nerdd-module 0.3.26__tar.gz → 0.3.28__tar.gz

{nerdd_module-0.3.26 → nerdd_module-0.3.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.26
+Version: 0.3.28
 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>
@@ -51,6 +51,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: rdkit>=2020.09.1
 Requires-Dist: pandas>=1.2.1
 Requires-Dist: pyyaml>=6.0
 Requires-Dist: filetype~=1.2.0
@@ -70,8 +71,6 @@ Requires-Dist: types-PyYAML; extra == "dev"
 Requires-Dist: types-decorator; extra == "dev"
 Requires-Dist: types-setuptools; extra == "dev"
 Requires-Dist: pre-commit>=2; extra == "dev"
-Provides-Extra: rdkit
-Requires-Dist: rdkit>=2022.3.3; extra == "rdkit"
 Provides-Extra: csp
 Requires-Dist: chembl_structure_pipeline>=1.0.0; extra == "csp"
 Provides-Extra: test

{nerdd_module-0.3.26 → nerdd_module-0.3.28}/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-0.3.26 → nerdd_module-0.3.28}/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-0.3.26 → nerdd_module-0.3.28}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.26
+Version: 0.3.28
 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>
@@ -51,6 +51,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: rdkit>=2020.09.1
 Requires-Dist: pandas>=1.2.1
 Requires-Dist: pyyaml>=6.0
 Requires-Dist: filetype~=1.2.0
@@ -70,8 +71,6 @@ Requires-Dist: types-PyYAML; extra == "dev"
 Requires-Dist: types-decorator; extra == "dev"
 Requires-Dist: types-setuptools; extra == "dev"
 Requires-Dist: pre-commit>=2; extra == "dev"
-Provides-Extra: rdkit
-Requires-Dist: rdkit>=2022.3.3; extra == "rdkit"
 Provides-Extra: csp
 Requires-Dist: chembl_structure_pipeline>=1.0.0; extra == "csp"
 Provides-Extra: test

{nerdd_module-0.3.26 → nerdd_module-0.3.28}/nerdd_module.egg-info/requires.txt

@@ -1,3 +1,4 @@
+rdkit>=2020.09.1
 pandas>=1.2.1
 pyyaml>=6.0
 filetype~=1.2.0
@@ -33,9 +34,6 @@ mkdocs
 mkdocs-material
 mkdocstrings
 
-[rdkit]
-rdkit>=2022.3.3
-
 [test]
 pytest
 pytest-sugar

{nerdd_module-0.3.26 → nerdd_module-0.3.28}/pyproject.toml

@@ -4,13 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.26"
+version = "0.3.28"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }
 authors = [{ name = "Steffen Hirte", email = "steffen.hirte@univie.ac.at" }]
 maintainers = [{ name = "Steffen Hirte", email = "steffen.hirte@univie.ac.at" }]
 dependencies = [
+    "rdkit>=2020.09.1",
     "pandas>=1.2.1",
     "pyyaml>=6.0",
     "filetype~=1.2.0",
@@ -59,12 +60,6 @@ dev = [
     "types-setuptools",
     "pre-commit>=2",
 ]
-rdkit = [
-    # Some old RDKit versions are not recognized by setuptools. For that reason,
-    # let the user install rdkit explicitly using an extra dependency.
-    # Note: rdkit 2022.3.3 is the oldest (working) version of rdkit on pypi.
-    "rdkit>=2022.3.3",
-]
 csp = [
     # Note 1: Version 1.0.0 of chembl_structure_pipeline is not available on
     # pypi, but maybe it was already installed in the current environment