Source: https://docs.nygen.io/CyteArc/api/datasets.html
Revision: bd4c9291910c21d57953c8e95149fd8ae6bfca57

Example datasets API reference
******************************

"cytearc.datasets" lists and downloads the public example datasets
that the CyteArc tutorials use. They live in top-level repositories of
the public "Nygen/cytebase" Hugging Face bucket, such as
"cytearc_docs" for the documentation datasets. Downloads need network
access but no credentials. A repository names each dataset by its
directory.

   import cytearc

   repository = cytearc.datasets.connect("cytearc_docs")
   repository.list_datasets()

   # Download and extract a prepared CyteArc store, then open it read-only.
   path = repository.download_dataset(
       "tenx_5K_pbmc_rnaseq", destination="cytearc_datasets", zarr=True
   )
   ds = cytearc.DataStore(f"{path}/data.zarr", zarr_mode="r")

"download_dataset(name, zarr=True)" downloads the dataset’s
"data.zarr.tar.gz" archive and extracts it to "data.zarr" in the
returned directory, keeping the archive beside it. Without
"zarr=True", it downloads the dataset’s other files, such as its
source count files. "download(path)" downloads one file, or every file
under a directory, and keeps its path within the repository.

cytearc.datasets.list_repositories()

   Return the top-level example repositories in the public bucket.

   Return type:
      "list"["str"]

cytearc.datasets.connect(repository)

   Connect to a public example repository, such as "cytearc_docs".

   Return type:
      "Repository"

class cytearc.datasets.Repository(name)

   Read files from one top-level example repository.

   download(path, destination='.')

      Download a file or directory while preserving its repository
      path.

      Return type:
         "list"["Path"]

   download_dataset(name, destination='.', *, zarr=False)

      Download one dataset, optionally selecting its Zarr archive.

      Return type:
         "Path"

   list_datasets()

      Return immediate dataset directories in this repository.

      Return type:
         "list"["str"]


CyteBase catalog
================

The CyteBase catalog of public datasets stored as cloud-hosted CyteArc
DataStores is the separate "cytebase" package, which CyteArc does not
install. CyteArc opens CyteBase datasets by their "hf://" URIs, as
https://docs.nygen.io/CyteArc/tutorials/cytebase-datasets shows. To
search the catalog, install and import the package:

   # Install the catalog client first: pip install cytebase
   import cytebase

   catalog = cytebase.Catalog()

See the CyteBase documentation at https://docs.nygen.io/CyteBase/ for
its API and tutorials.

"cytearc.cytebase" keeps the earlier names of the example downloads
through CyteArc 1.x: "Repository", "connect", and "list_repositories"
are the "cytearc.datasets" objects. The catalog names it once
exported, such as "Catalog", "releases", and "embedding", moved to the
"cytebase" package, and reading one from "cytearc.cytebase" raises an
"AttributeError" that says so. The catalog build pipeline moved to the
CyteBase repository at https://github.com/NygenAnalytics/CyteBase.