README.rst

Contributing to the Biopython Tutorial

Installing the requirements

In the Biopython directory, install the required packages for building the documentation with:

pip install -r .circleci/requirements-sphinx.txt

ReStructered Text Markup Language

The tutorials are written in ReStructered Text format. Read the Sphix reST Primer to learn how to use this format.

Building the documentation

Build the documentation in HTML by running make html in the Docs folder. Make sure that you have installed necessary requirements (see instructions above).

To view the generated documentation, open Doc/_build/html/index.html in your browser.

Build a PDF of the documentation using make latexpdf. This command depends on Latexmk and LaTeX tooling.

On Ubuntu, you can install these with the following commands:

sudo apt install hevea texlive-latex-base texlive-latex-extra python-pygments

On Fedora (tested for Workstation 33):

dnf install texlive-scheme-basic texlive-preprint \
            texlive-comment texlive-minted hevea

Testing code examples

The Biopython tutorial uses its own system for testing code examples, which is located in Tests/test_Tutorial.py. You can read more about this system in the testing chapter of the Biopython Tutorial.