BioNeMo2 Documentation

Viewing the current documentation on github pages

The documentation should be viewable at https://nvidia.github.io/bionemo-framework/.

Previewing the documentation locally

From the repository root:

# Build the Docker image
docker build -t nvcr.io/nvidian/cvai_bnmo_trng/bionemo2-docs -f docs/Dockerfile .

# Run the Docker container
docker run --rm -it -p 8000:8000 \
  -v ${PWD}/docs:/docs \
  -v ${PWD}/sub-packages:/sub-packages \
  -v ${PWD}/bionemo-recipes:/bionemo-recipes \
  nvcr.io/nvidian/cvai_bnmo_trng/bionemo2-docs:latest

And then navigate to http://0.0.0.0:8000 on your local machine.

Sub-package Documentation

When adding documentation for a new sub-package, ensure it is properly integrated into the documentation site by:

1. Adding an entry to docs/docs/user-guide/examples/SUMMARY.md to include it in the Tutorials section
2. Adding an entry to docs/docs/user-guide/developer-guide/SUMMARY.md to include it in the Developer Guide section

This ensures the sub-package documentation is properly indexed and accessible through the navigation menu.

The sub-package specific documentation itself must be placed alongside the sub-package code in the sub-packages/bionemo-<sub-package-name>/ directory:

• README.md - A root level file that describes the sub-package and how to use it.
• examples/ - A directory that contains documentation or examples specific to the sub-package, in the form of .md or .ipynb files.
• assets/ - A folder that contains any static assets used in any of the above files, e.g. .png files.

When the docs are built, these documentation files will be fetched (via the scripts/gen_ref_pages.py script) for rendering in the main documentation site.

• The README.md will be rendered as an individual page in the User Guide -> Developer Guide -> <sub-package-name>/ section of the documentation site.
• Every file in the examples/ directory will be rendered as an individual page in the User Guide -> Tutorials -> <sub-package-name>/ section of the documentation site.

An example sub-package structure is shown below:

bionemo-<sub-package-name>/
└── assets/
    ├── example_1.png
├── examples/
│   ├── example_1.md
│   └── example_2.ipynb
├── src/
├── tests/
├── LICENSE
├── pyproject.toml
├── README.md
├── VERSION

Hiding/collapsing .ipynb cells

To remove cells from the rendered mkdocs html you can add a remove-cell tag to the cell. Note that remove-output is also an option to hide outputs but not the code cell. Unfortunately remove-input does not seem to be supported.

To collapse jupyter-lab rendered code cells, for example in a brev.dev or user ran jupyter lab session, you can add a special jupyter block to the metadata block for that cell in the json representation of your .ipynb file. You can do this in vscode by clicking the ... above the cell and selecting Edit cell tags (JSON).

A metadata field with both changes, (removed from the rendered docs and collapsed in jupyter) would look like the following:

"metadata": {
    "jupyter": {
     "source_hidden": true
    },
    "tags": [
     "remove-cell"
    ]
   },

aliases for these options can be found in the - mkdocs-jupyter: section of mkdocs.yml in this folder.