Python API for efficient storage and retrieval of single-cell data using TileDB

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Project description

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.

Project details

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Avatar for atolopko-czi from gravatar.com atolopko-czi Avatar for bkmartinjr from gravatar.com bkmartinjr Avatar for johnkerl-tiledb from gravatar.com johnkerl-tiledb Avatar for mlin from gravatar.com mlin Avatar for nguyenv from gravatar.com nguyenv

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Release history Release notifications | RSS feed

1.15.0rc3 pre-release

1.15.0rc2 pre-release

1.15.0rc1 pre-release yanked

Reason this release was yanked:

pip allowed an rc anndata dependency to be included, which was unfortunate

1.15.0rc0 pre-release yanked

Reason this release was yanked:

Relese has post-tag failures

1.14.5

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1.14.2rc0 pre-release

1.14.1

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Reason this release was yanked:

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This version

1.3.0

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