tiledbsoma 2.3.0
Python API for efficient storage and retrieval of single-cell data using TileDB
License: MIT
Requires Python: >=3.9

# 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
```

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

- 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
  make data
  python -m pytest tests
  ```
- A note about the `spdlog` package: If you encounter an install-time error like `fatal error: spdlog/spdlog.h: No such file or directory` you should additionally recursively remove `/usr/local/lib/cmake/spdlog `, since the system uninstall of `spdlog` fails to remove this properly.

# 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).

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