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 ruff,
• 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.

python -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

Name	Default value	Explanation
directory_name	my-python-project	Name of the directory that contains the package. Avoid using spaces or uppercase letters for the best experience across operating systems. To get an impression of what will be generated, see the directory tree below
package_name	my_python_package	Name of the package. Avoid using spaces, dashes, or uppercase letters for the best experience across operating systems.
package_short_description	Short description of package	The information that you enter here will end up in the README, documentation, license, and pyproject.toml, so it may be a good idea to prepare something in advance.
keyword1	keyword1	A term that describes your package.
keyword2	keyword2	Another term that describes your package.
version	0.1.0
github_organization	<my-github-organization>	GitHub organization that will contain this project's repository. This can also be your GitHub user name.
license	Apache Software License 2.0	The software license under which the code is made available.
full_name	Jane Smith	Your full name, e.g. Jane Smith.
email	yourname@esciencecenter.nl	Your (work) email address.
copyright_holder	Netherlands eScience Center	Name(s) of the organization(s) or person(s) who hold the copyright of the software.
code_of_conduct_email	yourname@esciencecenter.nl	Email address of the person who should be contacted in case of violations of the Code of Conduct.

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/
├── 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
├── .pylintrc
├── pyproject.toml
├── README.dev.md
├── README.md
├── 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 (see this discussion). Make a PR to add your project here, or simply ping us in an issue!

How to contribute

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