Rework ZarrIO backend/Remove python3.7/Update HDMF and PyNWB min/Update workflows #120
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mavaylon1
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oruebel
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oruebel
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oruebel
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src/hdmf_zarr/zarr_utils.py
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| class BuilderResolverMixin(BuilderResolver):# refactor to backend/utils.py | ||
| """ | ||
| A mixin for adding to Zarr reference-resolving types | ||
| the get_object method that returns Builders | ||
| """ | ||
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| def get_object(self, zarr_obj): | ||
| """ | ||
| A class that maps an Zarr object to a Builder | ||
| """ | ||
| return self.io.get_builder(zarr_obj) | ||
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| class ContainerResolverMixin(ContainerResolver): # refactor to backend/utils.py | ||
| """ | ||
| A mixin for adding to Zarr reference-resolving types | ||
| the get_object method that returns Containers | ||
| """ | ||
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| def get_object(self, zarr_obj): | ||
| """ | ||
| A class that maps an Zarr object to a Container | ||
| """ | ||
| return self.io.get_container(zarr_obj) |
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I think BuilderResolverMixin and ContainerResolverMixin are not implementing any Zarr-specific functionality. I think we may be able to just import these from HDMF. As the comment says, for import we may want to move them to backend/utils.py in HDMF instead
oruebel
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rly
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Sep 29, 2023
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This looks good to me. I'll let @oruebel do the final approval. |
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Thanks for your hard work on this! |
oruebel
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Co-authored-by: Oliver Ruebel <[email protected]>
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Co-authored-by: Oliver Ruebel <[email protected]>
oruebel
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Co-authored-by: Oliver Ruebel <[email protected]>
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This was referenced Sep 29, 2023
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Motivation
What was the reasoning behind this change? Please explain the changes briefly.
This branch holds the re-work of the ZarrIO backend on how it handles object references. The changes are to follow the same workflow HDMF has when handling object references.
With the changes to the backend, we have a temporary ignore on dtype conversion. It is has been raised in this ticket: #120
This PR removes python 3.7, brings hdmf and pynwb to the most up to date, as well updates to the workflows.
How to test the behavior?
Run unit tests and gallery examples, specifically test_io_convert.py and plot_convert_nwb_hdf5.py
Checklist
rufffrom the source directory.