Fix synergy test for refactored output format and add missing docstrings

Co-authored-by: jlelia <[email protected]>

Author: Copilot

src/cellpyability/toolbox.py

@@ -15,9 +15,18 @@
 from scipy.optimize import curve_fit
 import shutil
 
-# Creates logging protocol for CellPyAbility
-# Include 'logger = cellpyability_logger()' at start of script
 def cellpyability_logger():
+    """
+    Creates and configures the CellPyAbility logger.
+    
+    Logs all messages (DEBUG and above) to cellpyability.log in current working directory.
+    Logs INFO and above to console output.
+    
+    Returns:
+    --------
+    logger : logging.Logger
+        Configured logger instance
+    """
     logger = logging.getLogger("CellPyAbility")
     logger.setLevel(logging.DEBUG) # print all messages to log
 
@@ -92,17 +101,45 @@ def get_output_base_dir(output_dir=None):
     logger.info(f'Output directory {output_base} established ...')
     return output_base
 
-# The next two functions will be used in get_cellprofiler_path()
 def save_txt(config_file, path):
+    """
+    Save a path string to a text file.
+    
+    Parameters:
+    -----------
+    config_file : str or Path
+        Path to the configuration file to write
+    path : str or Path
+        Path to save in the configuration file
+    """
     with open(config_file, 'w') as file:
         file.write(str(path))
     logger.info(f'Path saved successfully in {config_file} as: {path}')
 
 def prompt_path():
+    """
+    Prompt user to enter the CellProfiler executable path.
+    
+    Returns:
+    --------
+    str
+        User-provided path with quotes and whitespace stripped
+    """
     return input("Enter the path to the CellProfiler program: ").strip().strip('"').strip("'")
 
-# Include 'cp_path = get_cellprofiler_path()' at start of script
 def get_cellprofiler_path():
+    """
+    Get the path to the CellProfiler executable.
+    
+    Checks for saved path in cellprofiler_path.txt, then checks default installation
+    locations on Windows and macOS. If not found, prompts user for the path.
+    Saves the path for future use.
+    
+    Returns:
+    --------
+    str or Path
+        Path to the CellProfiler executable
+    """
     # Store CellProfiler path in current working directory (PyPI-compatible)
     config_file = Path.cwd() / "cellprofiler_path.txt"
 
@@ -300,9 +337,51 @@ def rename_counts(cp_csv, counts_csv):
 
 # Define models at module level so they are accessible
 def fivePL(x, A, B, C, D, G):
+    """
+    Five-parameter logistic (5PL) dose-response model.
+    
+    Parameters:
+    -----------
+    x : array-like
+        Dose/concentration values
+    A : float
+        Minimum asymptote (response at infinite dose)
+    B : float
+        Hill slope
+    C : float
+        Inflection point (IC50/EC50)
+    D : float
+        Maximum asymptote (response at zero dose)
+    G : float
+        Asymmetry factor
+    
+    Returns:
+    --------
+    array-like
+        Predicted response values
+    """
     return ((A - D) / (1.0 + (x / C) ** B) ** G) + D
 
 def hill(x, Emax, EC50, HillSlope):
+    """
+    Hill equation for dose-response curves.
+    
+    Parameters:
+    -----------
+    x : array-like
+        Dose/concentration values
+    Emax : float
+        Maximum effect
+    EC50 : float
+        Half-maximal effective concentration
+    HillSlope : float
+        Hill coefficient (slope factor)
+    
+    Returns:
+    --------
+    array-like
+        Predicted response values
+    """
     return Emax * (x**HillSlope) / (EC50**HillSlope + x**HillSlope)
 
 def fit_response_curve(x, y, name):

tests/data/test_synergy_BlissMatrix.csv

@@ -1,7 +1,7 @@
-Row Drug Concentration,0.0,6.103515625e-09,2.44140625e-08,9.765625e-08,3.90625e-07,1.5625e-06,6.25e-06,2.5e-05,0.0001,0.0004
+Drug Y (M),0.0,6.103515625e-09,2.441406249999996e-08,9.765624999999987e-08,3.906249999999996e-07,1.5624999999999988e-06,6.249999999999997e-06,2.4999999999999994e-05,0.0001,0.0004
 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
 3.90625e-07,0.0,0.030946751592267896,0.012015661544450884,0.2531808625591223,0.6142383771150097,0.9677389960256152,0.9316918731297796,0.8047634312298755,0.5467837824072979,0.028962647109758904
-1.5625e-06,0.0,0.07953190897452611,0.08496439416815316,0.20301738215191545,0.8519715881066756,1.0107631828643693,0.9533215365698291,0.8280294113993946,0.5639091273981162,0.029023472726199484
-6.25e-06,0.0,0.05351524691666354,0.03513250669772261,0.2735871309968979,0.8264150570068889,0.9841027476438996,0.9358210303233951,0.8131855924198923,0.5586656313813382,0.045500815203827163
-2.5e-05,0.0,0.05319167649583978,0.08349744897983535,0.2062700613718521,0.729943966890402,0.9789236654841811,0.9260712538469191,0.835268209513788,0.61121571152568,0.09249274025676549
+1.562500000000002e-06,0.0,0.07953190897452611,0.08496439416815316,0.20301738215191545,0.8519715881066756,1.0107631828643693,0.9533215365698291,0.8280294113993946,0.5639091273981162,0.029023472726199484
+6.249999999999997e-06,0.0,0.05351524691666354,0.03513250669772261,0.2735871309968979,0.8264150570068889,0.9841027476438996,0.9358210303233951,0.8131855924198923,0.5586656313813382,0.045500815203827163
+2.4999999999999994e-05,0.0,0.05319167649583978,0.08349744897983535,0.2062700613718521,0.729943966890402,0.9789236654841811,0.9260712538469191,0.835268209513788,0.61121571152568,0.09249274025676549
 0.0001,0.0,0.09873056490781451,0.14723825085831954,0.3103372264416291,0.8537961590820602,1.0162890964616222,0.9656480763683999,0.8882421695100602,0.6392428401127285,0.09648776720545657

tests/test_module_outputs.py

@@ -138,7 +138,7 @@ def test_synergy_module():
 
     test_data_dir = Path(__file__).parent / "data"
     counts_file = test_data_dir / "test_synergy_counts.csv"
-    expected_stats = test_data_dir / "test_synergy_stats.csv"
+    expected_bliss = test_data_dir / "test_synergy_BlissMatrix.csv"
 
     # Run Synergy analysis (output goes to ./cellpyability_output/synergy_output/)
     print(f"Running Synergy analysis with counts file: {counts_file}")
@@ -156,40 +156,40 @@ def test_synergy_module():
     )
 
     # Check output file (in current working directory)
-    output_stats = Path.cwd() / "cellpyability_output/synergy_output/test_synergy_stats.csv"
+    output_bliss = Path.cwd() / "cellpyability_output/synergy_output/test_synergy_BlissMatrix.csv"
 
     try:
-        if not output_stats.exists():
-            print(f"[FAIL] FAILED: Output file not created: {output_stats}")
+        if not output_bliss.exists():
+            print(f"[FAIL] FAILED: Output file not created: {output_bliss}")
             return False
 
-        print(f"Output file created: {output_stats}")
+        print(f"Output file created: {output_bliss}")
 
         # Compare files
-        match, message = compare_csv_files(output_stats, expected_stats, tolerance=1e-10)
+        match, message = compare_csv_files(output_bliss, expected_bliss, tolerance=1e-10)
 
         if match:
-            print(f"[PASS] PASSED: Synergy Stats output matches expected file")
+            print(f"[PASS] PASSED: Synergy BlissMatrix output matches expected file")
             print(f"   {message}")
             result = True
         else:
-            print(f"[FAIL] FAILED: Synergy Stats output does not match")
+            print(f"[FAIL] FAILED: Synergy BlissMatrix output does not match")
             print(f"   {message}")
 
             # Show first few rows for debugging
             print("\n   First rows of output:")
-            df_out = pd.read_csv(output_stats)
+            df_out = pd.read_csv(output_bliss)
             print(df_out.head())
             print("\n   First rows of expected:")
-            df_exp = pd.read_csv(expected_stats)
+            df_exp = pd.read_csv(expected_bliss)
             print(df_exp.head())
 
             result = False
     finally:
         # Clean up output files - use ignore_errors for Windows compatibility
-        if output_stats.exists():
+        if output_bliss.exists():
             try:
-                shutil.rmtree(output_stats.parent, ignore_errors=True)
+                shutil.rmtree(output_bliss.parent, ignore_errors=True)
             except Exception as e:
                 print(f"Warning: Could not clean up output directory: {e}")