pheval 0.6.1__py3-none-any.whl → 0.6.3__py3-none-any.whl

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/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/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/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(

{pheval-0.6.1.dist-info → pheval-0.6.3.dist-info}/METADATA

@@ -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.dist-info → pheval-0.6.3.dist-info}/RECORD

@@ -1,6 +1,6 @@
 pheval/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/analyse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pheval/analyse/benchmark.py,sha256=sfjReLmodXwCT9ZyZDE6Oli0j1S5ygicJshb7n4-x4U,6916
+pheval/analyse/benchmark.py,sha256=s4ZHsvnZY9XNsbbBp_0JEny1bUpxLbcg0ls3J-wUtC8,7085
 pheval/analyse/benchmark_db_manager.py,sha256=zS1TI76YuV2_YXLipHLSyh-XDR5kTxyOwhRhHRFHfjQ,764
 pheval/analyse/benchmark_output_type.py,sha256=CBZmRhfz_g7cegYlZtcK2j18YY0iwjjAgNdb70sQiSM,1513
 pheval/analyse/binary_classification_curves.py,sha256=Crb45rJWc5rxDdx82sgoHRvYHE2D5pus91fgl39FyRw,5007
@@ -8,7 +8,7 @@ pheval/analyse/binary_classification_stats.py,sha256=sOuEp6IxZ6SVp-KC6MJkZNTkZuc
 pheval/analyse/generate_plots.py,sha256=g98DxhTw1dPRfRRYoKBmt51XfIa2KzlL_Z7weFSoBUg,14550
 pheval/analyse/generate_rank_comparisons.py,sha256=KcQJ9rm1nvvTcqLNuxAkXRXuV18vEsiP0giQ-ryHyYc,1684
 pheval/analyse/rank_stats.py,sha256=JLgbaumayUzVzpRh0IXlY7454HWShVJQVImifC0U4GA,8489
-pheval/analyse/run_data_parser.py,sha256=Lr0ao_Mlp8EYLaM4XmiEjo7P7jt_rCBR2y2hb_D3c70,3366
+pheval/analyse/run_data_parser.py,sha256=UjuC9R2Ag3v6BDU-xjVn1iFfYDQLlmE2ajl5gXwF9uQ,3688
 pheval/cli.py,sha256=Yow7JLwYvtFc8W1U0V1g5bzxMICsv05NWm2PAsFwqvM,1591
 pheval/cli_pheval.py,sha256=N8xp3r8avYqLswPhakxtTQyemVdgHAvnpAIj_FmoN5k,3510
 pheval/cli_pheval_utils.py,sha256=sh6kx36jYfuSIWBMlrdW3g-LPftxBy-xw4b7hg8bdj4,16545
@@ -19,8 +19,8 @@ pheval/infra/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/infra/exomiserdb.py,sha256=pM9-TfjrgurtH4OtM1Enk5oVhIxGQN3rKRlrxHuObTM,5080
 pheval/post_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/post_processing/mondo_mapping.py,sha256=Vetk0acOtR__FXnx9wy2pcDDWFz1mQkc88alKUn0muI,937
-pheval/post_processing/phenopacket_truth_set.py,sha256=oD2072hrv0xdiJdPv8X6bSHPCp771ApgJB9q0ZODqAg,10241
-pheval/post_processing/post_processing.py,sha256=8COHwzjEPzX8AxDanfXnNdM1WG1ojqbAZ04ahlXFogs,10079
+pheval/post_processing/phenopacket_truth_set.py,sha256=xSP9uu6Qxuog4HFXJiRJdBdQXn6GLSKBgSDpH4TtgD4,10301
+pheval/post_processing/post_processing.py,sha256=g99MBjGzl5qPi8CK6CLKH0XAFdkt1uSye25VbzqV1Kg,10166
 pheval/post_processing/validate_result_format.py,sha256=w7zbpbS-fxwQuUwkqJPsD2nQV4SZxxVk3e7-MZEBV8I,2891
 pheval/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/prepare/create_noisy_phenopackets.py,sha256=kYFwQjBJN6gla2I51X3zfucVmnRB7kwH2uqi1ElWzkg,12291
@@ -50,8 +50,8 @@ pheval/utils/logger.py,sha256=5DZl5uMltUDQorhkvg_B7_ZhFwApAmEkWneFIOKfRGQ,1566
 pheval/utils/phenopacket_utils.py,sha256=XGnFLarvXezFR0W5frzyGTwEbhcA3zuGJPg1r5YBscg,27326
 pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
 pheval/utils/utils.py,sha256=23bQPL-HmzHnMRJSe4doJdj6rtmFyfO77FOH3wyFZZI,4518
-pheval-0.6.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-pheval-0.6.1.dist-info/METADATA,sha256=134LdEW9TDwCN8vCKnFnXjs2qnC5vscaWGaODPwqhHQ,6494
-pheval-0.6.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pheval-0.6.1.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
-pheval-0.6.1.dist-info/RECORD,,
+pheval-0.6.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+pheval-0.6.3.dist-info/METADATA,sha256=Q0AX7IoMMvNPMpEYNLY2Ijdp5vSZgmpvDB6r2Q9zZgA,6494
+pheval-0.6.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pheval-0.6.3.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
+pheval-0.6.3.dist-info/RECORD,,