For Developers

Anyone can contribute to the development of PyCogent3, not just registered developers. If you figure out a solution to something using PyCogent3 that you’d like to share, or if you have ideas for improving the current documentation, please consider forking and submitting a pull request and we’ll look into including it in PyCogent3!

Grabbing from Bitbucket

To grab PyCogent3 from Bitbucket, do the following:

$ hg clone ssh:// PyCogent3

Building/testing the documentation

To build the documentation or doctest the contents, you’ll need to install Sphinx:

$ pip install sphinx

Generating the html form of the documentation requires changing into the doc directory and executing a make command:

$ cd path/to/PyCogent3/doc
$ make html
... # bunch of output
Build finished. The HTML pages are in _build/html.

The index file czan be found in PyCogent3/doc/_build/html/index.html is the root of the documentation.

You can also generate a pdf file, using the Sphinx latex generation capacity. This is slightly more involved. (It also requires that you have an installation of TeTex.)

First generate the latex

$ make latex
... # bunch of output
Build finished; the LaTeX files are in _build/latex.
Run `make all-pdf' or `make all-ps' in that directory to run these through (pdf)latex.

then change into the latex dir and build the pdf

$ cd _build/latex
$ make all-pdf

You can now open PyCogent3.pdf.

To actually test the documentation, you need to be in the doc directory and then execute another make command:

$ cd path/to/PyCogent3/doc
$ make doctest

The results are in _build/doctest/output.txt.


The documentation does not test for presence of 3rd party dependencies (such as applications or python modules) like the PyCogent3 unittest test suite. If you don’t have all the 3rd party applications installed you will see failures. At this point no effort is being expended to hide such failures.

Adding to the documentation

You can maximise the cogent3 user experience for yourself and others by contributing to the documentation. If you solve a problem that you think might prove useful to others then fork, add it into the documentation and do a pull request. If you can think of ways to improve the existing documents let us know via a ticket.

For guidance on adding documentation, look at any of the existing examples. The restructured text format is pretty easy to write (for overview see the Sphinx rest overview). The conventions adopted by PyCogent3 are to use heading levels to be consistent with the standard (taken from Sphinx headings). They are

  • # with overline, for parts
  • * with overline, for chapters
  • =, for sections
  • -, for subsections
  • ^, for subsubsections
  • “, for paragraphs
  • +, added for sub-paragraphs (non-standard)

If it’s a use-case, create your file in the examples directory, giving it a .rst suffix. Link it into the documentation tree, adding a line into the examples/index.rst file. If it’s something you think should be added into the cookbook, add it into the appropriate cookbook document.

The new documentation checklist

Things you should check before committing your new document:

  • Add a line at the beginning with yourself as author (.. sectionauthor:: My Name) so people can contact you with feedback.

  • Add any data files used in your documentation under PyCogent3/doc/data/

  • Add a download link to those files to PyCogent3/doc/data_file_links.rst following the style employed in that file.

  • Spellcheck!!

  • Check what you wrote is valid restructured text by building the documents for both html and latex. If your document isn’t connected into the table of contents, Sphinx will print a warning to screen.

  • Check you have correctly marked up the content and that it looks OK. Make sure that python code and shell commands are correctly highlighted and that literals are marked up as literals. In particular, check the latex build since it is common for text to span beyond the page margins. If the latter happens, revise your document!

  • Check that it works (rather than testing the entire suite, you can use the convenience script within doc). For instance, the following is a single test of one file:

    $ cd path/to/PyCogent3/doc
    $ python examples/reverse_complement.rst

Adding TODOs

Add todo’s into the rst files using the todo directive as in

.. todo::

    some task

To see the list of todo’s in the project, uncomment the line that sets todo_include_todos=True in doc/, then cd into the doc/ and make the html docs again. The todo’s are listed on the main page.


Be sure to revert the file back to it’s original state so you don’t accidentally commit the change as this affects everyone else’s documentation too!

Developing C-extensions

Extensions for PyCogent3 should be written in Cython.

If you have any questions, contact Gavin.