pheval-exomiser 0.2.4__tar.gz → 0.2.6__tar.gz

{pheval_exomiser-0.2.4 → pheval_exomiser-0.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pheval_exomiser
-Version: 0.2.4
+Version: 0.2.6
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk
@@ -10,6 +10,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: click (>=8.1.3,<9.0.0)
 Requires-Dist: docker (>=6.0.1,<7.0.0)
 Requires-Dist: google (>=3.0.0,<4.0.0)

{pheval_exomiser-0.2.4 → pheval_exomiser-0.2.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pheval_exomiser"
-version = "0.2.4"
+version = "0.2.6"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
     "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",

{pheval_exomiser-0.2.4 → pheval_exomiser-0.2.6}/src/pheval_exomiser/post_process/post_process_results_format.py

@@ -182,7 +182,12 @@ class PhEvalDiseaseResultFromExomiserJsonCreator:
                     )
             except KeyError:
                 pass
-        return simplified_exomiser_result
+        return list(
+            {
+                (result.disease_identifier, result.score): result
+                for result in simplified_exomiser_result
+            }.values()
+        )
 
 
 def create_standardised_results(

{pheval_exomiser-0.2.4 → pheval_exomiser-0.2.6}/src/pheval_exomiser/prepare/tool_specific_configuration_options.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List
+from typing import List, Optional
 
 from pydantic import BaseModel, Field
 
@@ -20,17 +20,17 @@ class ApplicationProperties(BaseModel):
         cache_caffeine_spec (int): Cache limit
     """
 
-    remm_version: str = Field(None)
-    cadd_version: str = Field(None)
-    hg19_data_version: str = Field(None)
-    hg19_local_frequency_path: Path = Field(None)
-    hg19_whitelist_path: Path = Field(None)
-    hg38_data_version: str = Field(None)
-    hg38_local_frequency_path: Path = Field(None)
-    hg38_whitelist_path: Path = Field(None)
-    phenotype_data_version: str = Field(None)
-    cache_type: str = Field(None)
-    cache_caffeine_spec: int = Field(None)
+    remm_version: Optional[str] = Field(None)
+    cadd_version: Optional[str] = Field(None)
+    hg19_data_version: Optional[str] = Field(None)
+    hg19_local_frequency_path: Optional[Path] = Field(None)
+    hg19_whitelist_path: Optional[Path] = Field(None)
+    hg38_data_version: Optional[str] = Field(None)
+    hg38_local_frequency_path: Optional[Path] = Field(None)
+    hg38_whitelist_path: Optional[Path] = Field(None)
+    phenotype_data_version: Optional[str] = Field(None)
+    cache_type: Optional[str] = Field(None)
+    cache_caffeine_spec: Optional[int] = Field(None)
 
 
 class PostProcessing(BaseModel):
@@ -64,5 +64,5 @@ class ExomiserConfigurations(BaseModel):
     analysis_configuration_file: Path = Field(...)
     max_jobs: int = Field(...)
     application_properties: ApplicationProperties = Field(...)
-    output_formats: List[str] = Field(None)
+    output_formats: Optional[List[str]] = Field(None)
     post_process: PostProcessing = Field(...)