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-1.2.7.tar.gz
(153.3 kB
view hashes)
Built Distributions
Close
Hashes for tiledbsoma-1.2.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c78e539e864fcdf796f15173023afdcc962dfd8b84d184d901fb05f4f6d565dd |
|
MD5 | 1ebcdd3974b8066e85ed0b0921620976 |
|
BLAKE2b-256 | 71791e121cb946a40f9bee263631b46b837ab215b68f98f69be876ff3490cc92 |
Close
Hashes for tiledbsoma-1.2.7-cp311-cp311-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1063a5cece5003d1cee99e7beff1f226f0e2651b0c372a3d900c6513588d5749 |
|
MD5 | c2623210e37c147326f948bc5947d96d |
|
BLAKE2b-256 | c6d2e5dd18dfb5f814eb619da91e5d14a4aed0fe5cd4863daf974cf110e4ed48 |
Close
Hashes for tiledbsoma-1.2.7-cp311-cp311-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 325b8c573789f4cf510e1d2f1cf94d292800fcea39f07ca473e24aa5af2d7105 |
|
MD5 | 2d2cf75e4c3a1a85e978aea061d843d3 |
|
BLAKE2b-256 | d352686f15c2d6e43b2c58df0a410252010cbd1110ac6547e3f3045826d7b685 |
Close
Hashes for tiledbsoma-1.2.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5b207f2427715531e9a64e55b3b36d2b4886fada6bb81cfc84e0f03a022a00fe |
|
MD5 | af5e70ccbc19578331bf98b9c605359c |
|
BLAKE2b-256 | b2a629b5d4676cf1eafc04a9e0e58dc34ce791ad74d4e292fdd90bd7132b9976 |
Close
Hashes for tiledbsoma-1.2.7-cp310-cp310-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | cd9e0d45bec79990559e2bbbfafb337be17536724c5fb79126809659869dee83 |
|
MD5 | 73c22948c1136bb188ccd87a80e8017f |
|
BLAKE2b-256 | 345a35bef7290959f0e3d4f61b452f9972f47610d467d3643636bfb3f8b7238d |
Close
Hashes for tiledbsoma-1.2.7-cp310-cp310-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a8b18ebab63e55102ca6181d92ae3d2d39820fa8027068c7915c62fc5617023b |
|
MD5 | 9e63b620d8771552f15bc76f2c47aa36 |
|
BLAKE2b-256 | 8cbf9a3c6f85f28980fd62b79e5233109db4c919cb7d2dfbfcede4918e86a8f7 |
Close
Hashes for tiledbsoma-1.2.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | cbdf8b010bd394ba4bee05c9a1b6710c130f24b839297be2e6d6bff8ba128ac0 |
|
MD5 | e85498eaa7031343e33eb69f954ff321 |
|
BLAKE2b-256 | bd21489fe617a6757e36b1bb94dbf0f2701fd57106b2c135994c16e0bda3420e |
Close
Hashes for tiledbsoma-1.2.7-cp39-cp39-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ccc5e76580628390104ab3ba0d423df5b7534acc95f2224031ed1c3ffa19fe8f |
|
MD5 | 454f87d8956fe2deb745138f3adfd277 |
|
BLAKE2b-256 | 7892b9b32d8d90ab2ef130b8e53b6eaf12fb2861828424c572777dd539f580f3 |
Close
Hashes for tiledbsoma-1.2.7-cp39-cp39-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 16c85fb90321fc9b2f038e3af7f95ed16d176105b1e4ec5b53cf7cbdef3dcc71 |
|
MD5 | b24ccc52a92751f26d40eb54cdf49f51 |
|
BLAKE2b-256 | 3a97bf21bde0f53411845b7b45e37e0193b8fe49b41041a0902dda40443fe72f |
Close
Hashes for tiledbsoma-1.2.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4bc1e7ccb5a4025eee2058a0c316da17b30aa4ce18e2f01d4fd6dec6a47e68fb |
|
MD5 | 4e91e107f96c39c870fd6906cb5fb2db |
|
BLAKE2b-256 | 1eded66efbfe6a781ba69cb4ee04d8819073ba5c752176e5cf850ef431383873 |
Close
Hashes for tiledbsoma-1.2.7-cp38-cp38-macosx_11_0_arm64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 271d270e41e45765e63e2066383cef25fa5f537e8c2fe999113077d083c68691 |
|
MD5 | 9ca2c9b48902f007f0fa3789024770fe |
|
BLAKE2b-256 | 982aa607e424ea178be73126df5122d5cb2cdba4da3916ca1a8347c5f1cb46cb |
Close
Hashes for tiledbsoma-1.2.7-cp38-cp38-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b7bc4e123bc3411e844422cdf846ec867402e83331329dfa3d88ce0f9c97d34c |
|
MD5 | 4866aa102e1c872e73e45be4875d6c7d |
|
BLAKE2b-256 | 36129bfd52c9b22b677562ca73f62770c46919b5e6ed49451597bf4c45fd2b6b |
Close
Hashes for tiledbsoma-1.2.7-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 23e004b6a68d701345ed250bee054ae73762cc9af891f2ca019149f3352018df |
|
MD5 | fc20efa5326d9074e13a4fa97bfbdaf4 |
|
BLAKE2b-256 | 61cd541614fe720d327a9324e3f39f554b08c89f2f27033cdd93025dccd39023 |
Close
Hashes for tiledbsoma-1.2.7-cp37-cp37m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 30116be9cbcac8be2609efa24538cb7081bd6b065369a6e85d7fe714bb0a2b2e |
|
MD5 | 1f57c5dc5f3eb36f7babae998511807c |
|
BLAKE2b-256 | 3b9fd985bdf4d1b8416f36b42630752ee566b2e923a5ba6397d7a9f704f0a15a |