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@abombin abombin commented Apr 24, 2025

add extensive comments for complex data set generation in UTAG tests.
Replaced one instance of a camel case with a snake case.

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Pull Request Overview

This PR enhances the UTAG tests by adding extensive inline comments for clarity in complex synthetic data generation and updates variable naming for consistency.

  • Adds detailed, step-by-step comments to the UTAG clustering data creation in the tests
  • Replaces a camel case variable with snake case for improved consistency in the clustering function

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File Description
tests/test_transformations/test_utag_clustering.py Added detailed comments to describe the data generation steps for synthetic spatial gene expression data.
src/spac/transformations.py Renamed a camel case variable to snake case to maintain naming consistency in UTAG clustering.
Comments suppressed due to low confidence (1)

tests/test_transformations/test_utag_clustering.py:124

  • It appears that spatial coordinates are generated randomly with a shape of (n_cells_complex, n_cells_complex), while earlier computed x_coord and y_coord suggest that a two-dimensional coordinate array is intended. Consider using np.column_stack((x_coord, y_coord)) to set the spatial coordinates with the correct dimensions.
adata_complex.obsm["spatial"] = np.random.rand(n_cells_complex, n_cells_complex)

@abombin abombin self-assigned this Apr 24, 2025
@abombin abombin closed this Apr 24, 2025
@abombin abombin reopened this Apr 24, 2025
@georgezakinih georgezakinih merged commit fddb5ca into dev Apr 24, 2025
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@abombin abombin deleted the add_comments_utag branch July 2, 2025 18:25
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3 participants