I've prepared a test build of this package with Zarr 3 which shows it is not compatible yet: https://copr.fedorainfracloud.org/coprs/qulogic/zarr3/build/8547559/ Note, I believe this is actually an issue with Zarr 3: https://github.com/zarr-developers/zarr-python/issues/2631#issuecomment-2601122791 So I'm opening this bug for tracking purposes only. Reproducible: Always Steps to Reproduce: Build against the linked copr Actual Results: =================================== FAILURES =================================== ______________________________ test_save_to_zarr _______________________________ tmp_path = PosixPath('/tmp/pytest-of-mockbuild/pytest-0/test_save_to_zarr0') def test_save_to_zarr(tmp_path): # Generate a dummy probe instance probe = generate_dummy_probe() # Define file path in the temporary directory folder_path = Path(tmp_path) / "probe.zarr" # Save the probe object to Zarr format > probe.to_zarr(folder_path=folder_path) tests/test_probe.py:176: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../BUILDROOT/usr/lib/python3.13/site-packages/probeinterface/probe.py:1138: in to_zarr self.add_probe_to_zarr_group(zarr_group) ../BUILDROOT/usr/lib/python3.13/site-packages/probeinterface/probe.py:1104: in add_probe_to_zarr_group group.create_dataset(name=field_name, data=data, dtype=dtype, chunks=False) /usr/lib64/python3.13/warnings.py:637: in wrapper return arg(*args, **kwargs) /usr/lib/python3.13/site-packages/zarr/core/group.py:2398: in create_dataset return Array(self._sync(self._async_group.create_dataset(name, **kwargs))) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ args = (<AsyncGroup file:///tmp/pytest-of-mockbuild/pytest-0/test_save_to_zarr0/probe.zarr>, 'x') kwargs = {'chunks': False, 'data': array([ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 25., 25., 25., 25., 25., 25., 25., 25., 25., 25., 25., 25., 50., 50., 50., 50., 50., 50., 50., 50., 50., 50.]), 'dtype': dtype('float64')} @functools.wraps(arg) def wrapper(*args, **kwargs): warn(msg, category=category, stacklevel=stacklevel + 1) > return arg(*args, **kwargs) E TypeError: AsyncGroup.create_dataset() missing 1 required keyword-only argument: 'shape' /usr/lib64/python3.13/warnings.py:637: TypeError Expected Results: Build should pass
Assigning to myself; as noted I think it's a Zarr bug.
Upstream is now tracking this in https://github.com/SpikeInterface/probeinterface/issues/313, and in the latest probeinterface 0.2.25 release they’ve upper-bounded Zarr to <3, https://github.com/SpikeInterface/probeinterface/pull/314. The good news is that Zarr is only a test dependency, and I’m able to conditionalize the tests that need it, so I’ll be shipping python-probeinterface-0.2.25 with a new "zarr" bcond that can be turned off if probeinterface is still incompatible when it’s time to actually ship Zarr 3: https://src.fedoraproject.org/rpms/python-probeinterface/pull-request/4
This bug appears to have been reported against 'rawhide' during the Fedora Linux 42 development cycle. Changing version to 42.
I have orphaned this package as part of the Neuro SIG’s strategy change to drop packages that are easily pip installable. Assuming nobody picks it back up, this may help unblock your Zarr update.
This is no longer relevant since python-probeinterface was retired in Rawhide.