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BohndiekLab / patato

PATATO: A Python PhotoAcoustic Tomography Analysis Toolkit
MIT License
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errors when running tests #26

Closed MengjieSHI closed 1 year ago

MengjieSHI commented 1 year ago

Hi @tomelse,

I tested the option 1: using pip to install PATATO and tried to run tests. It seems the 'tests' folder is not downloaded, so I manually added it. The test failed because of three errors. I attached the screenshot of the error below.

image

The last two errors seem caused by the missing files due to the default relative path. Any suggestions to fix these?

tomelse commented 1 year ago

Hi @MengjieSHI, Thanks so much for taking the time to review the code.

The layout of the package means that the tests have to be run on a locally installed version of PATATO. The way I've done this usually is the following. Hopefully this should allow you to reproduce the tests. 

git clone https://github.com/BohndiekLab/patato 
cd patato
pip install -e .
cd tests
python -m unittest

This means that we don't have to ship all of the test code and example data with the installable version, reducing the amount of download time required for installing PATATO.

I hope that's okay? I tested it on Google Colab, and it seems to work.

I'll update the documentation to suggest that people do it in this way.

Thanks, Tom

MengjieSHI commented 1 year ago

Thanks for your fast response! Tests were running without issues now.

A minor comment on the documentation page, I guess you forgot to update the file names included in the example. I replaced them with'invivo_oe.hdf5' and 'invivo_dce.hdf5' and it works perfectly.

This issue is related to JOSS https://github.com/openjournals/joss-reviews/issues/5686 review.