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peng-lab / BaSiCPy

MIT License
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Data in package #57

Closed yfukai closed 2 years ago

yfukai commented 2 years ago

Attempt to add getting-sample-data function to the package, following scikit-image etc.

yfukai commented 2 years ago

Now the test is quite slow (bounded by data download?) Maybe we can compress it a bit more, or skip downloading tests by default.

yfukai commented 2 years ago

I think I should consider compressing the data and making test data with the new implementation first and then come back to this pull request.

Nicholas-Schaub commented 2 years ago

Is this still WIP?

yfukai commented 2 years ago

Yes, the problem is that it's still slow to download the data. I'll first reorganize the data (in image size and bit depth), make an associated test data, and then open this pull request.

Nicholas-Schaub commented 2 years ago

@yfukai is there an ETA for this? I could assist if needed.

yfukai commented 2 years ago

Thanks, I'm waiting for myself to finish the implementation of the main routine #58 to generate test data, and hopefully, I'll be able to finish it by next week! If it seems to be taking more time, I'll think about an alternative way.

yfukai commented 2 years ago

Now it's ready. The test is failing for now, but I think it works once the data is added to the repo. (At least it's working if I changed the URL to https://github.com/yfukai/BaSiCpy/raw/data_in_package/data ). Please let me know if it's better to separate the tests into another PR.

yfukai commented 2 years ago

This is the test result with the URL https://github.com/yfukai/BaSiCpy/raw/data_in_package/data https://github.com/peng-lab/BaSiCPy/pull/57/checks?check_run_id=6551997384 @Nicholas-Schaub @tdmorello

yfukai commented 2 years ago

This will close #8.