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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Error downloading example dataset #1116

Closed cliu72 closed 7 months ago

cliu72 commented 7 months ago

Describe the bug I'm getting this error when I try to run example_dataset.get_example_dataset. I tried this line in notebooks 1, 2, and 3 - I get the same error. I tried on both Linux and Windows.

ValueError: BuilderConfig BuilderConfig(name='segment_image_data', version=0.0.5, data_dir=None, data_files=None, description='This configuration contains data used by notebook 1 - Segment Image Data.') doesn't have a 'trust_remote_code' key.

Expected behavior Successfully download example dataset in notebooks 1, 2, and 3.

To Reproduce Run notebook 1, 2, or 3 as is (delete any existing example datasets). image

srivarra commented 7 months ago

@cliu72 What version of the package datasets are you using?

cliu72 commented 7 months ago

Ah yes, that was the problem, thanks Sri. The version I was using was 2.14.6. In my old environment, I had just run pip install . to update ark. I created a completely new environment and ran pip install . to build ark from scratch and the datasets version was 2.17.1 (and then I was able to download the example dataset). So I guess re-installing ark in the same environment doesn't update datasets, but it does update when you create a new environment.