Netherlands eScience Center Python Template

Spend less time setting up and configuring your new Python packages and comply with the Netherlands eScience Center Software Development Guide from the start.

Use this Cookiecutter template to generate an empty Python package. Features include:

• Boilerplate unit tests and documentation,
• Python static setup configuration,
• Open source software license,
• Continuous integration with GitHub action workflows for building, testing, link checking and linting,
• Code style checking with prospector,
• Editorconfig,
• Usage and contribution documents:
  • README.md for package users,
  • README.dev.md for package developer,
  • project_setup.md with extensive documentation about project setup,
  • Change log,
  • Code of Conduct,
  • Contributing guidelines,
• Continuous code quality and code coverage reporting using Sonarcloud,
• Automatic creation of issues with instructions how to pass all GitHub action workflows and integrate with services like Zenodo and Read the Docs,
• Instructions how to make package citable
• FAIR software recommendation badge,
• Optional pre commit hook to catch lint errors early

Badges

fair-software.nl recommendations
(1/5) code repository
(2/5) license
(3/5) community registry
(4/5) citation
(5/5) checklist
overall
Other best practices
GitHub Actions
Citation metadata consistency
MarkDown link checker
Tests

How to use

Step 1/3: Install cookiecutter

We recommend installing cookiecutter in user space as per cookiecutter's instructions. This way, you don't have to install cookiecutter for every new project.

python3 -m pip install --user --upgrade cookiecutter

Step 2/3: Generate the files and directory structure

Run cookiecutter with the template:

# Notes:
#   1. See table below for explanation of each question
#   2. The files will be generated in a new directory
cookiecutter https://github.com/nlesc/python-template.git

Once the project files have been generated, follow the steps outlined in {{cookiecutter.directory_name}}/next_steps.md.

Step 3/3: Read about what was just generated

Good job! You have now generated the skeleton for your package:

my-python-project/
├── .bumpversion.cfg
├── CHANGELOG.md
├── CITATION.cff
├── CODE_OF_CONDUCT.md
├── CONTRIBUTING.md
├── docs
│   ├── conf.py
│   ├── index.rst
│   ├── make.bat
│   ├── Makefile
│   ├── _static
│   │   └── theme_overrides.css
│   └── _templates
│       └── .gitignore
├── .editorconfig
├── .githooks
│   └── pre-commit
├── .github
│   ├── next_steps
│   │   ├── 01_sonarcloud_integration.md
│   │   ├── 02_citation.md
│   │   ├── 03_readthedocs.md
│   │   ├── 04_zenodo_integration.md
│   │   └── 05_linting.md
│   └── workflows
│       ├── build.yml
│       ├── cffconvert.yml
│       ├── lint.yml
│       ├── markdown-link-check.yml
│       ├── next_steps.yml
│       └── sonarcloud.yml
├── .gitignore
├── LICENSE
├── MANIFEST.in
├── .mlc-config.json
├── my_python_package
│   ├── __init__.py
│   ├── my_module.py
│   └── __version__.py
├── next_steps.md
├── NOTICE
├── project_setup.md
├── .prospector.yml
├── .pylintrc
├── pyproject.toml
├── README.dev.md
├── README.md
├── setup.cfg
├── setup.py
├── sonar-project.properties
└── tests
    ├── __init__.py
    └── test_my_module.py

For an explanation of what's there, read on in the project_setup.md file. There are also instructions on how to apply the template to an existing Python package.

Examples

Many developers have gone before you in using this template to get started quickly. Check out their projects in the list below:

1. Cerise: https://github.com/MD-Studio/cerise
2. cerulean: https://github.com/MD-Studio/cerulean
3. cffconvert: https://github.com/citation-file-format/cff-converter-python
4. fairtally: https://github.com/fair-software/fairtally
5. howfairis: https://github.com/fair-software/howfairis
6. matchms: https://github.com/matchms/matchms
7. MUSCLE 3: https://github.com/multiscale/muscle3
8. pycff: https://github.com/citation-file-format/pycff
9. spec2vec: https://github.com/iomega/spec2vec
10. yatiml: https://github.com/yatiml/yatiml
11. ... And many more. Make a PR to add your project here!

How to contribute

Suggestions/improvements/edits are most welcome. Please read the contribution guidelines before creating an issue or a pull request.