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oruebel / ndx-icephys-meta

NWB extensions for origanizing intracellular electrophysiology metadata
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error on the README script when used with h5py>=3.1.0 #81

Closed anilbey closed 3 years ago

anilbey commented 3 years ago

It raises this error when used with h5py 3.1.0 or 3.2.0. TypeError: No conversion path for dtype: dtype('<U9')

It may be due to the h5py 3.0.0 update.

oruebel commented 3 years ago

Thanks for the heads up. We are still working on updating HDMF/PyNWB to support h5py >3.0. I'll have a look to see if this is an issue with the extension itself or HDMF, but I assume it is most likely the problem that updating HDMF to the latest h5py is still in the works. The corresponding issues and PR's on HDMF are

https://github.com/hdmf-dev/hdmf/issues/458 https://github.com/hdmf-dev/hdmf/pull/480

wvangeit commented 3 years ago

hi @oruebel, is there any ETA on the h5py>3.0 support? We need this extension for some open source code, and it would be good if our users don't have problems installing this dependency. Thanks.

oruebel commented 3 years ago

We are currently working on integrating the extension with NWB core. I would expect this will probably take another 2 weeks. h5py 3.x support is related to HDMF issue https://github.com/hdmf-dev/hdmf/issues/458 and the corresponding PR https://github.com/hdmf-dev/hdmf/pull/480. Can you please re-post your question there. CC @ajtritt

oruebel commented 3 years ago

@wvangeit sorry of the delay on this issue. h5py3 support has been in released in PyNWB and HDMF. Porting of the extension to NWB core is largely complete now. I anticipate that we will finish the release by the end of this month. The relevant PRs on PyNWB are https://github.com/NeurodataWithoutBorders/pynwb/pull/1349 and the related PR https://github.com/NeurodataWithoutBorders/pynwb/pull/1383.