README.rst

Contributing to the Biopython Tutorial

Installing the tools you need

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

Formatting code examples

Code examples should be formatted using minted. Also, the Biopython tutorial uses its own system for testing code examples, which is located in test_Tutorial.py. You can read more about this system in the testing chapter of the Biopython Tutorial.

Here is an example of Python code that uses the console to show output:

%doctest path-to-folder
\begin{minted}{pycon}
>>> from Bio import SeqIO
\end{minted}

These examples should use %doctest to verify that the output is correct.

Here is an example of Python code that does not show output:

\begin{minted}{python}
from Bio import SeqIO
\end{minted}

Formatting text

Format headings as follows:

Chapter titles:

\chapter{Title of Chapter}
\label{chapter:chapterlabel}

Section titles:

\section{Title of Section}
\label{sec:sectionlabel}

Subsection titles:

\subsection{Title of Subsection}

When referring to code in the middle of a paragraph, format it as follows:

\verb|variable_name|

This will render variable_name in a monospace font. Within the pipe characters, underscores will be interpreted literally, so they do not need to be escaped.

Building the documentation

Build the documentation by running "make" in the Docs folder.

Once the documentation has been generated, you can inspect either Tutorial.pdf or Tutorial.html in the Docs directory to see if the output is correct.