Metadata-Version: 2.1
Name: tiledbsc
Version: 0.1.2
Summary: Python API for efficient storage and retrieval of single-cell data using TileDB
Home-page: https://github.com/single-cell-data/TileDB-SingleCell/apis/python
Author: TileDB, Inc.
Author-email: help@tiledb.io
Maintainer: TileDB, Inc.
Maintainer-email: help@tiledb.io
License: MIT
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Information Technology
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >3.7
Description-Content-Type: text/markdown
Requires-Dist: tiledb (>=0.16.2)
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: pyarrow
Requires-Dist: anndata
Requires-Dist: scanpy
Provides-Extra: dev
Requires-Dist: black ; extra == 'dev'
Requires-Dist: isort ; extra == 'dev'
Requires-Dist: flake8-bugbear ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'

# Overview

This is a POC Python implementation of the proposed [Unified Single-cell Data Model](https://github.com/single-cell-data/SOMA).

# Installation

## Using pip

This code is hosted at [PyPI](https://pypi.org/project/tiledbsc/), so you can do

```
python -m pip install tiledbsc
```

To install a specific version:

```
python -m pip install git+https://github.com/single-cell-data/TileDB-SingleCell.git@0.0.6#subdirectory=apis/python
```

To update to the latest version:

```
python -m pip install --upgrade tiledbsc
```

## From source

* This requires [`tiledb`](https://github.com/TileDB-Inc/TileDB-Py) (see [./setup.cfg](setup.cfg) for version), in addition to other dependencies in [setup.cfg](./setup.cfg).
* Clone [this repo](https://github.com/single-cell-data/TileDB-SingleCell)
* `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-SingleCell/issues](https://github.com/single-cell-data/TileDB-SingleCell/issues).
