Additional Pandas v2.0 fixes (#922)

src/tlo/methods/rti.py

@@ -2390,7 +2390,7 @@ def rti_assign_injuries(self, number):
                        'Polytrauma': sum(i > 2 for i in injais) > 1,
                        'MAIS': max(injmais),
                        'Number_of_injuries': ninj}
-            inj_df = inj_df.append(new_row, ignore_index=True)
+            inj_df.loc[len(inj_df)] = new_row
             # If person has an ISS score less than 15 they have a mild injury, otherwise severe
             if new_row['ISS'] < 15:
                 severity_category.append('mild')

tests/test_healthsystem.py

@@ -838,7 +838,7 @@ def apply(self, person_id, squeeze_factor):
          }).unstack().fillna(0.0).astype(int)
 
     assert summary_hsi_event['Number_By_Appt_Type_Code'].apply(pd.Series).sum().to_dict() == \
-           counts_of_appts_by_level.sum(axis=1, level=1).sum(axis=0).to_dict()
+           counts_of_appts_by_level.groupby(axis=1, level=1).sum().sum().to_dict()
 
 
 @pytest.mark.slow

tests/test_hiv_tb_scenarios.py

@@ -162,12 +162,12 @@ def test_check_tb_test_under_each_scenario(seed):
     hiv_pos_person = 1
     both_people = [hiv_neg_person, hiv_pos_person]
 
-    df.at[both_people, 'tb_inf'] = 'active'
-    df.at[both_people, 'tb_strain'] = 'ds'
-    df.at[both_people, 'tb_date_active'] = sim.date
-    df.at[both_people, 'tb_smear'] = True
-    df.at[both_people, 'age_exact_years'] = 20
-    df.at[both_people, 'age_years'] = 20
+    df.loc[both_people, 'tb_inf'] = 'active'
+    df.loc[both_people, 'tb_strain'] = 'ds'
+    df.loc[both_people, 'tb_date_active'] = sim.date
+    df.loc[both_people, 'tb_smear'] = True
+    df.loc[both_people, 'age_exact_years'] = 20
+    df.loc[both_people, 'age_years'] = 20
 
     # set HIV status
     df.at[hiv_neg_person, 'hv_inf'] = False
@@ -236,12 +236,12 @@ def test_check_tb_test_under_each_scenario(seed):
     hiv_pos_person = 1
     both_people = [hiv_neg_person, hiv_pos_person]
 
-    df.at[both_people, 'tb_inf'] = 'active'
-    df.at[both_people, 'tb_strain'] = 'ds'
-    df.at[both_people, 'tb_date_active'] = sim.date
-    df.at[both_people, 'tb_smear'] = True
-    df.at[both_people, 'age_exact_years'] = 20
-    df.at[both_people, 'age_years'] = 20
+    df.loc[both_people, 'tb_inf'] = 'active'
+    df.loc[both_people, 'tb_strain'] = 'ds'
+    df.loc[both_people, 'tb_date_active'] = sim.date
+    df.loc[both_people, 'tb_smear'] = True
+    df.loc[both_people, 'age_exact_years'] = 20
+    df.loc[both_people, 'age_years'] = 20
     # set HIV status
     df.at[hiv_neg_person, 'hv_inf'] = False
     df.at[hiv_pos_person, 'hv_inf'] = True