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

In case of illegal instruction errors when running on older architectures --- e.g. Opteron, non-AVX2 --- the issue is that the pre-compiled binaries available at Conda or PyPI aren't targeted for all processor variants over time. You can install from source, as shown below.

To see if this is the issue, on Linux:

grep avx2 /proc/cpuinfo

If this comes up empty for your system, you'll definitely need to build from source to run TileDB-SOMA on that system.

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

1.14.4

1.14.3

1.14.2

1.14.2rc0 pre-release

1.14.1

1.14.0 yanked

Reason this release was yanked:

Broken release; 1.14.1 upcoming
This version

1.13.1

1.13.1rc0 pre-release

1.13.0

1.13.0rc0 pre-release

1.12.3

1.12.2

1.12.1

1.12.0

1.11.4

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1.9.5

1.8.1

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Reason this release was yanked:

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0.1.19

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