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
Using pip
This code is hosted at PyPI, so you can install using pip
:
$ 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 -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
tiledbsoma-1.2.5.tar.gz
(153.2 kB
view hashes)
Built Distributions
Close
Hashes for tiledbsoma-1.2.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 9b90159802b3f510a3e59f09f33367a1e1fb3fa38e97c57cfdaf0a7f17b05bc5 |
|
MD5 | c67af8a9e138d80584eabfe8acfeaea4 |
|
BLAKE2b-256 | 6d98e6aa30928361979a224cc348b3c85ab81132c747ba3aa4ebdf3343f03dac |
Close
Hashes for tiledbsoma-1.2.5-cp311-cp311-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1c698c5610ffbb7ffe0d3a3277f5a8eff0b8003b21ff1f4e3944d1d7637566e5 |
|
MD5 | 98aba0e1d6bf80d7640ca4dc44e77b9e |
|
BLAKE2b-256 | d70dbc36a5be8bb256dd9749c3fb3cab45c6a8ccc45854d3ffb3460d0471fd5c |
Close
Hashes for tiledbsoma-1.2.5-cp311-cp311-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b2eb654e65733f2a5a23ec996794078c419ff1e5b722f39c2b92c98e118cd817 |
|
MD5 | a79fc5969b9d3d7f69b1a1e9e2280b07 |
|
BLAKE2b-256 | c9c41ad99726195fb70ae472b5369f3c9ea075ea9282f8fad572bf954f05c95e |
Close
Hashes for tiledbsoma-1.2.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fb534803c93138167887f18c6f31b1cfc933f333f9c7d301e35b722102211b87 |
|
MD5 | 0759b6ca687c715ce955190ebdf70da0 |
|
BLAKE2b-256 | 8b45869804f91f05a69fe1f47b08e6010eaa9ff8afb679379fbeadde481e87bf |
Close
Hashes for tiledbsoma-1.2.5-cp310-cp310-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e3f7994e6456be61fc734445d30ad2eb15f361bfeeb5774bad875bbeec938e1f |
|
MD5 | 4e9e7cfdfa1ce17dac984a2fd2a3efa1 |
|
BLAKE2b-256 | 5db0080b758c08d5e6b14e871ad7f647aac9369ee890cfdd63d9c4f255ecca8d |
Close
Hashes for tiledbsoma-1.2.5-cp310-cp310-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 008dc95fd8e9a4fa7c605c39f8307eb2d11dbac1e8eb8aadb1dca9718ff43196 |
|
MD5 | 613605210363b8ff361256249898ea18 |
|
BLAKE2b-256 | 9f389439183b11d169e7cdf499bd05d9951a8c66c7ff680ec63432782f2b0701 |
Close
Hashes for tiledbsoma-1.2.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 898a3da1bd3da31353d735dbf716bcfafbe9edbc928370bdfe1dd240cda941ff |
|
MD5 | c47194b9cb279bb8911cf8bbb1eff16c |
|
BLAKE2b-256 | 8c48e4438ea7ec69f60f2081658eb9e2136a67f27e1f51e2e6a764d82ad92b05 |
Close
Hashes for tiledbsoma-1.2.5-cp39-cp39-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2109c792a55fbd1eca3fc07b582518165be4c29fc541791306231200e57b48c4 |
|
MD5 | 10ac25534f91047402ddcb1e2a159f19 |
|
BLAKE2b-256 | 26c7a2c1027c453e274d195ef621b54509a76bb2f91ee97fd295fbad9347845e |
Close
Hashes for tiledbsoma-1.2.5-cp39-cp39-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ff1707f907a47ced98197373b8731e82af9e91a90721dfa3e716a5610baabbd8 |
|
MD5 | ddb64934b8ebb550fc621f86edaaa05a |
|
BLAKE2b-256 | 045594e45bb6ccaa48b08ff59f017b624bb6da098ef2ee073ea9534ffd1a3151 |
Close
Hashes for tiledbsoma-1.2.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 78bc3e84d2098aeaf0f921c5a4b652656110fe63def515841f0f0ba4982be296 |
|
MD5 | bd45c4340e6b9bf3deee8ee5b343f31a |
|
BLAKE2b-256 | c18c5660eb179dcb70254190e59a2ac5c9e62a05e81630e36d0f8ab3636794e2 |
Close
Hashes for tiledbsoma-1.2.5-cp38-cp38-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 6877a16def3ecf9338b1bcc24994ed6aeed0753d1971d1159e1b11bcb810b246 |
|
MD5 | 9345cdb46030bcac8b5e2b08c97b178b |
|
BLAKE2b-256 | 37f972ad5c90c8358316c0c4ddd5a23e8bafcb39131bc5d5c1d4b2fbe7006be3 |
Close
Hashes for tiledbsoma-1.2.5-cp38-cp38-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 77d5df8abf7be2f14d1a8c1ce660aacec2f5d7aa7eb08d90d6d6b2d45b05c123 |
|
MD5 | 3593ada904d1def88a432a5c78540ea6 |
|
BLAKE2b-256 | 525a1ac102d7e37c6074351aa509dab54fa7c7bcdcebcd32753ead44cfbe9729 |
Close
Hashes for tiledbsoma-1.2.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | deae36e663f4278eb40f203325c4cba9493e48ca958cc5a12f13a93a5bde187b |
|
MD5 | e1c4d23786b223f46dea754238e3d858 |
|
BLAKE2b-256 | 278cb6522e56748f95cdad2c7491ee1082e8b6cefee707a3dfd0377f8a816971 |
Close
Hashes for tiledbsoma-1.2.5-cp37-cp37m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | bebb64d590560999b71d16c7e557d8e812dcae63e3153b05984cf8fd22cae82b |
|
MD5 | 8a9594b0e0fbbfcf4d19d7b2b11326da |
|
BLAKE2b-256 | e9dad283149c13fd7b0019f939870ecba1003b730d9faba09682bf073efa04fc |