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This is a Python implementation of the SOMA API specification for interacting with the Unified Single-cell Data Model.
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
In case of illegal instruction
errors when running on older architectures --- e.g. Opteron, non-AVX2 --- the issue is that the pre-compiled binaries available at Conda or PyPI aren't targeted for all processor variants over time. You can install from source, as shown below.
To see if this is the issue, on Linux:
grep avx2 /proc/cpuinfo
If this comes up empty for your system, you'll definitely need to build from source to run TileDB-SOMA on that system.
cd
into your checkout and then cd apis/python
python -m pip install .
python -m pip install -v -e .
/usr/local
, set the path with environment variables TILEDB_PATH
and TILEDBSOMA_PATH
, TILEDB_PATH=/usr/local python -m pip install -v -e .
venv
:
$ python -m venv venv
$ . ./venv/bin/activate
$ python -m pip install -v -e .
make data
python -m pytest tests
spdlog
package: If you encounter an install-time error like fatal error: spdlog/spdlog.h: No such file or directory
you should additionally recursively remove /usr/local/lib/cmake/spdlog
, since the system uninstall of spdlog
fails to remove this properly.Please see https://github.com/single-cell-data/TileDB-SOMA/issues.
platform_config
formatWhen 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;
}
Please see the TileDB-SOMA wiki.
FAQs
Python API for efficient storage and retrieval of single-cell data using TileDB
We found that tiledbsoma demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 5 open source maintainers collaborating on the project.
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