project_setup.md

Project Setup

Here we provide some details about the project setup. Most of the choices are explained in the guide. 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.

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.

• Runtime dependencies should be added to setup.cfg in the install_requires list under [options].
• Development dependencies should be added to setup.cfg in one of the lists under [options.extras_require].

Packaging/One command install

You can distribute your code using PyPI. The guide 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
  • PyTest introduction
  • PyTest is listed as a development dependency
  • This is configured in pyproject.toml
• The project uses GitHub action workflows to automatically run tests on GitHub infrastructure against multiple Python versions
  • Workflows can be found in .github/workflows
• Relevant section in the guide

Documentation

• Documentation should be put in the docs/ directory.
• We recommend writing the documentation using MkDocs and Google style docstrings.
• Relevant section in the guide

Coding style conventions and code quality

• Relevant section in the NLeSC guide and README.dev.md.

Continuous code quality

Sonarcloud is used to perform quality analysis and code coverage report

• sonar-project.properties is the SonarCloud configuration file
• .github/workflows/sonar-cloud.yml is the GitHub action workflow which performs the SonarCloud analysis

Package version number

• We recommend using semantic versioning.
• For convenience, the package version is stored in a single place: nplinker/.bumpversion.cfg.
• Don't forget to update the version number before making a release!

Logging

• We recommend using the logging module for getting useful information from your module (instead of using print).
• Relevant section in the guide

CHANGELOG.md

• Document changes to your software package
• Relevant section in the guide

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).
• Follow the making software citable section in the guide.

CODE_OF_CONDUCT.md

• Information about how to behave professionally
• Relevant section in the guide

CONTRIBUTING.md

• Information about how to contribute to this software package
• Relevant section in the guide

MANIFEST.in

• List non-Python files that should be included in a source distribution
• Relevant section in the guide

NOTICE

• List of attributions of this project and Apache-license dependencies
• Relevant section in the guide