hdmf-zarr

library0.12.0pypypi✓ verified 83d ago

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.

data serialization database

pip install hdmf-zarr

github ↗package ↗

INSTALL

IMPORT

SIG · HDMF-ZARR

hdmf-zarr

datapythonv0.12.0

Install

11.6s avg

Import

4120ms

Disk

230MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.12.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 11.6s · import 4.120s · 220MB

230MB installed

● package 230MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

ZarrIO

✓ from hdmf_zarr import ZarrIO

Minimal import example. Full usage requires an HDMF container object (e.g., from pynwb).

from hdmf_zarr import ZarrIO from hdmf.common import NWBContainer # Create an NWBFile (requires pynwb) or a simple HDMF container # For demonstration, assume 'container' is an HDMF object # container = NWBContainer('test') # Write with ZarrIO # ZarrIO(container).export('output.zarr') print(ZarrIO.__name__)

Debug

Known issues

breakingIn 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.

fix

Re-export files using hdmf-zarr >=0.10.0 or keep older files only for reading.

affects: >=0.10.0,<0.12.0

gotchaThe `ZarrIO.file` property was renamed to `ZarrIO._file` in version 0.12.0. Direct access to the underlying Zarr group is now private.

fix

Use `ZarrIO._file` instead of `ZarrIO.file` for direct Zarr group access, or rely on public methods like `read()`.

affects: >=0.12.0

deprecated`NestedDirectoryStore` is deprecated in Zarr and may be removed. hdmf-zarr >=0.8.0 added a warning for its usage.

fix

Set environment variable `ZARR_DEPRECATED_NESTED_DIRECTORY_STORE` or switch to default Zarr store (e.g., `zarr.DirectoryStore`).

affects: >=0.8.0

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'hdmf_zarr'

Missing installation of hdmf-zarr. Often occurs when using pynwb without explicit hdmf-zarr install.

fix

Run `pip install hdmf-zarr` or include it in your requirements.

ImportError: cannot import name 'ZarrIO' from 'hdmf_zarr'

Incorrect import path or outdated version. HDMF-Zarr may not be installed correctly.

fix

Verify installation: `pip show hdmf-zarr`. Correct import: `from hdmf_zarr import ZarrIO`.

TypeError: '_io.BufferedWriter' object has no attribute 'name'

Using an uninitialized file-like object instead of a path string. ZarrIO expects a path, not a file handle.

fix

Pass a string path (e.g., 'output.zarr') instead of an open file object.

Upgrade

Version history

0.12.0latest on PyPI · released Oct 8, 2025

Audit

Dependencies

hdmfrequiredCore framework; hdmf-zarr provides a Zarr backend for HDMF.

zarrrequiredZarr storage backend for arrays and groups.

h5pyoptionalRequired for HDF5 compatibility in some conversion utilities.

Agent activity

9 hits · last 30 days

node

Resources

githubhttps://github.com/hdmf-dev/hdmf-zarr ↗

packagehttps://pypi.org/project/hdmf-zarr/ ↗