Merge dev branch into master to release version 2.1.2 #282
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I tried out this update myself. Thanks @JeanMainguy for the dendrogram! I encountered one issue when dealing with pangenomes containing more than 65k gene families, as the current browsers cannot support a tile plot with that many gene families. This limitation stems from the browser, not PPanGGOLiN (https://stackoverflow.com/questions/78431835/plotly-heatmap-has-limit-on-data-size). Therefore, I approved this PR after advising to add warnings to inform users in such cases. I also improved the doc.
Fix random.sample call to be compatible with python 3.12
<path>/ppanggolin/cluster/cluster.py:440: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
Fix error when using an external clustering
Fixing some ruff warnings
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This pull request merges the dev branch into the master branch to release version 2.1.1
It includes the following bug fixes and enhancements:
Improved tile plot : PR Improve tile plot figure #277
Fixed an issue in the partition module to support Python 3.12: PR Fix error when using an external clustering #278
Fixed issues with the cluster command: PR Fix error when using an external clustering #278
Fixed ruff warnings: PR Fixing some ruff warnings #274