Python API for efficient storage and retrieval of single-cell data using TileDB
Reason this release was yanked:
This was tagged on the wrong branch. Do not use.
Project description
Overview
This is a POC Python implementation of the proposed Unified Single-cell Data Model.
This branch, main, implements the updated specfication. Please also see the main-old branch which implements the original specification.
Installation
Using pip
This code is hosted at PyPI, so you can do
$ python -m pip install tiledbsoma
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
cdinto your checkout and thencd apis/pythonpython -m pip install .- Or, if you wish to modify the code and run it,
python setup.py develop - Optionally, if you prefer, you can run that inside
venv:$ python -m venv venv $ . ./venv/bin/activate $ python -m pip install .
- 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 };
offsets_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.
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