A template repository for new projects

This template uses cookiecutter to create a new project instance.

The contents of the template can be seen here. Varibles with {{ cookiecuter... }} will be replaced with the values given at the time of repository creation from the template.

Usage

Install cookiecutter and use it in the following manner:

python -m pip install cookiecutter
cookiecutter gh:rendeirolab/_project_template

You can also clone the repository and point to its path as sole argument.

Fields to be provided are:

• [required] project_slug: A consise and unique string for the project (no whitespace).
• project_description: A human readable description of the project.
• editor: Which text editor is being used - will generate a few auxiliary files for specific editors.
• zenodo_doi: A DOI for data used/produced by the project.
• biorxiv_doi: A DOI for the project's preprint.
• full_name: The user's full name.
• username: The user's username (no whitespace).
• email: The user's email.
• [do not change] template_version: This will keep track of what template version was used to

Defaults

To have default values filled in (e.g. username, email) create a .cookiecutterrc file or use a COOKIECUTTER_CONFIG environmental variable as described here. The file should have, for example:

default_context:
    full_name: "Audrey Roy"
    username: "aroy"
    email: "[email protected]"

Authenticating with git/Github

To use SSH to authenticate with Github (recommended):

1. Generate a ssh-key with the command: ssh-keygen
2. Add the generated public key to your Github profile settings
3. Make cookiecutter use SSH by default by adding to your ~/.cookiecutterrc file:

abbreviations:
    gh: [email protected]:{0}.git

Alternatively, you can continue to use HTTPS (default) but if you have two factor authentication activated in your Github profile (highly recommended), you will have to:

1. Create a Github application token.
2. Provide that as your Github password when interacting with Github using git/cookiecutter.

Editing

To make modifications/improvements to the template open a pull request on GitHub.

When merging the PR, make sure to:

1. Add the modifications to the Changelog
2. Increment the version number on cookiecutter.json.