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Adding toy samplesheet (synthetic data)#1851

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quentinblampey wants to merge 3 commits intonf-core:sopafrom
quentinblampey:sopa
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Adding toy samplesheet (synthetic data)#1851
quentinblampey wants to merge 3 commits intonf-core:sopafrom
quentinblampey:sopa

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@quentinblampey
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This is a dummy samplesheet. Under the hood, Sopa will create a synthetic toy dataset to run the tests.

@mashehu
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mashehu commented Jan 28, 2026

please add a more detailed description about that in the readme

@quentinblampey
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Thanks @mashehu, I updated it!

@mashehu
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mashehu commented Jan 29, 2026

Sorry to be a pain, but why not just put the toy dataset directly in this branch instead of going through a generation step?

@quentinblampey
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For multiple reasons:

  1. The generation is very quick, so it's easier to run it rather than reading from a static file
  2. The input of Sopa is raw data that we process into a SpatialData object (via a process called TO_SPATIALDATA). There is no "raw data" for the toy dataset since it's synthetic (but we still call TO_SPATIALDATA with a specific technology argument). Instead, if I directly save the toy dataset as a SpatialData object, this would skip the TO_SPATIALDATA process, and I think it's better to keep all processes in the tests.

In brief, doing this would be both more complex and would remove some parts of the process being tested.

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okay, makes sense. 🙂

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2 participants