adding a docstring and switching a couple dependencies' sources

bin/multisample_plot.py

@@ -194,6 +194,30 @@ def accumulate_cov_dfs(directory: str, sample_lookup: dict[str, str]) -> pl.Data
 
 
 def fix_dataframe(df: pl.DataFrame) -> pl.DataFrame:
+ """
+ Fix and preprocess the input DataFrame for analysis.
+
+ This function takes a Polars DataFrame containing coverage data and performs
+ the following operations:
+ 1. Converts the DataFrame to a list of dictionaries.
+ 2. Iterates through the rows, adding new rows where there are large
+ jumps in coverage (greater than 50).
+ 3. Creates a new row with zero coverage between segments where large
+ jumps occur.
+
+ Parameters:
+ df (pl.DataFrame): Input DataFrame containing coverage data.
+ Expected columns: 'start', 'stop', 'coverage',
+ 'sample', and 'chromosome'.
+
+ Returns:
+ pl.DataFrame: A new DataFrame with additional rows inserted to
+ represent gaps in coverage.
+
+ Note:
+ The function assumes that the input DataFrame is sorted by position
+ within each chromosome and sample.
+ """
  rows = df.to_dicts()
  new_rows = []
  for i in range(len(rows) - 1):

pyproject.toml

@@ -44,6 +44,8 @@ dependencies = [
  "numpy",
  "scipy",
  "paramiko",
+ "plotnine",
+ "loguru",
 ]
 
 [build-system]
@@ -82,7 +84,6 @@ pyyaml = ">=5.4.1,<5.5"
 rasusa = ">=2.0.0,<2.1"
 python-edlib = ">=1.3.9,<1.4"
 mosdepth = ">=0.3.8,<0.4"
-plotnine = ">=0.13.6,<0.14"
 pyarrow = ">=16.1.0,<16.2"
 rust = ">=1.77.2,<1.80"
 csvtk = ">=0.30.0,<0.31"