tox lint

monarch-initiative · Jan 7, 2025 · 8930cd2 · 8930cd2
1 parent c6604ff
commit 8930cd2
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Showing 4 changed files with 34 additions and 22 deletions.
diff --git a/src/pheval/analyse/disease_prioritisation_analysis.py b/src/pheval/analyse/disease_prioritisation_analysis.py
@@ -64,9 +64,13 @@ def assess_disease_prioritisation(
             elif len(result) == 0:
                 relevant_ranks.append(0)
         binary_classification_stats.add_classification(
-            self.db_connection.parse_table_into_dataclass(
-                str(standardised_disease_result_path), RankedPhEvalDiseaseResult
-            ) if standardised_disease_result_path.exists() else [],
+            (
+                self.db_connection.parse_table_into_dataclass(
+                    str(standardised_disease_result_path), RankedPhEvalDiseaseResult
+                )
+                if standardised_disease_result_path.exists()
+                else []
+            ),
             relevant_ranks,
         )
 

diff --git a/src/pheval/analyse/gene_prioritisation_analysis.py b/src/pheval/analyse/gene_prioritisation_analysis.py
@@ -61,9 +61,13 @@ def assess_gene_prioritisation(
             if not result:
                 relevant_ranks.append(0)
         binary_classification_stats.add_classification(
-            self.db_connection.parse_table_into_dataclass(
-                str(standardised_gene_result_path), RankedPhEvalGeneResult
-            ) if standardised_gene_result_path.exists() else [],
+            (
+                self.db_connection.parse_table_into_dataclass(
+                    str(standardised_gene_result_path), RankedPhEvalGeneResult
+                )
+                if standardised_gene_result_path.exists()
+                else []
+            ),
             relevant_ranks,
         )
 

diff --git a/src/pheval/analyse/variant_prioritisation_analysis.py b/src/pheval/analyse/variant_prioritisation_analysis.py
@@ -15,10 +15,10 @@ class AssessVariantPrioritisation(AssessPrioritisationBase):
     """Class for assessing variant prioritisation based on thresholds and scoring orders."""
 
     def assess_variant_prioritisation(
-            self,
-            standardised_variant_result_path: Path,
-            phenopacket_path: Path,
-            binary_classification_stats: BinaryClassificationStats,
+        self,
+        standardised_variant_result_path: Path,
+        phenopacket_path: Path,
+        binary_classification_stats: BinaryClassificationStats,
     ) -> None:
         """
         Assess variant prioritisation.
@@ -73,18 +73,22 @@ def assess_variant_prioritisation(
             elif len(result) == 0:
                 relevant_ranks.append(0)
         binary_classification_stats.add_classification(
-            self.db_connection.parse_table_into_dataclass(
-                str(standardised_variant_result_path), RankedPhEvalVariantResult
-            ) if standardised_variant_result_path.exists() else [],
+            (
+                self.db_connection.parse_table_into_dataclass(
+                    str(standardised_variant_result_path), RankedPhEvalVariantResult
+                )
+                if standardised_variant_result_path.exists()
+                else []
+            ),
             relevant_ranks,
         )
 
 
 def assess_phenopacket_variant_prioritisation(
-        phenopacket_path: Path,
-        run: RunConfig,
-        variant_binary_classification_stats: BinaryClassificationStats,
-        variant_benchmarker: AssessVariantPrioritisation,
+    phenopacket_path: Path,
+    run: RunConfig,
+    variant_binary_classification_stats: BinaryClassificationStats,
+    variant_benchmarker: AssessVariantPrioritisation,
 ) -> None:
     """
     Assess variant prioritisation for a Phenopacket by comparing PhEval standardised variant results
@@ -107,10 +111,10 @@ def assess_phenopacket_variant_prioritisation(
 
 
 def benchmark_variant_prioritisation(
-        benchmark_name: str,
-        run: RunConfig,
-        score_order: str,
-        threshold: float,
+    benchmark_name: str,
+    run: RunConfig,
+    score_order: str,
+    threshold: float,
 ):
     """
     Benchmark a directory based on variant prioritisation results.

diff --git a/tests/test_analysis.py b/tests/test_analysis.py
@@ -1,7 +1,7 @@
 import unittest
 from copy import copy
 from pathlib import Path
-from unittest.mock import patch, MagicMock
+from unittest.mock import MagicMock, patch
 
 import duckdb