CLI commands

Four commands cover the normal path: init writes a dataset yaml from your data, build turns it into a bundle (and updates the bundle after every edit), serve opens it, site build writes the folder to publish. Every command is also available as sscape <command>, and spatialscape <command> --help prints the same information as these pages.

pip install spatialscape
spatialscape --help

Command	Purpose
init	Write a dataset yaml that doubles as a menu of what the data contains.
build	Build or update a bundle from the dataset yaml. Rerun it after any edit.
serve	Open your bundles in the viewer locally: one origin for the app and the data.
site init	Write a starter site.yaml listing your datasets.
site build	Write a folder you can upload to any static host.
inspect	Print what a sample file contains, to help edit the dataset yaml.
validate	Check a bundle on disk or over HTTP.
thumbnails	Re-render thumbnail.png for the dataset and for each sample.
synth	Write a tiny synthetic dataset for tests and demos.

Typical sequence

spatialscape init analysis/spe_visium.rds --id my_atlas     # writes my_atlas.yaml, a menu of the data
# edit my_atlas.yaml: annotations, names, colors, the opening gene
spatialscape build my_atlas.yaml                            # -> bundles/my_atlas; rerun after any edit
spatialscape serve bundles --open
spatialscape site init my_atlas.yaml && spatialscape site build site.yaml   # only for a gallery with settings
# ... upload site/ (or the bundles alone) ...
spatialscape validate https://data.example.org/my_atlas

Exit codes

build and validate exit with status 1 when validation reports problems, so they can gate a deployment script. Every other command exits 0 on success and prints a one-line error otherwise (SPATIALSCAPE_DEBUG=1 shows the traceback).

Generated reference

These pages are generated from the CLI's own help text by python/scripts/gen_cli_docs.py. If a page and --help ever disagree, --help is right and the generator needs re-running.