Metadata-Version: 2.1
Name: spatialdata
Version: 0.0.4
Summary: Spatial data format.
Project-URL: Documentation, https://spatialdata.readthedocs.io/
Project-URL: Source, https://github.com/scverse/spatialdata.git
Project-URL: Home-page, https://github.com/scverse/spatialdata.git
Author: scverse
Maintainer-email: scverse <giov.pll@gmail.com>
License: BSD 3-Clause License
        
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License-File: LICENSE
Requires-Python: >=3.9
Requires-Dist: anndata>=0.9.1
Requires-Dist: dask-image
Requires-Dist: geopandas
Requires-Dist: multiscale-spatial-image>=0.11.2
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: ome-zarr>=0.7.0
Requires-Dist: pyarrow
Requires-Dist: pygeos
Requires-Dist: rich
Requires-Dist: shapely>=2.0.1
Requires-Dist: spatial-image>=0.3.0
Requires-Dist: typing-extensions>=4.0.0
Requires-Dist: xarray
Requires-Dist: xarray-schema
Requires-Dist: xarray-spatial>=0.3.5
Requires-Dist: zarr
Provides-Extra: dev
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Provides-Extra: extra
Requires-Dist: napari-spatialdata; extra == 'extra'
Requires-Dist: spatialdata-io; extra == 'extra'
Requires-Dist: spatialdata-plot; extra == 'extra'
Provides-Extra: test
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Provides-Extra: torch
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Description-Content-Type: text/markdown

# Work in progress ⚠

-   **The library is not ready.** We aim at a beta release in the following months. If interested in a demo/early beta, please reach out to us.
-   To get involved in the discussion you are welcome to join our Zulip workspace and/or our community meetings every second week; [more info here](https://imagesc.zulipchat.com/#narrow/stream/329057-scverse/topic/SpatialData.20meetings).
-   Links to the OME-NGFF specification: [0.4](https://ngff.openmicroscopy.org/latest/), [0.5-dev (tables)](https://github.com/ome/ngff/pull/64), [0.5-dev (transformations and coordinate systems)](https://github.com/ome/ngff/pull/138)

# spatialdata

[![Tests][badge-tests]][link-tests]
[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/scverse/spatialdata/main.svg)](https://results.pre-commit.ci/latest/github/scverse/spatialdata/main)
[![codecov](https://codecov.io/gh/scverse/spatialdata/branch/main/graph/badge.svg?token=X19DRSIMCU)](https://codecov.io/gh/scverse/spatialdata)
[![DOI](https://zenodo.org/badge/487366481.svg)](https://zenodo.org/badge/latestdoi/487366481)

[badge-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml/badge.svg
[link-tests]: https://github.com/scverse/spatialdata/actions/workflows/test.yaml

<img src='https://github.com/giovp/spatialdata-sandbox/raw/main/graphics/overview.png'/>

## Getting started

Please refer to the [documentation][link-docs]. In particular:

-   [API documentation][link-api].
-   [Design doc][link-design-doc].
-   [Example notebooks][link-notebooks].

## Installation

Check out the docs for more complete installation instructions. For now you can install `spatialdata` with:

```bash
pip install git+https://github.com/scverse/spatialdata.git@main
```

## Contact

For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].

## Citation

> t.b.a

You can cite the scverse publication as follows:

> **The scverse project provides a computational ecosystem for single-cell omics data analysis**
>
> Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis
>
> _Nat Biotechnol._ 2022 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).

<!-- Links -->

[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/scverse/spatialdata/issues
[changelog]: https://spatialdata.readthedocs.io/latest/changelog.html
[design doc]: https://scverse-spatialdata.readthedocs.io/en/latest/design_doc.html
[link-docs]: https://spatialdata.scverse.org/en/latest/
[link-api]: https://spatialdata.scverse.org/en/latest/api.html
[link-design-doc]: https://spatialdata.scverse.org/en/latest/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks.html
