Python API for efficient storage and retrieval of single-cell data using TileDB
Project description
Overview
This is a POC Python implementation of the proposed Unified Single-cell Data Model.
This branch conforms to this version of the specification -- for the latest version please see the main branch of this repository.
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.
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