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

These details have been verified by PyPI

Maintainers

atolopko-czi bkmartinjr johnkerl-tiledb mlin nguyenv

These details have not been verified by PyPI

Project links

Homepage

Project description

Overview

This is a Python implementation of the 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
# or
$ python -m pip install --pre tiledbsoma

Without --pre you will get version 0.1.* (the main-old branch); with --pre, you will get 0.5.0a* (the main branch).

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 .

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

These details have been verified by PyPI

Maintainers

atolopko-czi bkmartinjr johnkerl-tiledb mlin nguyenv

These details have not been verified by PyPI

Project links

Homepage

Release history Release notifications | RSS feed

1.15.0rc3 pre-release

Oct 30, 2024

1.15.0rc2 pre-release

Oct 7, 2024

1.15.0rc1 pre-release yanked

Oct 5, 2024

Reason this release was yanked:

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

1.15.0rc0 pre-release yanked

Oct 4, 2024

Reason this release was yanked:

Relese has post-tag failures

1.14.5

Oct 23, 2024

1.14.4

Oct 22, 2024

1.14.3

Oct 8, 2024

1.14.2

Sep 26, 2024

1.14.2rc0 pre-release

Sep 26, 2024

1.14.1

Sep 18, 2024

1.14.0 yanked

Sep 17, 2024

Reason this release was yanked:

Broken release; 1.14.1 upcoming

1.13.1

Aug 16, 2024

1.13.1rc0 pre-release

Aug 16, 2024

1.13.0

Aug 6, 2024

1.13.0rc0 pre-release

Aug 6, 2024

1.12.3

Jul 8, 2024

1.12.2

Jul 4, 2024

1.12.1

Jun 23, 2024

1.12.0

Jun 17, 2024

1.11.4

Jun 3, 2024

1.10.2

Apr 29, 2024

1.9.5

Apr 11, 2024

1.8.1

Mar 19, 2024

1.7.3

Mar 7, 2024

1.6.2

Jan 10, 2024

1.5.3

Jan 9, 2024

1.4.4

Oct 18, 2023

1.3.0

Jul 18, 2023

1.2.5

May 30, 2023

This version

1.1.1

Mar 16, 2023

1.0.1

Mar 21, 2023

1.0.0

Mar 13, 2023

0.1.22

Jan 17, 2023

0.1.21

Jan 12, 2023

0.1.20 yanked

Jan 12, 2023

Reason this release was yanked:

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

0.1.19

Dec 19, 2022

0.1.18

Nov 18, 2022

0.1.17

Nov 16, 2022

0.1.16

Nov 10, 2022

0.1.15

Nov 10, 2022

0.1.14

Nov 4, 2022

0.1.13

Nov 3, 2022

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