README.rst

January 7, 2020 ยท View on GitHub

################################################################################ PyCFF ################################################################################

A Python library for reading and writing CFF files.

Note that this is an early prototype. Please do not use this for anything beyond playing with things, it is completely untested and probably buggy.

Project Setup

Here we provide some details about the project setup. Most of the choices are explained in the guide <https://guide.esciencecenter.nl>_. Links to the relevant sections are included below. Feel free to remove this text when the development of the software package takes off.

For a quick reference on software development, we refer to the software guide checklist <https://guide.esciencecenter.nl/best_practices/checklist.html>_.

Version control

Once your Python package is created, put it under version control <https://guide.esciencecenter.nl/best_practices/version_control.html>! We recommend using git <http://git-scm.com/> and github <https://github.com/>_.

.. code-block:: console

cd pycff git init git add -A git commit

To put your code on github, follow this tutorial <https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/>_.

Python versions

This repository is set up with Python versions:

  • 3.5
  • 3.6
  • 3.7

Add or remove Python versions based on project requirements. The guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html>_ contains more information about Python versions and writing Python 2 and 3 compatible code.

Package management and dependencies

You can use either pip or conda for installing dependencies and package management. This repository does not force you to use one or the other, as project requirements differ. For advice on what to use, please check the relevant section of the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#dependencies-and-package-management>_.

  • Dependencies should be added to setup.py in the install_requires list.

Packaging/One command install

You can distribute your code using pipy or conda. Again, the project template does not enforce the use of either one. The guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#building-and-packaging-code>_ can help you decide which tool to use for packaging.

Testing and code coverage

  • Tests should be put in the tests folder.

  • The testing framework used is PyTest <https://pytest.org>_

    • PyTest introduction <http://pythontesting.net/framework/pytest/pytest-introduction/>_

  • Tests can be run with python setup.py test

    • This is configured in setup.py and setup.cfg

  • Use Travis CI <https://travis-ci.com/>_ to automatically run tests and to test using multiple Python versions

    • Configuration can be found in .travis.yml
    • Getting started with Travis CI <https://docs.travis-ci.com/user/getting-started/>_

  • TODO: add something about code quality/coverage tool?

  • Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#testing>_

Documentation

  • Documentation should be put in the docs folder. The contents have been generated using sphinx-quickstart (Sphinx version 1.6.5).

  • We recommend writing the documentation using Restructured Text (reST) and Google style docstrings.

    • Restructured Text (reST) and Sphinx CheatSheet <http://openalea.gforge.inria.fr/doc/openalea/doc/_build/html/source/sphinx/rest_syntax.html>_
    • Google style docstring examples <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>_.

  • To generate html documentation run python setup.py build_sphinx

    • This is configured in setup.cfg
    • Alternatively, run make html in the docs folder.

  • The docs/_static and docs/_templates contain an (empty) .gitignore file, to be able to add them to the repository. These two files can be safely removed (or you can just leave them there).

  • To put the documentation on Read the Docs <https://readthedocs.org>_, log in to your Read the Docs account, and import the repository (under 'My Projects').

    • Include the link to the documentation in this README_.

  • Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#writingdocumentation>_

Coding style conventions and code quality

  • Check your code style with prospector
  • You may need run pip install .[dev] first, to install the required dependencies
  • You can use yapf to fix the readability of your code style and isort to format and group your imports
  • Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#coding-style-conventions>_

CHANGELOG.rst

  • Document changes to your software package
  • Relevant section in the guide <https://guide.esciencecenter.nl/software/releases.html#changelogmd>_

CITATION.cff

  • To allow others to cite your software, add a CITATION.cff file
  • It only makes sense to do this once there is something to cite (e.g., a software release with a DOI).
  • To generate a CITATION.cff file given a DOI, use doi2cff <https://github.com/citation-file-format/doi2cff>_.
  • Relevant section in the guide <https://guide.esciencecenter.nl/software/documentation.html#citation-file>_

CODE_OF_CONDUCT.rst

  • Information about how to behave professionally
  • Relevant section in the guide <https://guide.esciencecenter.nl/software/documentation.html#code-of-conduct>_

CONTRIBUTING.rst

  • Information about how to contribute to this software package
  • Relevant section in the guide <https://guide.esciencecenter.nl/software/documentation.html#contribution-guidelines>_

MANIFEST.in

  • List non-Python files that should be included in a source distribution
  • Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/language_guides/python.html#building-and-packaging-code>_

NOTICE

  • List of licenses of the project and dependencies
  • Relevant section in the guide <https://guide.esciencecenter.nl/best_practices/licensing.html#notice>_

Installation

To install pycff, do:

.. code-block:: console

git clone https://github.com/NLeSC/pycff.git cd pycff pip install .

Run tests (including coverage) with:

.. code-block:: console

python setup.py test

Documentation

.. _README:

Include a link to your project's full documentation here.

Contributing

If you want to contribute to the development of PyCFF, have a look at the contribution guidelines <CONTRIBUTING.rst>_.

License

Copyright (c) 2018, Netherlands eScience Center

Apache Software License 2.0

Credits

This package was created with Cookiecutter <https://github.com/audreyr/cookiecutter>_ and the NLeSC/python-template <https://github.com/NLeSC/python-template>_.