tiledbsoma 0.1.18

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

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
• 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 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.