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Mandelbrot demo requires Zarr-Python update #234

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d33bs opened this issue Jan 17, 2025 · 3 comments
Open

Mandelbrot demo requires Zarr-Python update #234

d33bs opened this issue Jan 17, 2025 · 3 comments

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@d33bs
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d33bs commented Jan 17, 2025

Hello, thanks for the great work on this project! I noticed that there's an error with the 5th cell on the demonstration Google Colab notebook linked here: https://colab.research.google.com/github/hms-dbmi/vizarr/blob/main/python/notebooks/mandelbrot.ipynb . This happened when I tried a "run all cells" on the notebook.

The error states:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
[<ipython-input-3-eee44cbf5fed>](https://localhost:8080/#) in <cell line: 0>()
     57 
     58 
---> 59 class MandlebrotStore(zarr.storage.BaseStore):
     60 
     61     def __init__(self, levels, tilesize, maxiter=255, compressor=None):

AttributeError: module 'zarr.storage' has no attribute 'BaseStore'

I imagine but don't know whether the Zarr API might have changed since the time the notebook was written.

@manzt
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manzt commented Jan 17, 2025

Hi there, the Mandelbrot notebook requires Zarr-Python <3 (pip install "zarr<3"). I haven't had time to migrate to the latest release to accommodate the new APIs. However, the required changes should be to just the notebook (ie the use of zarr module to define a custom store) and not vizarr itself since vizare supports both the v2 and v3 zarr format.

@d33bs
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d33bs commented Jan 17, 2025

Thanks @manzt - I'll give that a try!

@manzt
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manzt commented Jan 18, 2025

...and i'll try to migrate the example to zarr-python v3!

@manzt manzt changed the title Google Colab demo within readme results in an error Mandelbrot demo requires Zarr-Python update Jan 18, 2025
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