- switch from unstructured dictionaries to DataClasses for more transparent data handling
- add explanation / example of dimorphism
- 3d plots
- neuroglancer links
- network graphs
- partner summaries
- dendrogram/umap of the N closest types
- for sex-specific neurons: closest type in the other sex
- Install uv
- Clone this repository
The website is build using mkdocs and jinja2 templates. Dependencies are managed using uv.
In addition, you need to set a number of environment variables to set up for fetching meta data. They are either secrets (credentials) for accessing data, or they are servers whose internal names we don't want to make public.
They are:
CAVE_SECRET: API token for CAVE (FlyWire); this should not be needed, and I will remove it in the futureSEATABLE_SERVER: URL for our FlyTable instanceSEATABLE_TOKEN: API token for FlyTableDVID_SERVER,DVID_NODE: URL and UUID for DVID for accessing meshes for generating thumbnailsNEUPRINT_SERVER: URL for accessing neuron connectivity, etc.NEUPRINT_APPLICATION_CREDENTIALS: A neuPrint API token
These variables are only required for the first step of the build, when the .md pages are built from the gatherered data. They are not required for the mkdocs step that builds the .html files from the .md files.
To build the website locally, run:
uv run build_pages.py
uv run mkdocs buildYou can set various flags to control the build process:
--skip-thumbnails: Skip generation of the thumbnails (by far the most expensive part)--skip-tables: Skip generation of the connections tables--update-metadata: Force updating the metadata (neuPrint/FlyTable)--clear-build: Clear the build directory before building
5E04
--clear-site: Clear the site directory before building
Obsolete:
--skip-graphs: Skip generation of the network graphs (second most expensive part)- graphs are no longer included on the pages
- the option now defaults to
True
To serve the website locally, run:
uv run mkdocs serveOn Github the website is built and deployed using a Github actions
workflow that is triggered on every push to the main branch. It
can also be triggered manually using the workflow dispatch feature.
GitHub Actions are not enabled in the Janelia Fly EM repo, and the necessary secrets are not configured there.
To manually deploy the website to GitHub pages, run:
uv run mkdocs gh-deploy --force