cleanup

pyproject.toml

@@ -13,7 +13,8 @@ matplotlib = "^3.9.2"
 seaborn = "^0.13.2"
 pandas-stubs = "^2.2.2.240807"
 click = "^8.1.7"
-snakemake = "^8.20.4"
+# Pinned as later snakemake version fail to unit test generation
+snakemake = "8.18.1" 
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.1"

workflow/.tests/unit/common.py

@@ -11,33 +11,8 @@
 import csv
 import math
 
-import pandas as pd
 
-
-def compare_csv_files(
-    file1_path: str, file2_path: str, tolerance: float = 1e-4
-) -> bool:
-    """
-    Compare two CSV files with a given tolerance.
-    """
-    df1 = pd.read_csv(file1_path, skiprows=[1])
-    df2 = pd.read_csv(file2_path, skiprows=[1])
-
-    if df1.shape != df2.shape:
-        raise ValueError("DataFrames have different shapes")
-
-    # check that the data frames contrain the same data types
-    assert df1.dtypes.equals(df2.dtypes)
-
-    # check that the data frames contain the same data
-    pd.testing.assert_frame_equal(
-        df1, df2, check_exact=False, rtol=tolerance, atol=tolerance
-    )
-
-    return True
-
-
-class OutputCheckerV2:
+class OutputChecker:
     """
     Check the output of a Snakemake rule given only the directories
     of the input data, expected output, and the working directory and

workflow/.tests/unit/test_amplicon_cov.py

@@ -6,7 +6,7 @@
 import shutil
 from pathlib import Path
 
-from common import OutputCheckerV2
+from common import OutputChecker
 
 
 def print_directory_contents(path):
@@ -85,7 +85,7 @@ def test_get_coverage_for_batch():
                 print(f"  {file}")
 
         # Compare output with expected result using the OutputChecker
-        checker = OutputCheckerV2(
+        checker = OutputChecker(
             workdir / "data",
             expected_path,
             workdir,