abundance fraction per cluster column

[Alex-Davydov]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @Alex-Davydov, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request introduces a valuable new data point, the abundance fraction per cluster, to the clustering results, enhancing the analytical output by providing a normalized measure of cluster size. Concurrently, a comprehensive update of various project dependencies was performed to maintain the codebase's health and integrate the latest library versions.

Highlights

• New Feature: Abundance Fraction: A new column, "abundance_fraction_per_cluster", has been added to the "abundances-per-cluster.tsv" output file. This column represents the fraction of total abundance for each cluster, providing a normalized view of cluster size.
• Dependency Updates: Several project dependencies, including various @milaboratories and @platforma-sdk packages, as well as Vue.js related packages, have been updated to their latest minor or patch versions to ensure stability and leverage recent improvements.

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[gemini-code-assist]

Code Review

This pull request adds a new column abundance_fraction_per_cluster to the output, which represents the fraction of total abundance for each cluster. The changes involve updating the python scripts to calculate this new value and to include it in the output files. The logic for the calculation is sound. I've provided one suggestion to make the implementation more idiomatic and efficient using polars expressions, avoiding unnecessary data transfer between the polars engine and Python.

[gemini-code-assist]

The calculation of abundance_fraction_per_cluster can be made more efficient and idiomatic by performing the entire operation within the polars expression, avoiding the need to extract total_abundance into a Python variable using .item(). This keeps the computation entirely within the polars engine.

You can define the sum as a polars expression and reuse it.

Suggested change

	total_abundance = abundances_per_cluster.select(pl.sum('abundance_per_cluster')).item()
	abundances_per_cluster = abundances_per_cluster.with_columns(
	pl.when(pl.lit(total_abundance) > 0)
	.then(pl.col('abundance_per_cluster') / pl.lit(total_abundance))
	.otherwise(pl.lit(0.0, dtype=pl.Float64))
	.alias('abundance_fraction_per_cluster')
	)
	total_abundance_expr = pl.sum('abundance_per_cluster')
	abundances_per_cluster = abundances_per_cluster.with_columns(
	pl.when(total_abundance_expr > 0)
	.then(pl.col('abundance_per_cluster') / total_abundance_expr)
	.otherwise(pl.lit(0.0, dtype=pl.Float64))
	.alias('abundance_fraction_per_cluster')
	)