https://github.com/hdmf-dev/hdmf-zarr
Zarr I/O backend for HDMF
https://github.com/hdmf-dev/hdmf-zarr
Last synced: 4 months ago
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Zarr I/O backend for HDMF
- Host: GitHub
- URL: https://github.com/hdmf-dev/hdmf-zarr
- Owner: hdmf-dev
- License: other
- Created: 2022-04-12T08:35:18.000Z (about 3 years ago)
- Default Branch: dev
- Last Pushed: 2024-07-13T23:03:10.000Z (11 months ago)
- Last Synced: 2024-07-14T11:08:21.133Z (10 months ago)
- Language: Python
- Homepage: https://hdmf-zarr.readthedocs.io/
- Size: 3.8 MB
- Stars: 7
- Watchers: 6
- Forks: 5
- Open Issues: 38
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.md
- Contributing: docs/CONTRIBUTING.rst
- License: LICENSE.txt
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
.. image:: docs/source/figures/logo_hdmf_zarr.png
:width: 400
hdmf-zarr
=========
The ``hdmf-zarr`` library implements a Zarr v2 backend for HDMF as well as convenience classes for integration of Zarr with PyNWB to support writing of NWB files to Zarr.
**Status:** The Zarr backend is **under development** and may still change. See the `overiew page `_ for an overview of the available features and known limitations of hdmf-zarr.
Support for Zarr v3 is planned. You can track progress of the support in https://github.com/hdmf-dev/hdmf-zarr/issues/202.
Documentation Status
--------------------
Latest release: .. image:: https://readthedocs.org/projects/hdmf-zarr/badge/?version=stable
:target: https://hdmf-zarr.readthedocs.io/en/stable/?badge=stable
:alt: Documentation status for latest release
Dev branch: .. image:: https://readthedocs.org/projects/hdmf-zarr/badge/?version=dev
:target: https://hdmf-zarr.readthedocs.io/en/dev/?badge=dev
:alt: Documentation status for dev branch
CI / Health Status
------------------
.. image:: https://codecov.io/gh/hdmf-dev/hdmf-zarr/branch/dev/graph/badge.svg
:target: https://codecov.io/gh/hdmf-dev/hdmf-zarr
.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_coverage.yml/badge.svg
:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_coverage.yml
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:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_tests.yml
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:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/run_all_tests.yml
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:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/check_external_links.yml
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:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/deploy_release.yml
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:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/ruff.yml
.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/codespell.yml/badge.svg
:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/codespell.yml
.. image:: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/HDMF_dev.yaml/badge.svg
:target: https://github.com/hdmf-dev/hdmf-zarr/actions/workflows/HDMF_dev.yaml
----------------
If you use HDMF or hdmf_zarr in your research, please use the following citation:
* A. J. Tritt, O. Ruebel, B. Dichter, R. Ly, D. Kang, E. F. Chang, L. M. Frank, K. Bouchard,
*"HDMF: Hierarchical Data Modeling Framework for Modern Science Data Standards,"*
2019 IEEE International Conference on Big Data (Big Data),
Los Angeles, CA, USA, 2019, pp. 165-179, doi: 10.1109/BigData47090.2019.9005648.
* HDMF-Zarr, RRID:SCR_022709
Documentation
-------------
See the ``hdmf-zarr`` documentation for details: https://hdmf-zarr.readthedocs.io
Usage
-----
The library is intended to be used in conjunction with HDMF. ``hdmf-zarr`` mainly provides
with the ``ZarrIO`` class an alternative to the ``HDF5IO`` I/O backend that ships with HDMF.
To support customization of I/O settings, ``hdmf-zarr`` provides ``ZarrDataIO`` (similar to
``H5DataIO`` in HDMF). Using ``ZarrIO`` and ``ZarrDataIO`` works much in the same way as ``HDF5IO``.
To ease integration with the NWB data standard and PyNWB, ``hdmf-zarr`` provides the ``NWBZarrIO``
class as alternative to ``pynwb.NWBHDF5IO``. See the tutorials included with the documentation for more details.