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Fix reading dtype from zarr dataset #72
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@alejoe91 it sounds like the hdmf-zarr/src/hdmf_zarr/backend.py Lines 671 to 675 in e4e9543
is likely the problem and should be updated to set the
The fix you propose helps work around the issue if an invalid file is encountered but doesn't fix the issue of creating bad files. |
Yeah I figured there was probably a better solution! Should I update the PR with the fix you suggested @oruebel ? |
Yes please. I think we can keep your fix as well as since it fixes potential issues on read, but it would be best to make sure we write the file correctly. |
Should be done ;) |
fixed flake8. I don't think failing tests are due to this change |
I'll take a look at fixing tests tomorrow. One issue is that codecov has been pulled from PyPi and it looks like there are some other issues in the gallery tests. I'll work on that to make sure we can get all tests passing. |
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## dev #72 +/- ##
==========================================
- Coverage 82.02% 81.94% -0.08%
==========================================
Files 11 11
Lines 2642 2647 +5
==========================================
+ Hits 2167 2169 +2
- Misses 475 478 +3
☔ View full report in Codecov by Sentry. |
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Looks good.
I created #80 to make sure we add roundtrip tests to cover this case and the changes from this PR
Hi guys,
I'm experimenting now with writing to Zarr using a custom DataChunkIterator from neuroconv bassed to the
ZarrDataIO
.Everything works fine, but upon reading the file, I get that the
zarr_type
is not found in the attirbutes. However, this can be inferred from thedtype
of thezarr.Dataset
.Not sure this is the most elegant solution and I didn't have time to dig in and find a better one, but it works in my case :)