pheval 0.5.7__py3-none-any.whl → 0.5.8__py3-none-any.whl

pheval/implementations/__init__.py

@@ -4,6 +4,7 @@ from functools import cache
 
 from class_resolver import ClassResolver
 
+from pheval.implementations.pheval_class_resolver import PhevalClassResolver
 from pheval.runners.runner import PhEvalRunner
 
 
@@ -14,9 +15,11 @@ def get_implementation_resolver() -> ClassResolver[PhEvalRunner]:
     Returns:
         ClassResolver[PhEvalRunner]: _description_
     """
-    implementation_resolver: ClassResolver[PhEvalRunner] = ClassResolver.from_subclasses(
-        PhEvalRunner,
-        suffix="Implementation",
+    implementation_resolver: PhevalClassResolver[PhEvalRunner] = (
+        PhevalClassResolver.from_subclasses(
+            PhEvalRunner,
+            suffix="Implementation",
+        )
     )
 
     # implementation_resolver.synonyms.update(
@@ -34,5 +37,6 @@ def get_implementation_resolver() -> ClassResolver[PhEvalRunner]:
     # See also:
     # https://packaging.python.org/en/latest/specifications/entry-points/
     # https://class-resolver.readthedocs.io/en/latest/api/class_resolver.ClassResolver.html#class_resolver.ClassResolver.register_entrypoint
+
     implementation_resolver.register_entrypoint("pheval.plugins")
     return implementation_resolver

pheval/implementations/pheval_class_resolver.py

@@ -0,0 +1,40 @@
+# Dependencies taken from class_resolver:
+# https://github.com/cthoyt/class-resolver/blob/5e51b41d08381e1754f3445c5ce4fcea4f6612d6/src/class_resolver/base.py#L276
+from importlib.metadata import entry_points
+
+# Dependency from importlib.metadata:
+# https://github.com/cthoyt/class-resolver/blob/5e51b41d08381e1754f3445c5ce4fcea4f6612d6/src/class_resolver/utils.py#L45
+from typing import TypeVar
+
+from class_resolver import ClassResolver
+
+from pheval.utils.logger import get_logger
+
+X = TypeVar("X")
+logger = get_logger()
+
+
+# Create a custom ClassResolver class to modify the _from_entrypoint method.
+class PhevalClassResolver(ClassResolver):
+    def __init__(self, *args, **kwargs) -> None:
+        super().__init__(*args, **kwargs)
+
+    # Modified _from_entrypoint method to raise error instead of warning
+    @staticmethod
+    def _from_entrypoint_custom(group: str) -> set[X]:
+        elements: set[X] = set()
+        for entry in entry_points(group=group):
+            try:
+                element = entry.load()
+                logger.info(f"Loaded {entry.name} correctly")
+            except (ImportError, AttributeError):
+                logger.warn(f"could not load {entry.name}. See error message below.")
+                raise
+            else:
+                elements.add(element)
+        return elements
+
+    def register_entrypoint(self, group: str) -> None:
+        """Register additional entries from an entrypoint."""
+        for element in self._from_entrypoint_custom(group).difference(self.lookup_dict.values()):
+            self.register(element)

{pheval-0.5.7.dist-info → pheval-0.5.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pheval
-Version: 0.5.7
+Version: 0.5.8
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk

{pheval-0.5.7.dist-info → pheval-0.5.8.dist-info}/RECORD

@@ -13,7 +13,8 @@ pheval/cli.py,sha256=rpvTTCKAvH75XkZUh0xaKv7Ftl9zIt2RncsMGIlrq9U,1556
 pheval/cli_pheval.py,sha256=iVvPby44EvVHkZsOFNQ_DovhYdwIkKir1Kf8uVJ_GCw,2872
 pheval/cli_pheval_utils.py,sha256=sh6kx36jYfuSIWBMlrdW3g-LPftxBy-xw4b7hg8bdj4,16545
 pheval/config_parser.py,sha256=eUa1wMRuCy2iq-oRSxTZGltLxaw5NjsISN2GRBpuQWM,1358
-pheval/implementations/__init__.py,sha256=BMUTotjTdgy5j5xubWCIQgRXrSQ1ZIcjooer7r299Zo,1228
+pheval/implementations/__init__.py,sha256=L0y_qPxKGcm4zCi-YmPa_YgtYoD9QsL7IHqoB7bfO4Y,1346
+pheval/implementations/pheval_class_resolver.py,sha256=YNNk3PoQbSvbKmbihlt_bsHNxRM95O-VrtUIbQnfBcw,1567
 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
@@ -46,8 +47,8 @@ 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=9V6vCT8l1g4O2-ZATYqsVyd7AYZdWGd-Ksy7_oIC3eE,2343
-pheval-0.5.7.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-pheval-0.5.7.dist-info/METADATA,sha256=jGVgjj__bZaODcDdjdpugcPUIlAfAiX6rKygGfBVmQ4,6494
-pheval-0.5.7.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pheval-0.5.7.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
-pheval-0.5.7.dist-info/RECORD,,
+pheval-0.5.8.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+pheval-0.5.8.dist-info/METADATA,sha256=q9bYdrUPdf_QAgOxXxXhct0HaEGSme45_0DVAaIXHr4,6494
+pheval-0.5.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pheval-0.5.8.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
+pheval-0.5.8.dist-info/RECORD,,