Python API for efficient storage and retrieval of single-cell data using TileDB
Project description
Overview
This is a POC Python implementation of the proposed Unified Single-cell Data Model.
This branch, main
, implements the updated specfication. Please also see the main-old
branch which implements the original specification.
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 thencd 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.
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 };
offsets_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-0.5.0a3-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ffd46dc54c71cfd09e15859c4068f988f5415968904bcd8f4d5ba478092ab697 |
|
MD5 | a1d469544493cc4186aa5464ef4f76aa |
|
BLAKE2b-256 | b7b7755720daddf4376e81d31b7bfc6c96eadfc2c6ec8f7083745007158f7ece |
Hashes for tiledbsoma-0.5.0a3-pp39-pypy39_pp73-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7b1ed0ee811a9f5e9930200fe1a68625c2a0884b012c6a16285710d11a95b020 |
|
MD5 | d835e64e24fec950498b27cdc439efcf |
|
BLAKE2b-256 | 7c464d75bf04d8ef991c62ea8976a8df99d0d78584b9fc486cd83a15ac702dda |
Hashes for tiledbsoma-0.5.0a3-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 89c914b461d530990c1e39446079ce3ac9a3c1ee3f7298b6bebac4afe10db85f |
|
MD5 | 467319c7b49f92372ae78bba9302e330 |
|
BLAKE2b-256 | 929e9fb8d3cb9e40b688f0e987e0b7fe28074e4114ac431e866b15e94e0dd056 |
Hashes for tiledbsoma-0.5.0a3-pp38-pypy38_pp73-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | dac2d8c378792dcdb0e0e92c078ce466bda24c8c1db9d17d35cf7334b7fc4b9e |
|
MD5 | 6c7c789718d1128350fd0abe52af4b3e |
|
BLAKE2b-256 | cf421a4c83cba9878fc3d6534bbf4905c9378e4e3b5939a11df574eea7dfec65 |
Hashes for tiledbsoma-0.5.0a3-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7a7d6a7c2865e0718b07d0e98a69f02e822f52a3002ed272a20a8c1ed1df04f0 |
|
MD5 | cd41e9f6cd7ff0a308efdb223f053d51 |
|
BLAKE2b-256 | 4bcada72e40da936a6b602ed795492a5c6a4851e821afd0f363f8adac6fd25fb |
Hashes for tiledbsoma-0.5.0a3-pp37-pypy37_pp73-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 9c1ebf2d9cdf760679e8f6cd15acca08902276eddb90b7b260157e17c10d0218 |
|
MD5 | 649b9fe839837bdd05e5ec6354b18f9f |
|
BLAKE2b-256 | 8bcd26aa2fb8872dc1373ed8ac738af6d0cc4ff77c76538a53c4c3b2d1cc342e |
Hashes for tiledbsoma-0.5.0a3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a7b6d00ab33bd6389a772d349146126bdfa2946fc653f5a6ccb61af80de58fa0 |
|
MD5 | 309e92bad622185de5e3d2f7ae7d0e73 |
|
BLAKE2b-256 | a87fa6939858039db7f03232c790d229e9782648b49cbdb80230693c899fc1b8 |
Hashes for tiledbsoma-0.5.0a3-cp311-cp311-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 02ac9d646a447422d5668af9b2c5786d86650e7de78125078fad9240e6593ed8 |
|
MD5 | d94c3101d84660e90008cb1de572b239 |
|
BLAKE2b-256 | a88d684715bd35dffc5ee564899dcda410b5384f97ef7e60161333ee46c7b862 |
Hashes for tiledbsoma-0.5.0a3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 6643736926cc0f46d88dcce6bc7acb501dc0fbdf885134094adcc3f055a4d727 |
|
MD5 | 8752ef8c54813672c22a8ef275f84ad6 |
|
BLAKE2b-256 | 218c8d4681c3bf4fe3338189eef0988544972e89a4666d5c1152acad298385cd |
Hashes for tiledbsoma-0.5.0a3-cp310-cp310-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 02fae9e4aadbff2f3c3e335b4a29dba4ee50a6e80d6fe3c9ae22b2cec25aa047 |
|
MD5 | f4fa1899f2bf8a4e07354250f5a2bb6f |
|
BLAKE2b-256 | 93ca06f53d2b27ed971ec42c9e3e1fa81b9dc9a442b2e27dc44dd9969db19afd |
Hashes for tiledbsoma-0.5.0a3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4e00095fd38aa6ceda92015a8aadabf47f6b1c447fa71129471cf9a10d0d493c |
|
MD5 | dfe357a6f42786ad9ba23df45b241ad6 |
|
BLAKE2b-256 | 45e9a47d22252642d4a2410699f9b1f2d27bb9ee25b457dcb81ea0aa93abb81c |
Hashes for tiledbsoma-0.5.0a3-cp39-cp39-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 64bf51b5dc61e55300f8dbbca1487d5a1401917cac851b28baa8b5f2f9eecd12 |
|
MD5 | c5c232d952d953339c8cb8bd506c2fe4 |
|
BLAKE2b-256 | 83140fa0c12ac3cbae4801911700efd42b7ae29f401548948a496cfe34e046f5 |
Hashes for tiledbsoma-0.5.0a3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4ead586b4cc833757438cc8fbd56014261cdde73d0d132cdc97b1c3d636815ff |
|
MD5 | deac659490b07a0fd7479957d35ae767 |
|
BLAKE2b-256 | 4559f98a8e3efef09285cad8e247be7ce31e9f8a0ad0032976b4ffbe11676027 |
Hashes for tiledbsoma-0.5.0a3-cp38-cp38-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1cb86e86e06ff02f2f7d932bc888c481a47ca53519f93981cf143bb04a0ae9fe |
|
MD5 | 190136153e5d8456b31e5f6f12da2920 |
|
BLAKE2b-256 | 88bfdec8b3beef3d02416e76bf2c4dd0cc37156ed56da35ad20975c480f48505 |
Hashes for tiledbsoma-0.5.0a3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 53b435da04a93968fb752a372b8e83bcef88da8be9c536b1f9dccb61f0bccaed |
|
MD5 | 47ae14285062ac5f0d8a2933acf282e2 |
|
BLAKE2b-256 | adf08bce75641a9af296dc86f5c994090046b923235b878df3b15807b7788281 |
Hashes for tiledbsoma-0.5.0a3-cp37-cp37m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 38624630c44f0038641cc23eb39e20ecada35a1ce6fd8cff2d4f8d8ee71d1ad4 |
|
MD5 | 2211dffb46a907f9e2209bcee304d00f |
|
BLAKE2b-256 | e5aba2c0b08766f934d84386f8805eb5d0f47560882988505093e9521ebe3c6a |