evancofer / manubot-rootstock

Clone me to create your manuscript

Continuous manuscripts written collaboratively on GitHub

Manubot Rootstock provides a system for collaboratively writing scholarly manuscripts via GitHub. This project aims to automate publishing. For example, citation and referencing are largely automated. This project originated with the Deep Review, but was moved here in hopes of making a general purpose template for the system.

A rootstock (or rhizome) is "a plant onto which another variety is grafted". This repository plays the role of a botanical trunk. Fork it and a manuscript will grow.

The most current version of the master branch is built by continuous integration and available via gh-pages. To see what's incoming, check the open pull requests.

Source

The manuscript source is located in content. Text should be written in markdown files, with a digit prefix for ordering (e.g. 01. or 02.) and a .md suffix.

Continuous Integration

When you make a pull request, Travis CI will test whether your changes break the build process to generate the formatted manuscript. The build process aims to detect common errors, such as invalid references. If your build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.

When a pull request is merged, Travis CI performs the build and writes the results to the gh-pages and references branches. The gh-pages branch hosts the following URLs:

• HTML manuscript at https://greenelab.github.io/manubot-rootstock/
• PDF manuscript at https://greenelab.github.io/manubot-rootstock/manuscript.pdf

For continuous integration configuration details, see .travis.yml.

License

This entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/greenelab/manubot-rootstock.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (LICENSE-CC0.md). All files matched by the following blog patterns are dual licensed under CC BY 4.0 and CC0 1.0:

• *.sh
• *.py
• *.yml
• *.json
• *.bib
• *.tsv
• .gitignore

All other files are only available under CC BY 4.0, including:

• *.md
• *.html
• *.pdf

Please open an issue for any question related to licensing.