molgenis-template-py

A template with boilerplate and pre-made configuration for Python projects

How to use

1. Click on the "Use this template" and name your repo. Choose molgenis as owner.
2. Fork it and clone it locally
3. In your favorite IDE:
   • Search for all occurrences of <#CHANGE-ME#> and replace them individually with something sensible
   • Search for all occurrences of <#REPO-NAME#> and replace them all with the name of your new repo (e.g. molgenis-py-foo)
   • Rename (refactor) the package src/molgenis/PROJECT to your project's name (e.g. src/molgenis/foo)
   • Search for <#PACKAGE-NAME#> and replace it with the name you gave the package in the previous step
   • Rename RENAME-Jenkinsfile to Jenkinsfile to activate the build pipeline
4. The example.py file under the src folder contains an example of how to set up the entry points of your library, application or command-line interface. You can use it as a starting point, or you can safely remove it. It's up to you!
5. Remove/edit this file :)

PyScaffold

This project has been set up with PyScaffold 4.1.1. To know more about the standards and best practices it configures, read the documentation. Here are some key points:

• All the configuration for your project should go in setup.cfg
• Development is done in a virtual environment. We use pipenv.
• Development dependencies should be added to the Pipfile (with pipenv install --dev <package>), normal dependencies should go in setup.cfg. pipenv will automatically pick these up when developing.
• You can use tox to build your project and run tests. Just run tox to run all tests. Take a look at tox.ini for the possibilities.
• Code styles are enforced at commit-time. Developers that have not installed the pre-commit hooks will probably see their pull request build fail, so make sure to make that clear to them. There are developer instructions that you can use in your README further below. The actual checks are configured in .pre-commit-config.yaml.

Other info

Here's some other useful information:

• By default, the project is configured to use Python 3.6. This can be changed in setup.cfg
• A build pipeline for Jenkins is added. If you want to add your own build pipeline, feel free to put up a pull request!
• The Jenkinsfile contains a release flow that uses tox to build and release to PyPi. The release can be triggered on Jenkins. A build is first published to TestPyPi, where you can try out the release before committing to the real thing.
• Your repository and its pull requests are automatically checked by Sonar.

Docs below this part can be used in your own README:

For developers

This project uses pre-commit and pipenv for the development workflow.

Install pre-commit and pipenv if you haven't already:

pip install pre-commit
pip install pipenv

Clone or check out this repository with git and install the git commit hooks:

pre-commit install

Create an environment and install the package including all (dev) dependencies:

pipenv install

Activate the virtual environment:

pipenv shell

Build and run the tests:

tox

Note: If you want automatic code formatting in your IDE, you need to configure file watchers for black (the code formatter) and isort (the formatter for import statements). Here are some examples of how to configure them in PyCharm: