# Overview
This is a Python implementation of the [SOMA API specification](https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md) for interacting with the [Unified Single-cell Data Model](https://github.com/single-cell-data/SOMA).
# Installation
TileDB-SOMA is available on [PyPI](https://pypi.org/project/tiledbsoma/) and [Conda](https://anaconda.org/tiledb/tiledbsoma-py), and can be installed via `pip` or `mamba` as indicated below.
```bash
python -m pip install tiledbsoma
```
```bash
mamba install -c conda-forge -c tiledb tiledbsoma-py
```
To install a specific version:
```shell
$ 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:
```shell
$ python -m pip install --upgrade tiledbsoma
```
## 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-SOMA)
* `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 -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 variables `TILEDB_PATH` and `TILEDBSOMA_PATH`, `TILEDB_PATH=/usr/local python -m pip install -v -e .`
* Optionally, if you prefer, you can run that inside `venv`:
```shell
$ python -m venv venv
$ . ./venv/bin/activate
$ python -m pip install -v -e .
```
* In either case:
```shell
python -m pytest tests
```
# Status
Please see [https://github.com/single-cell-data/TileDB-SOMA/issues](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`](https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md#platform-specific-configuration) parameter.
The options accepted by TileDB SOMA are described here, using [TypeScript interface syntax](https://www.typescriptlang.org/docs/handbook/2/objects.html):
```typescript
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](https://github.com/single-cell-data/TileDB-SOMA/wiki).
<!-- temp for readthedocs testing -->
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