[SPP] Completed basic setup package and CI integration.

.gitignore

@@ -0,0 +1,17 @@
+\.vscode/
+
+\.DS_Store
+
+__pycache__
+
+*/__pycache__/*
+
+**/__pycache__/*
+
+.notipy.json
+
+.single_run
+
+.coverage*
+
+coverage.xml

.spp_cache/badges.json

@@ -0,0 +1 @@
+{"code_climate": {"code_climate_maintainability_url": "https://api.codeclimate.com/v1/badges/64bfb8eb5a73959ea0d3/maintainability", "code_climate_coverage_url": "https://api.codeclimate.com/v1/badges/64bfb8eb5a73959ea0d3/test_coverage"}, "codacy": {"codacy": " image:: https://api.codacy.com/project/badge/Grade/85bc1e3d96bf4c43a2ca70ca233a1bca\n    :target: https://www.codacy.com/manual/LucaCappelletti94/epigenomic_dataset?utm_source=github.com&utm_medium=referral&utm_content=LucaCappelletti94/epigenomic_dataset&utm_campaign=Badge_Grade"}}

.travis.yml

@@ -0,0 +1,38 @@
+dist: trusty
+sudo: false
+git:
+  depth: false
+addons:
+  sonarcloud:
+    organization: lucacappelletti94-github
+    token:
+      secure: xJRLDhqyy2V/hsD5oN3HrvHkc3219NFnUfnoTbEJ10ZlzEaqjLOfz2TK2vWNNhvR8r/cQW/BVp/JMGxPi9X/WU8Yyz65mMd0h2vowxyTgr6sSit5P3fEkDlXpV6MJ/XRUIuSdGU1/qy4IrbdS+6tI7IaRZ9tEA4GuFjSQy0wEis90ciOUbZClMVrKDdq0joPrdmnRMyjf2q6gxY+y1wbn+TuFgOJ4bhsWoRyP0Ig7EhbQJTYc+KyXVlV9xK/7RocziZtYmTv/wPWTb3imamm3bg+bTCrZaPvP0zsInLkguyWO8fu2j3eTyKcoTmCZni6pJLhAx4JvVVlEyKuxLBxn4+v+V4YeBCK2Q/l+BAYGVXONuuudyHi2zAzmX4VdeXpd6cvO0NzIAm/vGiqbdI2Pslo6OAF7hr3dw11wKeVkdxuvWK3taIqaIUAqt7tdje6FpUXcfg6+EGr6gSeLAmfD5bg8OVW6mSkB1/fwkn9MD/9HxBaGTchu8NJc3LkNKaS7UYV3xP3rSXU/+NiKHTH0xkHbp4yPasZXgsRk7aM7t6K/EPQt+fBFO5V/GkyffgkrMIqdMkJde0lsqZ/dWiTg8oz89i3Wr6ihLowxaI/j/hMdXDQrMN+UfWSvDZasrRIQrjhCAXj7KC46ODh7lIe9ep70qd967khgrFoh7M9ivI=
+language: python
+python:
+- '3.6'
+before_install:
+- pip install --upgrade pytest
+install:
+- pip install .[test]
+before_script:
+- curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64
+  > ./cc-test-reporter
+- chmod +x ./cc-test-reporter
+- "./cc-test-reporter before-build"
+after_script:
+- "./cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT"
+script:
+- rm -rf .coverage
+- coverage erase
+- pytest --cov=epigenomic_dataset --cov-report xml:coverage.xml
+- coverage combine --append || true
+- coverage report
+- coverage xml
+- if [ "$TRAVIS_PULL_REQUEST" = "false" ]; then sonar-scanner; fi
+after_success:
+- coveralls
+- python-codacy-coverage -r coverage.xml
+env:
+  global:
+  - secure: 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
+  - secure: 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

README.rst

@@ -0,0 +1,62 @@
+epigenomic_dataset
+=========================================================================================
+|travis| |sonar_quality| |sonar_maintainability| |codacy| |code_climate_maintainability| |pip| |downloads|
+
+Python package wrapping ENCODE epigenomic data for a number of reference cell lines.
+
+How do I install this package?
+----------------------------------------------
+As usual, just download it using pip:
+
+.. code:: shell
+
+    pip install epigenomic_dataset
+
+Tests Coverage
+----------------------------------------------
+Since some software handling coverages sometime get slightly different results, here's three of them:
+
+|coveralls| |sonar_coverage| |code_climate_coverage|
+
+Python package wrapping ENCODE epigenomic data for a number of reference cell lines.
+
+
+.. |travis| image:: https://travis-ci.org/LucaCappelletti94/epigenomic_dataset.png
+   :target: https://travis-ci.org/LucaCappelletti94/epigenomic_dataset
+   :alt: Travis CI build
+
+.. |sonar_quality| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_epigenomic_dataset&metric=alert_status
+    :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_epigenomic_dataset
+    :alt: SonarCloud Quality
+
+.. |sonar_maintainability| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_epigenomic_dataset&metric=sqale_rating
+    :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_epigenomic_dataset
+    :alt: SonarCloud Maintainability
+
+.. |sonar_coverage| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_epigenomic_dataset&metric=coverage
+    :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_epigenomic_dataset
+    :alt: SonarCloud Coverage
+
+.. |coveralls| image:: https://coveralls.io/repos/github/LucaCappelletti94/epigenomic_dataset/badge.svg?branch=master
+    :target: https://coveralls.io/github/LucaCappelletti94/epigenomic_dataset?branch=master
+    :alt: Coveralls Coverage
+
+.. |pip| image:: https://badge.fury.io/py/epigenomic_dataset.svg
+    :target: https://badge.fury.io/py/epigenomic_dataset
+    :alt: Pypi project
+
+.. |downloads| image:: https://pepy.tech/badge/epigenomic_dataset
+    :target: https://pepy.tech/badge/epigenomic_dataset
+    :alt: Pypi total project downloads 
+
+.. |codacy|  image:: https://api.codacy.com/project/badge/Grade/85bc1e3d96bf4c43a2ca70ca233a1bca
+    :target: https://www.codacy.com/manual/LucaCappelletti94/epigenomic_dataset?utm_source=github.com&utm_medium=referral&utm_content=LucaCappelletti94/epigenomic_dataset&utm_campaign=Badge_Grade
+    :alt: Codacy Maintainability
+
+.. |code_climate_maintainability| image:: https://api.codeclimate.com/v1/badges/64bfb8eb5a73959ea0d3/maintainability
+    :target: https://codeclimate.com/github/LucaCappelletti94/epigenomic_dataset/maintainability
+    :alt: Maintainability
+
+.. |code_climate_coverage| image:: https://api.codeclimate.com/v1/badges/64bfb8eb5a73959ea0d3/test_coverage
+    :target: https://codeclimate.com/github/LucaCappelletti94/epigenomic_dataset/test_coverage
+    :alt: Code Climate Coverate

epigenomic_dataset/__version__.py

@@ -0,0 +1,2 @@
+"""Current version of package epigenomic_dataset"""
+__version__ = "1.0.0"

setup.py

@@ -0,0 +1,64 @@
+import os
+import re
+# To use a consistent encoding
+from codecs import open as copen
+
+from setuptools import find_packages, setup
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+# Get the long description from the relevant file
+with copen(os.path.join(here, 'README.rst'), encoding='utf-8') as f:
+    long_description = f.read()
+
+
+def read(*parts):
+    with copen(os.path.join(here, *parts), 'r') as fp:
+        return fp.read()
+
+
+def find_version(*file_paths):
+    version_file = read(*file_paths)
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              version_file, re.M)
+    if version_match:
+        return version_match.group(1)
+    raise RuntimeError("Unable to find version string.")
+
+
+__version__ = find_version("epigenomic_dataset", "__version__.py")
+
+test_deps =[
+    "pytest",
+    "pytest-cov",
+    "coveralls",
+    "validate_version_code",
+    "codacy-coverage"
+]
+
+extras = {
+    'test': test_deps,
+}
+
+setup(
+    name='epigenomic_dataset',
+    version=__version__,
+    description="Python package wrapping ENCODE epigenomic data for a number of reference cell lines.",
+    long_description=long_description,
+    url="https://github.com/LucaCappelletti94/epigenomic_dataset",
+    author="Luca Cappelletti",
+    author_email="[email protected]",
+    # Choose your license
+    license='MIT',
+    include_package_data=True,
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3'
+    ],
+    packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+    tests_require=test_deps,
+    # Add here the package dependencies
+    install_requires=[],
+    extras_require=extras,
+)

sonar-project.properties

@@ -0,0 +1,23 @@
+# =====================================================
+#   Meta-data for the project
+# =====================================================
+sonar.projectName=epigenomic_dataset
+sonar.projectKey=LucaCappelletti94_epigenomic_dataset
+sonar.projectVersion=1.0.0
+sonar.organization=lucacappelletti94-github
+sonar.host.url=https://sonarcloud.io
+sonar.login=epigenomic_dataset
+
+sonar.links.homepage=https://github.com/LucaCappelletti94/epigenomic_dataset
+sonar.links.ci=https://travis-ci.org/LucaCappelletti94/epigenomic_dataset
+sonar.links.scm=https://github.com/LucaCappelletti94/epigenomic_dataset
+sonar.links.issue=https://github.com/LucaCappelletti94/epigenomic_dataset/issues
+
+sonar.language=py
+
+sonar.sources=./epigenomic_dataset
+sonar.tests=./tests
+
+sonar.exclusions=**/__pycache__/*,*/__pycache__/*
+
+sonar.python.coverage.reportPath=coverage.xml

tests/test_version.py

@@ -0,0 +1,5 @@
+from validate_version_code import validate_version_code
+from epigenomic_dataset.__version__ import __version__
+
+def test_version():
+    assert validate_version_code(__version__)