Python API for efficient storage and retrieval of single-cell data using TileDB
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
cdinto your checkout and thencd apis/pythonpython -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 variablesTILEDB_PATHandTILEDBSOMA_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.
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