pheval 0.6.1__tar.gz → 0.6.3__tar.gz

{pheval-0.6.1 → pheval-0.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pheval
-Version: 0.6.1
+Version: 0.6.3
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk

{pheval-0.6.1 → pheval-0.6.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pheval"
-version = "0.6.1"
+version = "0.6.3"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
   "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",

{pheval-0.6.1 → pheval-0.6.3}/src/pheval/analyse/benchmark.py

@@ -1,3 +1,4 @@
+import sys
 import time
 from pathlib import Path
 from typing import List, Tuple
@@ -135,6 +136,9 @@ def benchmark_runs(benchmark_config_file: Path) -> None:
     start_time = time.perf_counter()
     logger.info("Initiated benchmarking process.")
     config = parse_run_config(benchmark_config_file)
+    if Path(f"{config.benchmark_name}.duckdb").exists():
+        logger.error(f"{config.benchmark_name}.duckdb already exists! Exiting.")
+        sys.exit(1)
     gene_analysis_runs = [run for run in config.runs if run.gene_analysis]
     variant_analysis_runs = [run for run in config.runs if run.variant_analysis]
     disease_analysis_runs = [run for run in config.runs if run.disease_analysis]

{pheval-0.6.1 → pheval-0.6.3}/src/pheval/analyse/run_data_parser.py

@@ -41,6 +41,15 @@ class RunConfig(BaseModel):
     def set_score_order(cls, score_order):
         return score_order or "descending"
 
+    @field_validator("results_dir", mode="after")
+    @classmethod
+    def check_results_dir_exists(cls, results_dir: Path):
+        if not results_dir.exists():
+            raise FileNotFoundError(
+                f"The specified results directory does not exist: {results_dir}"
+            )
+        return results_dir
+
 
 class SinglePlotCustomisation(BaseModel):
     """

{pheval-0.6.1 → pheval-0.6.3}/src/pheval/post_processing/phenopacket_truth_set.py

@@ -225,7 +225,9 @@ class PhenopacketTruthSet:
                 pl.lit(0).cast(pl.Int64).alias("rank"),
                 pl.lit(True).alias("true_positive"),
                 pl.col("disease_identifier")
-                .map_elements(lambda x: map_disease_id(x, mondo_mapping_table))
+                .map_elements(
+                    lambda x: map_disease_id(x, mondo_mapping_table), return_dtype=pl.Utf8
+                )
                 .alias("mondo_identifier"),
             ]
         )

{pheval-0.6.1 → pheval-0.6.3}/src/pheval/post_processing/post_processing.py

@@ -150,7 +150,10 @@ def _get_result_type(
         case ResultType.VARIANT:
             return phenopacket_truth_set.classified_variant, _write_variant_result
         case ResultType.DISEASE:
-            return phenopacket_truth_set.classified_disease, _write_disease_result
+            return (
+                lambda id_: phenopacket_truth_set.classified_disease(id_, mondo_mapping_table),
+                _write_disease_result,
+            )
 
 
 def create_empty_pheval_result(