fix recall and enable workflow again

Author: IoannaNika

.github/workflows/python-package.yaml

@@ -1,6 +1,6 @@
 name: CI
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   build:

src/utils/evaluation.py

@@ -69,11 +69,11 @@ def calculate_recall(number_of_haplotypes_per_region:dict, true_number_haps_per_
         if true_number_haps_per_sample_region[sample_name][region]['Wuhan'] == 0:
             recall_wuhan_region = 1
         else:
-            recall_wuhan_region = max (number_of_haplotypes_per_region[region]['Wuhan'] / true_number_haps_per_sample_region[sample_name][region]['Wuhan'], 1)
+            recall_wuhan_region = min (number_of_haplotypes_per_region[region]['Wuhan'] / true_number_haps_per_sample_region[sample_name][region]['Wuhan'], 1)
         if true_number_haps_per_sample_region[sample_name][region]['Omicron'] == 0:
             recall_omicron_region = 1
         else:
-            recall_omicron_region = max (number_of_haplotypes_per_region[region]['Omicron'] / true_number_haps_per_sample_region[sample_name][region]['Omicron'], 1)
+            recall_omicron_region = min (number_of_haplotypes_per_region[region]['Omicron'] / true_number_haps_per_sample_region[sample_name][region]['Omicron'], 1)
 
         recall_wuhan.append(recall_wuhan_region)
         recall_omicron.append(recall_omicron_region)

tests/test_evaluation.py

@@ -48,6 +48,18 @@ def test_calculate_recall_and_duplication_ratio(self):
 
         dup_ratio = calculate_duplication_ratio(num_haps_per_region, true_num_of_haps_per_sample_per_region, sample_name)
         self.assertEqual(dup_ratio, 2)
+    
+    def test_calculate_recall_not_all_haps_reconstructed(self):
+        num_haps_per_region = {"test_region":{"Wuhan": 1, "Omicron": 0}}
+        sample_name = "test"
+        true_num_of_haps_per_sample_per_region = {"test": {"test_region": {"Wuhan": 1, "Omicron": 1}}}
+        recall_wuhan, recall_omicron = calculate_recall(num_haps_per_region, true_num_of_haps_per_sample_per_region, sample_name)
+
+        self.assertEqual(recall_wuhan, 1)
+        self.assertEqual(recall_omicron, 0)
+
+        dup_ratio = calculate_duplication_ratio(num_haps_per_region, true_num_of_haps_per_sample_per_region, sample_name)
+        self.assertEqual(dup_ratio, 0.5)
 
     def test_calculate_absolute_relative_abundance_error(self): 
         true_abs_per_sample_per_region  = {"test": {"test_region":{"Wuhan": 0.25, "Omicron": 0.75}}}