Documentation “how to” in depth

Our documentation is build using Sphinx, which uses reStructuredText (and with extensions Markdown) to compile documentation as html, LaTeX, PDF and more. It takes care of linking all pages together, building a search index and also extraction the documentation written in the docstrings of the code.

How to use Sphinx in general

First you have enter your virtual env (if you don’t know how, have a look here: Get Started! or Virtual envs “how to” in depth)

When you are in your virtual env (here called glotaran) navigate to glotarans docs folder:

(glotaran)$cd docs


Consider for the following steps that, if you are on a Posix system (Linux, MacOS, BSD or Git Bash/migwin on Windows) use make, on normal Windows cmd/PS use make.bat instead. If your Git Bash is missing the make functionality you can follow this guide.

Once you are in the docs folder, generating/compiling the documentation is as easy as running:

(glotaran)$make html

The documentation than can be found is the folder docs/_build/html, where you can open it by double clicking index.html


The reStructuredText Syntax isn’t as forgiving as html (where browsers correct most of the falsey). It’s more like LaTeX, which is why it is recommended to compile often, for errors not to stack up.

It might happen, that you change the documentation and can’t see the changes after a refresh in the browser. Since Sphinx to reduce the compile time, it only recompiles the changed files, which can lead to problems if you add new files, because the indexing wasn’t updated. If this happens, you can force Sphinx to rebuild the whole documentation by first running:

(glotaran)$make clean


  1. Change the docs

  2. Build the docs:

    (glotaran)$make html
  3. Look at the commandline interface and make sure no errors happened.

  4. Refresh the you browser to see the changes.

  5. If there are no changes, even so there was no error, force Sphinx to rebuild all:

    (glotaran)$make clean html
  6. Start with step 1 again.

Useful resources:
Often used commands (for Windows replace `make with `make.bat):
  • (glotaran)$make html
  • (glotaran)$make clean
  • (glotaran)$make clean html
  • (glotaran)$make help

Generate API Documentation

The API Documentation will be generated automatically form the docstrings. Those Docstrings should be formatted in the NumPyDoc style. Please make use of all available features as you see fit.

The features are:
  • Parameters
  • Returns
  • Raises
  • See Also
  • Notes
  • References
  • Examples

If you add packages, modules, classes, methods, attributes, functions or exceptions, please read the introduction of Api Documentation Creation Helper.

Often used commands (for Windows replace `make with `make.bat):

  • (glotaran)$make html
  • (glotaran)$make clean_all
  • (glotaran)$make api_docs
  • (glotaran)$make clean_all api_docs html

Api Documentation Creation Helper

The helper Module to generate the API documentation is located at docs/

The functionality is available by calling make api_docs on a Posix system or make.bat api_docs on Windows.

If you add packages, modules, classes, methods, attributes, functions or exceptions, you might need to run make clean_all on a Posix system or make.bat clean_all on Windows to see changes in the documentation.

The generation of the API is done by traversing the main package traverse_module and listing all child modules for autosummary to process (see write_api_documentation, api_documentation.rst and _templates/api_documentation_template.rst).

If the child module is also a package all its contained modules will be listed (see write_known_packages, known_packages.rst, _templates/known_packages_template.rst and _templates/autosummary/module.rst).

To understand how it works in detail the following links might be of help: