update unit tests

epic-open-source · Dec 5, 2024 · d40d9fd · d40d9fd
1 parent 29cd288
commit d40d9fd
Show file tree

Hide file tree

Showing 6 changed files with 38 additions and 22 deletions.
diff --git a/src/seismometer/__init__.py b/src/seismometer/__init__.py
@@ -63,4 +63,5 @@ def run_startup(
     config = config_provider or ConfigProvider(config_path, output_path=output_path, definitions=definitions)
     loader = loader_factory(config)
     sg = Seismogram(config, loader)
+
     sg.load_data(predictions=predictions_frame, events=events_frame)
diff --git a/src/seismometer/data/performance.py b/src/seismometer/data/performance.py
@@ -304,7 +304,7 @@ def calculate_bin_stats(
         fpr = fps / total_negatives
 
         ppv = tps / (tps + fps)
-        ppv[np.isnan(ppv)] = 0
+        ppv[np.isnan(ppv)] = 1
 
         # TN / TN + FN
         npv = np.divide(tns, tns + fns)

diff --git a/src/seismometer/table/analytics_table.py b/src/seismometer/table/analytics_table.py
@@ -135,6 +135,21 @@ def __init__(
         self.rows_group_length = len(self.target_columns) if self.top_level == "Score" else len(self.score_columns)
         self.num_of_rows = len(self.score_columns) * len(self.target_columns)
         self.per_context = per_context
+        # If polars package is not installed, overwrite is_na function in great_tables package to treat Agnostic
+        # as pandas dataframe.
+        try:
+            import polars as pl
+
+            # Use 'pl' to avoid the F401 error
+            _ = pl.DataFrame()
+        except ImportError:
+            from typing import Any
+
+            from great_tables._tbl_data import Agnostic, PdDataFrame, is_na
+
+            @is_na.register(Agnostic)
+            def _(df: PdDataFrame, x: Any) -> bool:
+                return pd.isna(x)
 
     def _validate_df_statistics_data(self):
         if not self._initializing:  # Skip validation during initial setup

diff --git a/tests/data/test_metric_to_threshold.py → tests/data/test_binary_performance.py b/tests/data/test_metric_to_threshold.py → tests/data/test_binary_performance.py
diff --git a/tests/data/test_cohorts.py b/tests/data/test_cohorts.py
@@ -20,24 +20,24 @@ def input_df():
 def expected_df(cohorts):
     data_rows = np.vstack(
         (
-            # TP,FP,TN,FN,   Acc,Sens,Spec,PPV,NPV,    Flag,      LR+, NNE, NNT1/2,  cohort,ct,tgtct,
-            [[0, 0, 1, 1, 0.5, 0.0, 1.0, 0.0, 0.5, 0.0, np.nan, np.inf, np.inf, "<1.0", 2, 1]] * 70,
-            [[0, 1, 0, 1, 0, 0, 0, 0, 0, 0.5, 0, np.inf, np.inf, "<1.0", 2, 1]] * 10,
-            [[1, 1, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 2, 4, "<1.0", 2, 1]] * 21,
-            # TP,FP,TN,FN,   Acc,Sens,Spec, PPV, NPV,    Flag,      LR+, NNE, NNT1/2,  cohort,ct,tgtct
-            [[0, 0, 2, 2, 0.5, 0.0, 1.0, 0.0, 0.5, 0.0, np.nan, np.inf, np.inf, ">=1.0", 4, 2]] * 30,
-            [[1, 0, 2, 1, 0.75, 0.5, 1, 1, 2 / 3, 0.25, np.inf, 1, 2, ">=1.0", 4, 2]] * 10,
-            [[1, 1, 1, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 1.0, 2, 4, ">=1.0", 4, 2]] * 10,
-            [[2, 1, 1, 0, 0.75, 1, 0.5, 2 / 3, 1, 0.75, 2, 1.5, 3, ">=1.0", 4, 2]] * 10,
-            [[2, 2, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 2, 4, ">=1.0", 4, 2]] * 41,
-            # TP,FP,TN,FN,   Acc,Sens,Spec,PPV,NPV,    Flag,      LR+, NNE, NNT1/2,  cohort,ct,tgtct
-            [[0, 0, 1, 1, 0.5, 0.0, 1.0, 0.0, 0.5, 0.0, np.nan, np.inf, np.inf, "1.0-2.0", 2, 1]] * 50,
-            [[1, 0, 1, 0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.5, np.inf, 1, 2, "1.0-2.0", 2, 1]] * 10,
-            [[1, 1, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 2, 4, "1.0-2.0", 2, 1]] * 41,
-            # TP,FP,TN,FN,   Acc,Sens,Spec,PPV,NPV,    Flag,      LR+, NNE, NNT1/2,  cohort,ct,tgtct
-            [[0, 0, 1, 1, 0.5, 0.0, 1.0, 0.0, 0.5, 0.0, np.nan, np.inf, np.inf, ">=2.0", 2, 1]] * 30,
-            [[1, 0, 1, 0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.5, np.inf, 1, 2, ">=2.0", 2, 1]] * 10,
-            [[1, 1, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 2, 4, ">=2.0", 2, 1]] * 61,
+            # TP,FP,TN,FN,   Acc,Sens,Spec,PPV,NPV,    Flag,      LR+,  NNT1/2,  cohort,ct,tgtct,
+            [[0, 0, 1, 1, 0.5, 0.0, 1.0, 1.0, 0.5, 0.0, np.nan, 2.0, "<1.0", 2, 1]] * 70,
+            [[0, 1, 0, 1, 0, 0, 0, 0, 0, 0.5, 0, np.inf, "<1.0", 2, 1]] * 10,
+            [[1, 1, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 4, "<1.0", 2, 1]] * 21,
+            # TP,FP,TN,FN,   Acc,Sens,Spec, PPV, NPV,    Flag,      LR+,  cohort,ct,tgtct
+            [[0, 0, 2, 2, 0.5, 0.0, 1.0, 1.0, 0.5, 0.0, np.nan, 2.0, ">=1.0", 4, 2]] * 30,
+            [[1, 0, 2, 1, 0.75, 0.5, 1, 1, 2 / 3, 0.25, np.inf, 2, ">=1.0", 4, 2]] * 10,
+            [[1, 1, 1, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 1.0, 4, ">=1.0", 4, 2]] * 10,
+            [[2, 1, 1, 0, 0.75, 1, 0.5, 2 / 3, 1, 0.75, 2, 3, ">=1.0", 4, 2]] * 10,
+            [[2, 2, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 4, ">=1.0", 4, 2]] * 41,
+            # TP,FP,TN,FN,   Acc,Sens,Spec,PPV,NPV,    Flag,      LR+,  cohort,ct,tgtct
+            [[0, 0, 1, 1, 0.5, 0.0, 1.0, 1.0, 0.5, 0.0, np.nan, 2.0, "1.0-2.0", 2, 1]] * 50,
+            [[1, 0, 1, 0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.5, np.inf, 2, "1.0-2.0", 2, 1]] * 10,
+            [[1, 1, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 4, "1.0-2.0", 2, 1]] * 41,
+            # TP,FP,TN,FN,   Acc,Sens,Spec,PPV,NPV,    Flag,      LR+,  cohort,ct,tgtct
+            [[0, 0, 1, 1, 0.5, 0.0, 1.0, 1.0, 0.5, 0.0, np.nan, 2.0, ">=2.0", 2, 1]] * 30,
+            [[1, 0, 1, 0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.5, np.inf, 2, ">=2.0", 2, 1]] * 10,
+            [[1, 1, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 4, ">=2.0", 2, 1]] * 61,
         )
     )
 

diff --git a/tests/data/test_perf_stats.py b/tests/data/test_perf_stats.py
@@ -31,7 +31,7 @@ def stats_case_base():
 
     expected = []
     # Threshold, TP, FP, TN, FN, Acc, Sens, Spec, PPV, NPV, Flag Rate, LR+, NNE, NBS, NNT1/3 |  Threshold
-    expected.append([100, 0, 0, 1, 2, 1 / 3, 0, 1, 0, 1 / 3, 0, np.nan, np.inf, np.nan, np.inf])  # 1
+    expected.append([100, 0, 0, 1, 2, 1 / 3, 0, 1, 1, 1 / 3, 0, np.nan, np.inf, np.nan, 3])  # 1
     expected.append([50, 1, 0, 1, 1, 2 / 3, 0.5, 1, 1, 0.5, 1 / 3, np.inf, 1, 1 / 3, 3])  # .5
     expected.append([10, 2, 1, 0, 0, 2 / 3, 1, 0, 2 / 3, 1, 1, 1, 1.5, 17 / 27, 4.5])  # .1
     expected.append([0, 2, 1, 0, 0, 2 / 3, 1, 0, 2 / 3, 1, 1, 1, 1.5, 2 / 3, 4.5])  # 0
@@ -46,7 +46,7 @@ def stats_case_0():
 
     expected = []
     # Threshold, TP, FP, TN, FN, Acc, Sens, Spec, PPV, NPV, Flag Rate, LR+, NNE, NBS, NNT1/3 |  Threshold
-    expected.append([100, 0, 0, 2, 2, 0.5, 0, 1, 0, 0.5, 0, np.nan, np.inf, np.nan, np.inf])  # 1
+    expected.append([100, 0, 0, 2, 2, 0.5, 0, 1, 1, 0.5, 0, np.nan, np.inf, np.nan, 3])  # 1
     expected.append([50, 1, 0, 2, 1, 0.75, 0.5, 1, 1, 2 / 3, 0.25, np.inf, 1, 1 / 4, 3])  # .5
     expected.append([10, 2, 1, 1, 0, 0.75, 1, 0.5, 2 / 3, 1, 0.75, 2, 1.5, 17 / 36, 4.5])  # .1
     expected.append([0, 2, 2, 0, 0, 0.5, 1, 0, 0.5, 1, 1, 1, 2, 1 / 2, 6])  # 0
@@ -90,7 +90,7 @@ def stats_case_0_4():
 
     expected = []
     # Threshold, TP, FP, TN, FN, Acc, Sens, Spec, PPV, NPV, Flag Rate, LR+, NNE, NBS, NNT1/3 |  Threshold
-    expected.append([100, 0, 0, 2, 2, 0.5, 0, 1, 0, 0.5, 0, np.nan, np.inf, np.nan, np.inf])  # 1
+    expected.append([100, 0, 0, 2, 2, 0.5, 0, 1, 1, 0.5, 0, np.nan, np.inf, np.nan, 3])  # 1
     expected.append([75, 1, 0, 2, 1, 0.75, 0.5, 1, 1, 2 / 3, 0.25, np.inf, 1, 1 / 4, 3])  # .75
     expected.append([50, 2, 0, 2, 0, 1, 1, 1, 1, 1, 0.5, np.inf, 1, 1 / 2, 3])  # .5
     expected.append([25, 2, 1, 1, 0, 0.75, 1, 0.5, 2 / 3, 1, 0.75, 2, 1.5, 5 / 12, 4.5])  # .25