Python API for efficient storage and retrieval of single-cell data using TileDB
Project description
Overview
This is a Python implementation of the SOMA API specification for interacting with the Unified Single-cell Data Model.
Installation
TileDB-SOMA is available on PyPI and Conda, and can be installed via pip
or mamba
as indicated below.
python -m pip install tiledbsoma
mamba install -c conda-forge -c tiledb tiledbsoma-py
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 thencd 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 variablesTILEDB_PATH
andTILEDBSOMA_PATH
,TILEDB_PATH=/usr/local python -m pip install -v -e .
- Optionally, if you prefer, you can run that inside
venv
:$ python -m venv venv $ . ./venv/bin/activate $ python -m pip install -v -e .
- In either case:
python -m pytest tests
Status
Please see 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
parameter.
The options accepted by TileDB SOMA are described here, using TypeScript interface syntax:
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for tiledbsoma-1.5.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 48de4020834275f8b1df69b898e33cd6186cadba9d4ed5a39bc59bff2b4065c9 |
|
MD5 | e3ee8bf878fa1e15f76c2c195e88fcc8 |
|
BLAKE2b-256 | feaf00aba61e51e6915b3d364b7c09951cf03658513bd855ba8c6edeb257159d |
Hashes for tiledbsoma-1.5.2-cp311-cp311-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 6399e62f4e8aad5d1dd08497ff7dcb7e19d998f79a5b6af34579b44e0b2b0e6b |
|
MD5 | 71d9529a909cbcf679fcaa8ca6c836b7 |
|
BLAKE2b-256 | 406dba7b902fa76dbfde324bdf7f0ce63bcee1243eac1584d2ea4074d3eda19d |
Hashes for tiledbsoma-1.5.2-cp311-cp311-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 551fc5ed05f35fc7bb34f6052325aa83aa6c4dc8d4dcf1bbcae6d7676c4f11be |
|
MD5 | 5d16b3115e4ebfb83e30f27c39e91e55 |
|
BLAKE2b-256 | 6b456f385cf196dc931ded951ab7406e2f7bf6715e3d6884123135807dec5bad |
Hashes for tiledbsoma-1.5.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 12e006aafab152618879b36ff73906668b4bbcf7c043065cf133dfa11c264be0 |
|
MD5 | 7e65161b58d79c2a3d6487a398c2ef5e |
|
BLAKE2b-256 | aeceaff58527893bead3eeb876f450d56ca193f156b6e3beb96f537c3ebc39a0 |
Hashes for tiledbsoma-1.5.2-cp310-cp310-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1ea4723d086e94642a05b3844782acf9db46122577a8ad589133dad7c5939e21 |
|
MD5 | b0193b1845121fd25bf0160d6a99bd13 |
|
BLAKE2b-256 | dee689ab83a94f618ef832e888e6ccef0f80195290ed4353a91ba12393c3d683 |
Hashes for tiledbsoma-1.5.2-cp310-cp310-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 21cc1a4f3745ba74f302ff7ec70b056e7110543c140a7d3b73921534d8e2ae7b |
|
MD5 | 542bcaa21c4a10b820da421d52cdc7b7 |
|
BLAKE2b-256 | 984d783f22ce9579a12f150e64f0c7f3d958b475ff16424aca7532a12398e179 |
Hashes for tiledbsoma-1.5.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c4f9cbaa43a07b79a5181c783c9b39deeb7460b525558c90c48a8dc807699ba1 |
|
MD5 | 286c1afcd4ca8a2aa100a235b8033a20 |
|
BLAKE2b-256 | ffeb418cd8adb78c507b0a96f8ee6c7e0f84bbc1a33d19cf0004639ac0a5e865 |
Hashes for tiledbsoma-1.5.2-cp39-cp39-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8ed7960fa93c6986387c86876369cafe10e26558190f2978d4a00a49ffe20db0 |
|
MD5 | 1142bfbe25b07180b2ae537d2e5a3da1 |
|
BLAKE2b-256 | cc0f4b824cecaea3f0ac8dc347afec975e151515c4fb3e753ee69f8d35ad9aaf |
Hashes for tiledbsoma-1.5.2-cp39-cp39-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5455c570773980f54b4351cfefa9d121f5f54ce76e6b3e67f1088c9ba8932e5c |
|
MD5 | b9635f3d8cd045ea12ac1e152740cdfe |
|
BLAKE2b-256 | 0e23a0864f90757bd82e76014e7b2387f23192beae121698b667f05192f4adf6 |
Hashes for tiledbsoma-1.5.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | dfee763232da997db4377d6ba72549489cfbd72364a5ee0d16285c54fd9ad21e |
|
MD5 | a00d865fcd430fb3fbb80f71d663d719 |
|
BLAKE2b-256 | 4dbc235a2961b478cc542cc226fb7fb70ded0502ebfd1c4b37c8e6605287288c |
Hashes for tiledbsoma-1.5.2-cp38-cp38-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a70882a8788c575a08ef0dbcfd1b17b8570841ca9fe4699b89aefa4c4af672e3 |
|
MD5 | 88da8d53fdd05603fb11c5d45aec547b |
|
BLAKE2b-256 | 6e4dc9ec17f5c278db862736bb2a22af4fbe942dfd31bb95034a87e33d0b4dcf |
Hashes for tiledbsoma-1.5.2-cp38-cp38-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c5ef89aee53ae068ce56c3596b51ed2e9d41a873c8888e14240e1b3182616370 |
|
MD5 | f23f8e2aaffbf596716777f549e9c450 |
|
BLAKE2b-256 | d99afd67d370efb4e87a66df0f9b17a0ba90516d5cb564df843be5edee618261 |
Hashes for tiledbsoma-1.5.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7766eaf309a32bfe5865c5f1c5e8fdd510f34a8bd032186a6108d7491eed426e |
|
MD5 | 4f2f068de1daa25d9a2d2e4cbc74cf7f |
|
BLAKE2b-256 | e717c2fa570879f0c9edf20c939a3a9899cb6051277ef3dc30f40459616fd307 |
Hashes for tiledbsoma-1.5.2-cp37-cp37m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | df6ea403375a1495b27f1bd112444619b77d9b3cf1523c070e20d951a2648822 |
|
MD5 | a0a7aa433c57b456532b0c961ab623cc |
|
BLAKE2b-256 | 62e9a04362c0dde50cffd675300700aa4542edd5940334170ace533941fc5b40 |