tiledbsoma

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#subdirectory=apis/python

To update to the latest version:

$ python -m pip install --upgrade tiledbsoma

From source

• This requires tiledb (see ./setup.cfg for version), in addition to other dependencies in setup.cfg.
• Clone this repo
• cd into your checkout and then cd apis/python
• python -m pip install .
• Or, if you wish to modify the code and run it, python -m pip install -v -e .
• If the TileDB and TileDB-SOMA libraries are locally installed to a custom directory, such as /usr/local, set the path with environment variables TILEDB_PATH and TILEDBSOMA_PATH, TILEDB_PATH=/usr/local python -m pip install -v -e .
• Optionally, if you prefer, you can run that inside venv:

  $ python -m venv venv
  $ . ./venv/bin/activate
  $ python -m pip install -v -e .
  

• In either case:

  python -m pytest tests
  

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[];
}

/**
 * Either the name of a filter (in which case it will use
 * the default arguments) or a specification with filter args.
 */
type TDBFilter = string | TDBFilterSpec;

interface TDBFilterSpec {
  /** The name of the filter. */
  _name: string;
  /** kwargs that are passed when constructing the filter. */
  [kwarg: string]: any;
}

Information for developers

Please see the TileDB-SOMA wiki.