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malariagen / malariagen-data-python

Analyse MalariaGEN data from Python
https://malariagen.github.io/malariagen-data-python/latest/
MIT License
13 stars 23 forks source link

Improve performance of dendrogram plotting and saving results to the cache #465

Closed alimanfoo closed 9 months ago

alimanfoo commented 9 months ago

This PR swaps out the implementation of plotly dendrogram which was borrowed from the web with a simpler and more performant implementation.

Also switches to using zarr to save data to the results cache to improve performance.

Also fix missing taxon colors for Ag3.

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codecov[bot] commented 9 months ago

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (356c1e7) 97.51% compared to head (0f7c121) 97.52%. Report is 2 commits behind head on master.

Files Patch % Lines
malariagen_data/anoph/base.py 95.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #465 +/- ## ========================================== + Coverage 97.51% 97.52% +0.01% ========================================== Files 26 26 Lines 2092 2103 +11 ========================================== + Hits 2040 2051 +11 Misses 52 52 ```

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alimanfoo commented 9 months ago

Going to merge but happy to follow up if any questions or suggestions.