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@BrianWhitneyAI BrianWhitneyAI commented Apr 4, 2025

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This PR does a few things all centered around updating our supported python versions to 3.10-3.13. It resolves #108, #104, #70, kind of resolves #10 maybe? And includes the changes from #105 and #80.

1.) Remove all past refrences to 3.9
2.) unpins imageio[ffmpeg], numpy, and tifffile
3.) Conditionally resolve 'ome_zarr_writer_2.py` dependencies to support all python versions
4.) define specific dependencies per python version
5.) update the time series writer tests which were broken and out of date. (this could probably be another PR but was trying to go green)

@BrianWhitneyAI BrianWhitneyAI marked this pull request as ready for review April 4, 2025 20:20
@BrianWhitneyAI BrianWhitneyAI requested a review from a team as a code owner April 4, 2025 20:20
@BrianWhitneyAI BrianWhitneyAI marked this pull request as draft April 4, 2025 20:26
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I am pretty unsure about my update to the time series writer tests which is broken due to the dependency scramble. The original test is full of TODOs and caveats. I really just wrote a test to correctly assert whats happening currently but I think i am missing some of the complexity of the RGBA portion. Could use some input here.

@BrianWhitneyAI BrianWhitneyAI marked this pull request as ready for review April 4, 2025 20:42
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@kmitcham kmitcham left a comment

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Thanks! I should have caught some of these when moved it to 3.9, but others I had no idea existed.

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Thanks! I should have caught some of these when moved it to 3.9, but others I had no idea existed.
No problem! still not sure its a fix but maybe a step forward! now for the readers...

pyproject.toml Outdated
"ome-types[lxml]>=0.4.0",
"ome-zarr>=0.6.1",
# Use ngff-zarr for Python 3.10 or lower and ome-zarr-models for Python 3.11 or higher.
'ngff-zarr>=0.8.2,<0.9.1; python_version < "3.11"',
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Why less than 0.9.1 still - I thought that was a 3.9 issue?

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@BrianWhitneyAI BrianWhitneyAI Apr 8, 2025

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Oh I didn't try it really. This is the version from before. The change here was mostly just the 'python_version < "3.11"''

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Tests should pass after #116 is merged

@BrianWhitneyAI BrianWhitneyAI mentioned this pull request Apr 10, 2025
@BrianWhitneyAI BrianWhitneyAI merged commit 601132f into main Apr 11, 2025
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@BrianWhitneyAI BrianWhitneyAI deleted the admin/python-support branch April 11, 2025 20:33
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Remove python 3.9 from bioio-czi CI & Readme timeseries writer tests break in actual use

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