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n5: prevent failure on missing group metadata #651

Merged
merged 3 commits into from Nov 18, 2020

Commits on Nov 12, 2020

  1. n5: prevent failure on missing group metadata

    In the N5 spec, https://github.com/saalfeldlab/n5#file-system-specification
    point 3, the `{"n5": "$version"}` metadata is only expected at the root level.
    Datasets missing the metadata on inner groups fail to load:
    
    ```
    In [43]: list(zarr.hierarchy.Group(store=zarr.n5.N5Store("ex.n5")).groups())
    ...
    ValueError: group not found at path 'setup0'
    ```
    
    This changes the group parsing logic to not fail if the metadata is
    missing. Suggestions welcome on how to detect the top group/array in
    order to special case the parsing.
    joshmoore committed Nov 12, 2020
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Commits on Nov 13, 2020

  1. Use pop rather than del

    Co-authored-by: jakirkham <jakirkham@gmail.com>
    joshmoore and jakirkham committed Nov 13, 2020
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  2. Re-add error handling

    joshmoore committed Nov 13, 2020
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