Overview
This is a Python implementation of the SOMA API specification for interacting with the Unified Single-cell Data Model.
Installation
TileDB-SOMA is available on PyPI and Conda, and can be installed via pip
or mamba
as indicated below.
python -m pip install tiledbsoma
mamba install -c conda-forge -c tiledb tiledbsoma-py
To install a specific version:
$ python -m pip install git+https://github.com/single-cell-data/TileDB-SOMA.git@0.0.6
To update to the latest version:
$ python -m pip install --upgrade tiledbsoma
From source
Status
Please see https://github.com/single-cell-data/TileDB-SOMA/issues.
platform_config
format
When accessing SOMA APIs, TileDB-specific settings can be configured with the platform_config
parameter.
The options accepted by TileDB SOMA are described here, using TypeScript interface syntax:
interface PlatformConfig {
tiledb?: TDBConfig;
}
interface TDBConfig {
create?: TDBCreateOptions;
}
interface TDBCreateOptions {
dims?: { [dim: string]: TDBDimension };
attrs?: { [attr: string]: TDBAttr };
allows_duplicates?: bool;
offsets_filters?: TDBFilter[];
validity_filters?: TDBFilter[];
capacity?: number;
cell_order?: string;
tile_order?: string;
}
interface TDBDimension {
filters?: TDBFilter[];
tile?: number;
}
interface TDBAttr {
filters?: TDBFilter[];
}
type TDBFilter = string | TDBFilterSpec;
interface TDBFilterSpec {
_name: string;
[kwarg: string]: any;
}
Information for developers
Please see the TileDB-SOMA wiki.