design testing for concentration routines

tests/test_concentrations.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Feb 27 17:22:43 2025
+
+@author: alraune
+"""
+
+import numpy as np
+import pandas as pd
+import pytest
+from mibipret.analysis.sample.concentrations import total_concentration, total_count
+
+class Test_total_concentration:
+    """Class for testing analysis module on NA screening of mibipret."""
+
+    columns1 = ['sample_nr', 'sulfate', 'benzene']
+    s01 = ['2000-001', 748, 263]
+    s02 = ['2000-002', 548, 103]
+
+    data1 = pd.DataFrame([s01,s02],
+                         columns = columns1)
+
+
+    def test_total_concentration_01(self):
+        """Testing routine total_concentration().
+
+        Correct calculation of total amount of contaminants (total concentration).
+        """
+
+        out = total_concentration(self.data1).values
+        test = self.data1.iloc[:,1:].sum(axis = 1).values
+        assert np.all(out == test)
+
+    def test_total_concentration_02(self):
+        """Testing routine total_concentration().
+
+        Testing inplace option adding calculated values as column to data.
+        """
+        data_test = self.data1.copy()
+        total_concentration(data_test,name_list=['sulfate'],include = True).values
+
+        assert data_test.shape[1] == self.data1.shape[1]+1 and \
+                np.all(data_test['total concentration selection'] == self.data1['sulfate'])
+
+    def test_total_concentration_03(self):
+        """Testing routine total_concentration().
+
+        Correct handling when no overlap of specified list of quantities 
+        with column names in data frame.
+        """
+        with pytest.raises(ValueError):
+            total_concentration(self.data1,name_list=['test1','test2'])
+
+
+    def test_total_concentration_04(self,capsys):
+        """Testing routine total_concentration().
+
+        Testing verbose flag.
+        """
+
+        total_concentration(self.data1,verbose=True)
+        out,err=capsys.readouterr()
+
+        assert len(out)>0
+
+
+class Test_total_count:
+    """Class for testing analysis module on NA screening of mibipret."""
+
+    columns1 = ['sample_nr', 'sulfate', 'benzene']
+    s01 = ['2000-001', 748, 263]
+    s02 = ['2000-002', 548, ]
+
+    data1 = pd.DataFrame([s01,s02],
+                         columns = columns1)
+
+
+    def test_total_count_01(self):
+        """Testing routine total_count().
+
+        Correct calculation of total count of contaminants with concentration > 0.
+        """
+
+        out = total_count(self.data1).values
+
+        assert np.all(out == [2,1])
+
+    def test_total_count_02(self):
+        """Testing routine total_count().
+
+        Correct calculation of total count of contaminants with concentration > specific threshold.
+        """
+
+        out = total_count(self.data1,threshold = 300).values
+
+        assert np.all(out == [1,1])
+
+    def test_total_count_03(self):
+        """Testing routine total_count().
+
+        Correct handling when no overlap of specified list of quantities 
+        with column names in data frame.
+        """
+        with pytest.raises(ValueError):
+            total_count(self.data1,threshold = -1)
+
+
+    def test_total_count_04(self):
+        """Testing routine total_count().
+
+        Testing inplace option adding calculated values as column to data.
+        """
+        data_test = self.data1.copy()
+        total_count(data_test,name_list=['sulfate'],include = True).values
+
+        assert data_test.shape[1] == self.data1.shape[1]+1 and \
+                np.all(data_test['total count selection'] == [1,1])
+
+    def test_total_count_05(self):
+        """Testing routine total_count().
+
+        Correct handling when no overlap of specified list of quantities 
+        with column names in data frame.
+        """
+        with pytest.raises(ValueError):
+            total_count(self.data1,name_list=['test1','test2'])
+
+
+    def test_total_count_06(self,capsys):
+        """Testing routine total_count().
+
+        Testing verbose flag.
+        """
+
+        total_count(self.data1,verbose=True)
+        out,err=capsys.readouterr()
+
+        assert len(out)>0
+
+
+