{"id":23846,"library":"hdmf-zarr","title":"hdmf-zarr","description":"A package defining a Zarr I/O backend for HDMF (Hierarchical Data Modeling Framework). Version 0.12.0 supports Python >=3.9 and provides Zarr-based reading/writing of HDMF files, including NWB (Neurodata Without Borders) files. Release cadence is irregular, with several minor releases per year.","status":"active","version":"0.12.0","language":"python","source_language":"en","source_url":"https://github.com/hdmf-dev/hdmf-zarr","tags":["neuroscience","NWB","Zarr","HDMF","I/O"],"install":[{"cmd":"pip install hdmf-zarr","lang":"bash","label":"Install from PyPI"}],"dependencies":[{"reason":"Core framework; hdmf-zarr provides a Zarr backend for HDMF.","package":"hdmf","optional":false},{"reason":"Zarr storage backend for arrays and groups.","package":"zarr","optional":false},{"reason":"Required for HDF5 compatibility in some conversion utilities.","package":"h5py","optional":true}],"imports":[{"note":"","wrong":"","symbol":"ZarrIO","correct":"from hdmf_zarr import ZarrIO"}],"quickstart":{"code":"from hdmf_zarr import ZarrIO\nfrom hdmf.common import NWBContainer\n# Create an NWBFile (requires pynwb) or a simple HDMF container\n# For demonstration, assume 'container' is an HDMF object\n# container = NWBContainer('test')\n# Write with ZarrIO\n# ZarrIO(container).export('output.zarr')\nprint(ZarrIO.__name__)","lang":"python","description":"Minimal import example. Full usage requires an HDMF container object (e.g., from pynwb)."},"warnings":[{"fix":"Re-export files using hdmf-zarr >=0.10.0 or keep older files only for reading.","message":"In version 0.10.0, the export functionality was refactored, breaking existing exported files by changing the default file source. Files exported with earlier versions may be invalid.","severity":"breaking","affected_versions":">=0.10.0,<0.12.0"},{"fix":"Use `ZarrIO._file` instead of `ZarrIO.file` for direct Zarr group access, or rely on public methods like `read()`.","message":"The `ZarrIO.file` property was renamed to `ZarrIO._file` in version 0.12.0. Direct access to the underlying Zarr group is now private.","severity":"gotcha","affected_versions":">=0.12.0"},{"fix":"Set environment variable `ZARR_DEPRECATED_NESTED_DIRECTORY_STORE` or switch to default Zarr store (e.g., `zarr.DirectoryStore`).","message":"`NestedDirectoryStore` is deprecated in Zarr and may be removed. hdmf-zarr >=0.8.0 added a warning for its usage.","severity":"deprecated","affected_versions":">=0.8.0"}],"env_vars":null,"search_vec":"'0.12.0':18 '3.9':21 'backend':10 'base':26 'border':35 'cadenc':38 'data':14 'defin':6 'file':30,36 'framework':16 'hdmf':2,12,29,50 'hdmf-zarr':1 'hierarch':13 'i/o':9,51 'includ':31 'irregular':40 'minor':43 'model':15 'neurodata':33 'neurosci':47 'nwb':32,48 'packag':5 'per':45 'provid':23 'python':20 'reading/writing':27 'releas':37,44 'sever':42 'support':19 'version':17 'without':34 'year':46 'zarr':3,8,25,49 'zarr-bas':24","created_at":"2026-05-01T08:09:56.666866+00:00","updated_at":"2026-05-01T08:09:56.666866+00:00","problems":[{"fix":"Run `pip install hdmf-zarr` or include it in your requirements.","cause":"Missing installation of hdmf-zarr. Often occurs when using pynwb without explicit hdmf-zarr install.","error":"ModuleNotFoundError: No module named 'hdmf_zarr'"},{"fix":"Verify installation: `pip show hdmf-zarr`. Correct import: `from hdmf_zarr import ZarrIO`.","cause":"Incorrect import path or outdated version. HDMF-Zarr may not be installed correctly.","error":"ImportError: cannot import name 'ZarrIO' from 'hdmf_zarr'"},{"fix":"Pass a string path (e.g., 'output.zarr') instead of an open file object.","cause":"Using an uninitialized file-like object instead of a path string. ZarrIO expects a path, not a file handle.","error":"TypeError: '_io.BufferedWriter' object has no attribute 'name'"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":"0.12.0","cli_name":"","cli_version":null,"type":"library","homepage":null,"github":"https://github.com/hdmf-dev/hdmf-zarr","docs":null,"changelog":null,"pypi":"https://pypi.org/project/hdmf-zarr/","npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["data","serialization","database"],"base_url":null,"auth_type":null,"provenance":{"verified_status":"passing","verified_at":"2026-06-29","last_verified":"2026-06-29","next_check":"2026-07-29","install_tag":null}}