Example datasets API reference

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 NygenAnalytics/CyteBase.