HDMF Documentation Utilities

This project is under active development. Its content, API and behavior may change at any time. We mean it.

Overview

This project is a collection of CLIs, scripts and modules useful to generate the HDMF documentation.

Using hdmf-docutils to generate documentation for an extension: http://pynwb.readthedocs.io/en/latest/extensions.html#documenting-extensions

To cite this tool use: (HDMF Documentation Utilities, RRID:SCR_021341)

Installation

pip install hdmf-docutils

Available Tools

• hdmf_generate_format_docs: Generate figures and RST documents from the HDMF YAML specification for the format specification documentation. Previously called "nwb_generate_format_docs".
• hdmf_init_sphinx_extension_doc: Create format specification SPHINX documentation for an HDMF extension. Previously called "nwb_init_sphinx_extension_doc".
• hdmf_gallery_prototype: Tool for prototyping sphinx gallery examples. Previously called "nwb_gallery_prototype".

Available Modules

• hdmf_docutils/doctools/*: This package contains modules used to generate figures of the hierarchies of HDMF files and specifications as well as to help with the programmatic generation of reStructuredText (RST) documents.

Available Notebooks

• compare-hdf5-files.ipynb: This notebook illustrates how to compare hdf5 files.

History

nwb-docutils was renamed to hdmf-docutils and generalized to be (mostly) independent of NWB in January, 2020.

nwb-docutils was initially a sub-directory of the nwb-schema project. Corresponding history was extracted during the 4th NWB Hackathon into a dedicated pip-installable project to facilitate its use by both core NWB documentation projects and various NWB extensions.

Usage

pip install hdmf-docutils

For the purpose of this example, we assume that our current directory has the following structure.

- my_extension/
  - my_extension_source/
      - mylab.namespace.yaml
      - mylab.specs.yaml
      - ...
      - docs/  (Optional)
          - mylab_description.rst
          - mylab_release_notes.rst

In addition to Python 3.x, you will also need sphinx (including the sphinx-quickstart tool) installed. Sphinx is available here http://www.sphinx-doc.org/en/stable/install.html .

We can now create the sources of our documentation as follows:

   python3 hdmf_init_sphinx_extension_doc  \
                --project my-extension \
                --author "Dr. Master Expert" \
                --version "1.2.3" \
                --release alpha \
                --output my_extension_docs \
                --spec_dir my_extension_source \
                --namespace_filename mylab.namespace.yaml \
                --default_namespace mylab
                --external_description my_extension_source/docs/mylab_description.rst \  (Optional)
                --external_release_notes my_extension_source/docs/mylab_release_notes.rst \  (Optional)

.. tip::

   Additional instructions for how to use and customize the extension documentations are also available
   in the ``Readme.md`` file that  ``init_sphinx_extension_doc.py`` automatically adds to the docs.

Tip

See make help for a list of available options for building the documentation in many different output formats (e.g., PDF, ePub, LaTeX, etc.).

Tip

See python3 init_sphinx_extension_doc.py --help for a complete list of option to customize the documentation directly during initialization.

Tip

The above example included additional description and release note docs as part of the specification. These are included in the docs via .. include commands so that changes in those files are automatically picked up when rebuilding to docs. Alternatively, we can also add custom documentation directly to the docs. In this case the options --custom_description format_description.rst and --custom_release_notes format_release_notes.rst of the init_sphinx_extension_doc.py script are useful to automatically generate the basic setup for those files so that one can easily start to add content directly without having to worry about the additional setup.