nerdd-module 0.3.27__tar.gz → 0.3.29__tar.gz

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.27
+Version: 0.3.29
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module/cli.py

@@ -67,8 +67,8 @@ def auto_cli(f: Callable[..., Model], *args: Any, **kwargs: Any) -> None:
 
     # compose footer with examples
     examples = []
-    if hasattr(model, "get_config"):
-        example_smiles = model.get_config().example_smiles
+    if hasattr(model, "config"):
+        example_smiles = model.config.example_smiles
         if example_smiles is not None:
             examples.append(example_smiles)
 

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module/model/enforce_schema_step.py

@@ -1,7 +1,7 @@
 import logging
 from typing import Iterator
 
-from ..config import Configuration
+from ..config import Module
 from ..steps import Step
 
 __all__ = ["EnforceSchemaStep"]
@@ -10,11 +10,9 @@ logger = logging.getLogger(__name__)
 
 
 class EnforceSchemaStep(Step):
-    def __init__(self, config: Configuration, output_format: str) -> None:
+    def __init__(self, config: Module, output_format: str) -> None:
         super().__init__()
-        self._property_names = [
-            p.name for p in config.get_dict().get_visible_properties(output_format)
-        ]
+        self._property_names = [p.name for p in config.get_visible_properties(output_format)]
 
         # check that properties are unique
         if len(self._property_names) != len(set(self._property_names)):
@@ -22,7 +20,7 @@ class EnforceSchemaStep(Step):
                 x for x in self._property_names if self._property_names.count(x) > 1
             }
             logger.warning(
-                f"Duplicate properties in result_properties: " f"{', '.join(duplicate_properties)}"
+                f"Duplicate properties in result_properties: {', '.join(duplicate_properties)}"
             )
 
     def _run(self, source: Iterator[dict]) -> Iterator[dict]:

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module/model/model.py

@@ -164,7 +164,7 @@ class PredictionStep(Step):
                 isinstance(record, dict) for record in predictions
             ), "The predictions must be a list of dictionaries."
         except Exception as e:
-            logger.error(e, exc_info=True)
+            logger.exception("An error occurred during prediction.", exc_info=e)
 
             # if an error occurs, we want to catch it and yield the error message
             predictions = [
@@ -214,13 +214,15 @@ class PredictionStep(Step):
             mol_id_to_record[record["mol_id"]].append(record)
 
         # add all records that are missing in the predictions
-        for mol_id, record in zip(temporary_mol_ids, batch):
+        for mol_id in temporary_mol_ids:
             if mol_id not in mol_id_to_record:
-                # notify the user that the molecule could not be predicted
-                record["problems"].append(IncompletePredictionProblem())
-
-                # add the record to the mapping
-                mol_id_to_record[mol_id].append(record)
+                # add a dummy record to the mapping
+                mol_id_to_record[mol_id].append(
+                    {
+                        # notify the user that the molecule could not be predicted
+                        "problems": [IncompletePredictionProblem()],
+                    }
+                )
 
         # If the result has multiple entries per mol_id, check that atom_id or
         # derivative_id is present in multi-entry results.

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module/model/simple_model.py

@@ -1,4 +1,5 @@
 from abc import abstractmethod
+from functools import cached_property
 from typing import Any, Iterable, List, Optional, Tuple, Union
 
 from rdkit.Chem import Mol
@@ -61,8 +62,8 @@ class SimpleModel(Model):
     def _get_postprocessing_steps(self, output_format: Optional[str], **kwargs: Any) -> List[Step]:
         output_format = output_format or "pandas"
         return [
-            EnforceSchemaStep(self._get_config(), output_format),
-            ConvertRepresentationsStep(self.get_config(), output_format, **kwargs),
+            EnforceSchemaStep(self.config, output_format),
+            ConvertRepresentationsStep(self.config, output_format, **kwargs),
             WriteOutputStep(output_format, **kwargs),
         ]
 
@@ -187,23 +188,24 @@ class SimpleModel(Model):
 
         return MergedConfiguration(*configs)
 
-    def get_config(self) -> Module:
+    @cached_property
+    def config(self) -> Module:
         return self._get_config().get_dict()
 
     def _get_batch_size(self) -> int:
         default = super()._get_batch_size()
-        return self.get_config().batch_size or default
+        return self.config.batch_size or default
 
     def _get_name(self) -> str:
         default = super()._get_name()
-        return self.get_config().name or default
+        return self.config.name or default
 
     def _get_description(self) -> str:
         default = super()._get_description()
-        return self.get_config().description or default
+        return self.config.description or default
 
     def _get_job_parameters(self) -> List[JobParameter]:
-        return super()._get_job_parameters() + self.get_config().job_parameters
+        return super()._get_job_parameters() + self.config.job_parameters
 
 
 class CustomPreprocessingStep(PreprocessingStep):

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module/problem.py

@@ -25,7 +25,7 @@ def UnknownProblem() -> Problem:
 def InvalidWeightProblem(weight: float, min_weight: float, max_weight: float) -> Problem:
     return Problem(
         type="invalid_weight",
-        message=(f"Molecular weight {weight:.2f} out of range " f"[{min_weight}, {max_weight}]"),
+        message=(f"Molecular weight {weight:.2f} out of range [{min_weight}, {max_weight}]"),
     )
 
 

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module/util/call_with_mappings.py

@@ -23,7 +23,7 @@ def call_with_mappings(
     # copy config
     config = config.copy()
 
-    # we check what arguments the constructor of the writer class can take
+    # check what arguments the class or function can take
     spec = inspect.getfullargspec(class_or_function)
     parameter_names = [a for a in spec.args if a != "self"]
     accept_any_args = spec.varargs is not None

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.27
+Version: 0.3.29
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.27 → nerdd_module-0.3.29}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.27"
+version = "0.3.29"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }