diff --git a/documentation/README.md b/documentation/README.md new file mode 100644 index 0000000..0c8a9e1 --- /dev/null +++ b/documentation/README.md @@ -0,0 +1,33 @@ +## Configuration for BioCompose Documentation. + +### This documentation is created using ``sphinx``. To get started with sphinx, run the following commands: + +1. Install sphinx into your environment with ``pip``: + ```bash + pip install sphinx sphinx-autodoc-typehints + ``` +2. Create a ``docs`` or ``documentation`` directory at the root of the ``bio-compose`` repo: + ```bash + mkdir documentation && cd documentation + ``` +3. Run sphinx quickstart in documentation directory: + ```bash + sphinx-quickstart + ``` +4. Ensure auto-complete of documentation is possible from the package's docstrings in the autogenerated ``conf.py`` from #3: + ```python + extensions = [ + 'sphinx.ext.autodoc', + 'sphinx_autodoc_typehints', + # other extensions that are preferred as per the sphinx documentation + ] + ``` +5. Auto-generate documentation from the docstrings: + ```bash + sphinx-apidoc -o /path/to/the/directory/with/index.rst /path/to/the/python/package/or/code/for/which/you/are/creating/the/documenation + ``` + +6. Ensure you are in the directory in which the ``Makefile`` is stored and create the HTML. Be sure to read the returning message from this step: + ```bash + make html + ``` \ No newline at end of file