From 560118d8062c580b2dd0ab390b3b5d65832fb90e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Valentin=20Grou=C3=A8s?= <valentin.groues@uni.lu>
Date: Tue, 19 Nov 2019 10:29:09 +0100
Subject: [PATCH] pep8 compliance

---
 .gitignore                     | 205 +++++++++++++++++++++++++++++++++
 interface/TextMiningService.py |   8 +-
 2 files changed, 209 insertions(+), 4 deletions(-)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..9148438
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,205 @@
+
+# Created by https://www.gitignore.io/api/python
+# Edit at https://www.gitignore.io/?templates=python
+
+### Python ###
+# 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
+
+# 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
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# 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
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/python
+
+# Created by https://www.gitignore.io/api/intellij
+# Edit at https://www.gitignore.io/?templates=intellij
+
+### Intellij ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Intellij Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator/
+
+# End of https://www.gitignore.io/api/intellij
+.idea
+*.iml
diff --git a/interface/TextMiningService.py b/interface/TextMiningService.py
index b22f8ac..8e76832 100644
--- a/interface/TextMiningService.py
+++ b/interface/TextMiningService.py
@@ -2,7 +2,7 @@ from abc import ABCMeta, abstractmethod
 from typing import List
 
 
-class Publication():
+class Publication:
     def __init__(self, pmc_id, pm_id, doi, preprint_id, other_id):
         self.pmc_id = pmc_id
         self.pm_id = pm_id
@@ -18,8 +18,8 @@ class TextMiningService(metaclass=ABCMeta):
         self.description = description
 
     @abstractmethod
-    def getMentions(self, entities: List[str], limit: int = 20) -> List[Publication]:
-        """Returs a list of publications for a given list of entity IDs in which the entities appear.
+    def get_mentions(self, entities: List[str], limit: int = 20) -> List[Publication]:
+        """Returns a list of publications for a given list of entity IDs in which the entities appear.
 
         Arguments:
             entities {List[str]} -- [description]
@@ -33,7 +33,7 @@ class TextMiningService(metaclass=ABCMeta):
         pass
 
     @abstractmethod
-    def getCoOccurrences(self, entity: str) -> List[str]:
+    def get_co_occurrences(self, entity: str) -> List[str]:
         """
         Co-occurrences at publication level.
 
-- 
GitLab