Initial commit

.gitignore

+# 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/
+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
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

.travis.yml

+language: python
+os: linux
+
+python:
+  - "3.8"
+
+env:
+  - TESTENV=test
+  - TESTENV=lint
+  - TESTENV=docs
+
+install:
+  - if [[ "$TESTENV" != "docs" ]]; then pip install -r requirements-test.txt; fi
+  - if [[ "$TESTENV" == "docs" ]]; then pip install -r requirements-doc.txt; fi
+  - pip install .
+
+script:
+  - if [[ "$TESTENV" == "test" ]]; then coverage run -m pytest; fi
+  - if [[ "$TESTENV" == "test" ]]; then coverage report -m; fi
+  - if [[ "$TESTENV" == "lint" ]]; then pylint src tests; fi
+  - if [[ "$TESTENV" == "lint" ]]; then mypy src tests; fi
+  - if [[ "$TESTENV" == "docs" ]]; then ./scripts/build_docs.sh; fi

LICENSE

+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
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+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
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+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
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+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
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+          include a readable copy of the attribution notices contained
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+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
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+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      risks associated with Your exercise of permissions under this License.
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+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
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+      on Your own behalf and on Your sole responsibility, not on behalf
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+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
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+      file or class name and description of purpose be included on the
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+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
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+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

MANIFEST.in

+include LICENSE
+include NOTICE
+include VERSION

NOTICE

+Ensembl Python Template
+Copyright 2018-2021 EMBL-European Bioinformatics Institute
+
+This product includes software developed at:
+- EMBL-European Bioinformatics Institute

README.md

+# Ensembl Python Template
+
+[![Documentation Status](https://readthedocs.org/projects/template-python/badge/?version=latest)](http://template-python.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/Ensembl/templat-python.svg?branch=master)](https://travis-ci.com/Ensembl/template-python)
+
+Example Ensembl Python Project.
+
+This repo structure can be forked and used as the base template for developing a
+Python package (app or library).
+It contains boilerplate code and configuration for unit testing,
+linting, type checking, automatic documentation and CI/CD.
+
+
+## Requirements
+
+- pyenv (with pyenv-virtualenv plugin)
+- Python 3.8+
+- Python packages
+  - Test
+    - pytest
+    - pylint
+    - mypy
+  - Docs
+    - Sphinx
+    - mock
+    - sphinx-rtd-theme
+  - Dev
+    - ipython
+    - black
+
+
+## Getting Started
+
+This template is a simple but fully functioning Python project.
+
+#### Template Project Layout
+
+```
+.
+├── .gitignore               <- File patterns to be ignored by Git
+├── .travis.yml              <- Travis CI instructions
+├── LICENSE                  <- License text
+├── MANIFEST.in              <- Files to be included in source distribution
+├── NOTICE                   <- Notice file (required by License)
+├── README.md                <- This file
+├── VERSION                  <- Version file (try using semantic versioning)
+├── docs                     <- Folder with boilerplate for auto-generated Sphinx docs
+│   ├── Makefile
+│   ├── _static
+│   │   └── style.css
+│   ├── _templates
+│   │   └── layout.html
+│   ├── conf.py              <- Sphinx configuration
+│   ├── index.rst
+│   ├── install.rst
+│   └── license.rst
+├── pylintrc                 <- Pylint (linter) configuration
+├── pyproject.toml           <- Various other Python tools packaging configuration
+├── requirements-dev.txt     <- Third-party packages required for development environment
+├── requirements-doc.txt     <- Third-party packages required for building Sphinx docs
+├── requirements-test.txt    <- Third-party packages required for running tests
+├── requirements.txt         <- Third-party packages required for this project
+├── scripts                  <- Utility scripts
+│   └── build_docs.sh        <- Script to generate modules files and build docs
+├── setup.py                 <- Module executed by pip when installing this project
+├── src                      <- Root folder for this project source code
+│   ├── ensembl
+│   │   ├── __init__.py
+│   │   └── hello_world.py
+└── tests                    <- Root folder for tests code
+    └── test_hello.py
+```
+
+#### Creating a new project
+
+Clone this template:
+```
+git clone --depth 1 -b master https://github.com/Ensembl/template-python.git
+```
+
+Remove Git repository data and rename the main folder:
+```
+rm -rf template-python/.git
+mv template-python <NEW_PROJECT_NAME>
+cd <NEW_PROJECT_NAME>
+git init
+```
+
+The following files (or folder names) will need to be modified:
+- `NOTICE`: Substitute "Ensembl Python Template" with your project's name
+- `setup.py`: Change package name and other settings
+- `docs/conf.py`: Change accordigly to project's name
+- `docs/install.rst`: Change installation instructions accordingly
+- `README.md`: Write a meaningful README for your project
+
+Once done with the basic customisation, create the initial commit:
+```
+cd <NEW_PROJECT_NAME>
+git add .
+git commit -m 'Initial commit'
+```
+
+#### Installing the development environment (with Pyenv)
+
+```
+pyenv virtualenv 3.8 <VIRTUAL-ENVIRONMENT-NAME>
+cd <NEW_PROJECT_NAME>
+pyenv local <VIRTUAL-ENVIRONMENT-NAME>
+pip install -r requirements-dev.txt
+pip install -e .
+```
+
+#### Testing
+
+Run test suite:
+```
+cd <NEW_PROJECT_NAME>
+pytest
+```
+
+To run tests, calculate and display testing coverage stats:
+```
+cd <NEW_PROJECT_NAME>
+coverage run -m pytest
+coverage report -m
+```
+
+
+#### Generate documentation
+```
+cd <NEW_PROJECT_NAME>
+./scripts/build_docs.sh
+```
+Open automatically generated documentation page at `docs/_build/html/index.html`
+
+
+#### Automatic Formatting
+```
+cd <NEW_PROJECT_NAME>
+black --check src tests
+```
+Use `--diff` to print a diff of what Black would change, without actually changing the files.
+
+To actually reformat all files contained in `src` and `test`:
+```
+cd <NEW_PROJECT_NAME>
+black src tests
+```
+
+#### Linting and type checking
+```
+cd <NEW_PROJECT_NAME>
+pylint src tests
+mypy src tests
+```
+Pylint will check the code for syntax, name errors and formatting style.
+Mypy will use type hints to statically type check the code.
+
+It should be relatively easy (and definitely useful) to integrate both `pylint` and `mypy`
+in your IDE/Text editor.
+
+
+## Resources
+
+#### Python Documentation
+- [Official Python Docs](https://docs.python.org/3/)
+
+#### Python distributions and virtual environments management
+- [Pyenv docs](https://github.com/pyenv/pyenv#readme)
+- [Pyenv virtualenv docs](https://github.com/pyenv/pyenv-virtualenv#readme)
+
+#### Auto-generating documentation
+- [Spinx Docs](https://www.sphinx-doc.org/en/master/index.html)
+
+#### Linting, type checking and formatting
+- [Pylint](https://www.pylint.org/)
+- [Mypy](https://mypy.readthedocs.io/en/stable/)
+- [Black](https://black.readthedocs.io/en/stable/)
+- [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings)
+
+#### Testing
+- [pytest](https://docs.pytest.org/en/6.2.x/)
+- [Coverage](https://coverage.readthedocs.io/)
+
+#### Development tools
+- [IPython](https://ipython.org/)
+
+#### Distributing
+- [Packaging Python](https://packaging.python.org/tutorials/packaging-projects/)
+- [Apache 2.0 License](https://www.apache.org/licenses/LICENSE-2.0#apply)
+- [Semantic Versioning](https://semver.org/)
+

VERSION

+0.0.1

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/style.css

+.rst-content .highlight > pre {
+	line-height: 1.5;
+}
\ No newline at end of file

docs/_templates/layout.html

+{% extends "!layout.html" %}
+{% block extrahead %}
+    <link href="{{ pathto("_static/style.css", True) }}" rel="stylesheet" type="text/css">
+{% endblock %}
\ No newline at end of file

docs/conf.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Documentation build configuration file, created by
+# sphinx-quickstart on Thu Feb 23 13:50:00 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+import os
+import sys
+from mock import Mock as MagicMock
+
+sys.path.insert(0, os.path.abspath('..'))
+
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+        return MagicMock()
+
+MOCK_MODULES = []
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
+import ensembl.hello_world
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    #'sphinx.ext.intersphinx',
+    #'sphinx.ext.todo',
+    #'sphinx.ext.coverage',
+    'sphinx.ext.viewcode'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'Ensembl Python Template'
+copyright = '2021 EMBL-European Bioinformatics Institute'
+author = 'Ensembl'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+#html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Ensembldoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'ensembl_template.tex', 'Ensembl - Template Documentation',
+     'Ensembl', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'ensembl-python-template', 'Ensembl - Python Template Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'Ensembl-Python-Template', 'Ensembl - Python Template Documentation',
+     author, 'Ensembl-Python-Template', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/index.rst

+.. See the NOTICE file distributed with this work for additional information
+   regarding copyright ownership.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+.. Documentation master file, created by sphinx-quickstart on Thu Feb 23 13:50:00 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Documentation for Template
+==========================
+
+.. toctree::
+   :caption: Table of Contents
+   :name: mastertoc
+   :maxdepth: 2
+
+   install
+   license
+   modules
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/install.rst

+.. See the NOTICE file distributed with this work for additional information
+   regarding copyright ownership.
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+Requirements and Installation
+=============================
+
+Requirements
+------------
+
+Software
+^^^^^^^^
+
+- Python 3.8+
+
+Python Modules
+^^^^^^^^^^^^^^
+
+- pylint
+- pytest
+
+Installation
+------------
+Directly from GitHub:
+
+.. code-block:: none
+   :linenos:
+
+   git clone https://github.com/Ensembl/template-python
+
+Using pip:
+
+.. code-block:: none
+   :linenos:
+
+   pip install git+https://github.com/Ensembl/template-python#egg=template-python

docs/license.rst

+License
+-------
+
+   Apache License
+   Version 2.0, January 2004
+   http://www.apache.org/licenses/
+
+
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+
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+
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+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

pylintrc

+[MASTER]
+
+# Use multiple processes to speed up Pylint.
+jobs=1
+
+[MESSAGES CONTROL]
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once).You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use"--disable=all --enable=classes
+# --disable=W"
+disable=similarities,invalid-name,too-many-statements,too-many-arguments,too-many-locals,too-few-public-methods,relative-import,no-self-use,wildcard-import
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=110
+
+# Remove error "Module 'py' has no 'path' member (no-member)" (https://py.readthedocs.io/en/latest/path.html)
+# Remove error "Generator 'generator' has no 'ne' member (no-member)": the variable is actually a pandas.DataFrame object
+generated-members=py.*

pyproject.toml

+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.mypy]
+python_version = 3.8
+mypy_path = "src"
+ignore_missing_imports = true
+
+[tool.coverage.run]
+source = ["src"]
+
+

requirements-dev.txt

+-r requirements-doc.txt
+-r requirements-test.txt
+black
+ipython

requirements-doc.txt

+Sphinx
+mock
+sphinx-rtd-theme

requirements-test.txt

+-r requirements.txt
+pytest
+pylint
+mypy
+coverage

requirements.txt

+# List third-party packages here