pytest-flake8 ; extra == "test"
+Requires-Dist: pytest-black ; extra == "test"
+Requires-Dist: flake8==3.9.2 ; extra == "test"
+Requires-Dist: tox ; extra == "test"
+Provides-Extra: dev
+Provides-Extra: docs
+Provides-Extra: test
+
+# pyconverters_cairn_xml
+
+[![license](https://img.shields.io/github/license/oterrier/pyconverters_cairn_xml)](https://github.com/oterrier/pyconverters_cairn_xml/blob/master/LICENSE)
+[![tests](https://github.com/oterrier/pyconverters_cairn_xml/workflows/tests/badge.svg)](https://github.com/oterrier/pyconverters_cairn_xml/actions?query=workflow%3Atests)
+[![codecov](https://img.shields.io/codecov/c/github/oterrier/pyconverters_cairn_xml)](https://codecov.io/gh/oterrier/pyconverters_cairn_xml)
+[![docs](https://img.shields.io/readthedocs/pyconverters_cairn_xml)](https://pyconverters_cairn_xml.readthedocs.io)
+[![version](https://img.shields.io/pypi/v/pyconverters_cairn_xml)](https://pypi.org/project/pyconverters_cairn_xml/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyconverters_cairn_xml)](https://pypi.org/project/pyconverters_cairn_xml/)
+
+Fetch articles from Pubmed
+
+## Installation
+
+You can simply `pip install pyconverters_cairn_xml`.
+
+## Developing
+
+### Pre-requesites
+
+You will need to install `flit` (for building the package) and `tox` (for orchestrating testing and documentation building):
+
+```
+python3 -m pip install flit tox
+```
+
+Clone the repository:
+
+```
+git clone https://github.com/oterrier/pyconverters_cairn_xml
+```
+
+### Running the test suite
+
+You can run the full test suite against all supported versions of Python (3.8) with:
+
+```
+tox
+```
+
+### Building the documentation
+
+You can build the HTML documentation with:
+
+```
+tox -e docs
+```
+
+The built documentation is available at `docs/_build/index.html.
+