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* replace infer_coordinates by parse_alignment_block * update * update * update * update * update * deprecate infer_coordinates * update * update * update * update * fix memory leak --------- Co-authored-by: Michiel de Hoon <mdehoon@tkx249.genome.gsc.riken.jp>
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 <https://en.m.wikipedia.org/wiki/ReStructuredText>`_ format.
Read the `Sphix reST Primer <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#hyperlinks>`_ 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 <https://mg.readthedocs.io/latexmk.html>`_ 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.