🚀 Big News: Socket Acquires Coana to Bring Reachability Analysis to Every Appsec Team.Learn more
Socket
Book a DemoInstallSign in
Socket

tiledbsoma

Package Overview
Dependencies
Maintainers
5
Alerts
File Explorer

Advanced tools

Socket logo

Install Socket

Detect and block malicious and high-risk dependencies

Install

tiledbsoma

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

1.17.0
PyPI
Maintainers
5

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

  • 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:
    make data
    python -m pytest tests
    
  • A note about the spdlog package: If you encounter an install-time error like fatal error: spdlog/spdlog.h: No such file or directory you should additionally recursively remove /usr/local/lib/cmake/spdlog , since the system uninstall of spdlog fails to remove this properly.

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.

FAQs

Did you know?

Socket

Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.

Install

Related posts