Python API for efficient storage and retrieval of single-cell data using TileDB

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for atolopko-czi from gravatar.com atolopko-czi Avatar for bkmartinjr from gravatar.com bkmartinjr Avatar for johnkerl-tiledb from gravatar.com johnkerl-tiledb Avatar for mlin from gravatar.com mlin Avatar for nguyenv from gravatar.com nguyenv

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

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 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: 
    $ 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

Verified details

These details have been verified by PyPI
Maintainers
Avatar for atolopko-czi from gravatar.com atolopko-czi Avatar for bkmartinjr from gravatar.com bkmartinjr Avatar for johnkerl-tiledb from gravatar.com johnkerl-tiledb Avatar for mlin from gravatar.com mlin Avatar for nguyenv from gravatar.com nguyenv

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

Release history Release notifications | RSS feed

1.15.0rc3 pre-release

1.15.0rc2 pre-release

1.15.0rc1 pre-release yanked

Reason this release was yanked:

pip allowed an rc anndata dependency to be included, which was unfortunate

1.15.0rc0 pre-release yanked

Reason this release was yanked:

Relese has post-tag failures

1.14.5

1.14.4

1.14.3

1.14.2

1.14.2rc0 pre-release

1.14.1

1.14.0 yanked

Reason this release was yanked:

Broken release; 1.14.1 upcoming

1.13.1

1.13.1rc0 pre-release

1.13.0

1.13.0rc0 pre-release

1.12.3

1.12.2

1.12.1

1.12.0

1.11.4

1.10.2

1.9.5

1.8.1

This version

1.7.3

1.6.2

1.5.3

1.4.4

1.3.0

1.2.5

1.1.1

1.0.1

1.0.0

0.1.22

0.1.21

0.1.20 yanked

Reason this release was yanked:

This was tagged on the wrong branch. Do not use.

0.1.19

0.1.18

0.1.17

0.1.16

0.1.15

0.1.14

0.1.13

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

tiledbsoma-1.7.3.tar.gz (227.6 kB view details)

Uploaded Source

Built Distributions

tiledbsoma-1.7.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.4 MB view details)

Uploaded CPython 3.11 manylinux: glibc 2.17+ x86-64

tiledbsoma-1.7.3-cp311-cp311-macosx_11_0_x86_64.whl (23.9 MB view details)

Uploaded CPython 3.11 macOS 11.0+ x86-64

tiledbsoma-1.7.3-cp311-cp311-macosx_11_0_arm64.whl (21.2 MB view details)

Uploaded CPython 3.11 macOS 11.0+ ARM64

tiledbsoma-1.7.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.4 MB view details)

Uploaded CPython 3.10 manylinux: glibc 2.17+ x86-64

tiledbsoma-1.7.3-cp310-cp310-macosx_11_0_x86_64.whl (23.9 MB view details)

Uploaded CPython 3.10 macOS 11.0+ x86-64

tiledbsoma-1.7.3-cp310-cp310-macosx_11_0_arm64.whl (21.2 MB view details)

Uploaded CPython 3.10 macOS 11.0+ ARM64

tiledbsoma-1.7.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.4 MB view details)

Uploaded CPython 3.9 manylinux: glibc 2.17+ x86-64

tiledbsoma-1.7.3-cp39-cp39-macosx_11_0_x86_64.whl (23.9 MB view details)

Uploaded CPython 3.9 macOS 11.0+ x86-64

tiledbsoma-1.7.3-cp39-cp39-macosx_11_0_arm64.whl (21.2 MB view details)

Uploaded CPython 3.9 macOS 11.0+ ARM64

tiledbsoma-1.7.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.4 MB view details)

Uploaded CPython 3.8 manylinux: glibc 2.17+ x86-64

tiledbsoma-1.7.3-cp38-cp38-macosx_11_0_x86_64.whl (23.9 MB view details)

Uploaded CPython 3.8 macOS 11.0+ x86-64

tiledbsoma-1.7.3-cp38-cp38-macosx_11_0_arm64.whl (21.2 MB view details)

Uploaded CPython 3.8 macOS 11.0+ ARM64

File details

Details for the file tiledbsoma-1.7.3.tar.gz.

File metadata

  • Download URL: tiledbsoma-1.7.3.tar.gz
  • Upload date:
  • Size: 227.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.11.8

File hashes

Hashes for tiledbsoma-1.7.3.tar.gz
Algorithm Hash digest
SHA256 f9444f75a0d5499e6ec5576d86c40f77bde9de56d24463626d7fa19d34a9c04d
MD5 9a937017a9b45554dca8a0cc92ee6693
BLAKE2b-256 7c1b2b0c46da7e93c0d640a0c7db825373189b9797be43a074dd6cf41c48ce36

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 5484216a2e615176ab7614edc63b217a34ab8e5e0dd9d8832fbafa04c0f8d30c
MD5 d68e458c99cd65358a17a62ac762ee1a
BLAKE2b-256 9723851ac95884b74291af810bd81237f052a1c5e575940e890c3af53eb9b041

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp311-cp311-macosx_11_0_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp311-cp311-macosx_11_0_x86_64.whl
Algorithm Hash digest
SHA256 3d5547c66d51e62c0915e42512c71df20396882070edb7b9485760aaa40d8ade
MD5 5d2030b072d3a0021b8b4fa17db800e1
BLAKE2b-256 abc7f177bac8bea2e0587d78786db3a6873934eff200e873bf807ccf19c80c5d

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp311-cp311-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp311-cp311-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 4f27f954855176260b04e30642b00f2dfcb0924620bd29a6f3844e260ed1b016
MD5 9a8976d79e486a1943e881793018ba44
BLAKE2b-256 7214cfed3165b3752d2d467560ff5fe0ff6d3faf45aaa6748bc5bc368df029d3

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 8b2ffcc6bedc0ad617d68f1e7cb1af85f5be1d5b1174af0acab74e072d3c574f
MD5 30318b5d996f1b5d4f230398a5a11c42
BLAKE2b-256 9532c2b1e8537c6f349a2f2070dff29a54ef838ce29f56da2b9f87950bd91f7e

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp310-cp310-macosx_11_0_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp310-cp310-macosx_11_0_x86_64.whl
Algorithm Hash digest
SHA256 7456b8c4e98411cb9de7705d5e99252f31d47df8561983306ebaf4f2b2c0faf9
MD5 876247862abe5118494ac0df4ed16235
BLAKE2b-256 eb09e2a2241714193d0a930855b09f9c6a3910c079466708723613fd3edbd188

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp310-cp310-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp310-cp310-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 fc3f7c6e2d582fda7c964c3cded312cf9970daae24bc1616b268ce1637447458
MD5 0d385b52ae298959aa63e69579936558
BLAKE2b-256 c7ea6d85d6f15dad28df00a21849878e40c8a9c7d0c55957ac74c360c4bb5364

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 3b075ad959779c8f27c1befdba2acff1b7805793b2edd5a5dd459a8d7600e3a1
MD5 0ae4992eb4229b36137b4e9749d69da6
BLAKE2b-256 54f85efb086611327463a9c11dffe4036ae6edcaa63f14e33165da23dc858987

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp39-cp39-macosx_11_0_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp39-cp39-macosx_11_0_x86_64.whl
Algorithm Hash digest
SHA256 3ea945c75ac78a20b01b2f0ea08456662d523a42e4ccd1788a162c7cbf74e78a
MD5 f723d858a39d243222893af6cbf9c303
BLAKE2b-256 6cc7ca7894d9b3a5316b3433f6b5892aaa144360095cdc1693133223b4479083

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp39-cp39-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp39-cp39-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 275dbcd5ea89a122c362cdfdaa6051ee739dd1094a5cb48464fddc9179662c8d
MD5 bf421dee727b46e42d1d1442d35647eb
BLAKE2b-256 b92cdfc0304d7fd64356eecda430c109b8483fd36102866e6e6d7010ca0c126e

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 d3f3060fd5796f4fe26f306ec9aa733f7da1d240144c2acdfcf6d062f6fc3427
MD5 2d15dbe953ce4c469eb4924e8f643d84
BLAKE2b-256 4bed4add27658617f8b22505840a65746ea6000c609042e427a574e13549263f

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp38-cp38-macosx_11_0_x86_64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp38-cp38-macosx_11_0_x86_64.whl
Algorithm Hash digest
SHA256 c4314e413b7361cc3a0d13816db45bbd20a04b490fdfc5fbda6323559dd8998c
MD5 0ebbf24026f17cf3da142f92cc5e15b1
BLAKE2b-256 bffd843f0a4dbfc6d456cf01bc083ea2339243737f542c062ac4cc953e30eb4b

See more details on using hashes here.

File details

Details for the file tiledbsoma-1.7.3-cp38-cp38-macosx_11_0_arm64.whl.

File metadata

File hashes

Hashes for tiledbsoma-1.7.3-cp38-cp38-macosx_11_0_arm64.whl
Algorithm Hash digest
SHA256 ff0bf4d4f0d4f5e6e46e76e47d6a64d2d00d8f3ff53124c6a753354e3119e4a4
MD5 99cc0201ba8818feee4940b3f456cfe1
BLAKE2b-256 6ea4f3f9d6dfa2c7ecd9262b53515ceddd273a6263f6c5281f293d3fdde0975b

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page