nerdd-module 0.3.52__tar.gz → 0.3.54__tar.gz

{nerdd_module-0.3.52 → nerdd_module-0.3.54}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.52
+Version: 0.3.54
 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-0.3.52 → nerdd_module-0.3.54}/nerdd_module/cli.py

@@ -30,7 +30,7 @@ def infer_click_type(param: JobParameter) -> click.ParamType:
         choices = [str(c.value) for c in param.choices]
         return click.Choice(choices)
 
-    type_map = {
+    type_map: dict[str, click.ParamType] = {
         "float": click.FLOAT,
         "integer": click.INT,
         "string": click.STRING,
@@ -67,10 +67,9 @@ def auto_cli(f: Callable[..., Model], *args: Any, **kwargs: Any) -> None:
 
     # compose footer with examples
     examples = []
-    if hasattr(model, "config"):
-        example_smiles = model.config.example_smiles
-        if example_smiles is not None:
-            examples.append(example_smiles)
+    example_smiles = model.config.example_smiles
+    if example_smiles is not None:
+        examples.append(example_smiles)
 
     for ReaderClass in Reader.get_reader_mapping():
         if hasattr(ReaderClass, "config"):

{nerdd_module-0.3.52 → nerdd_module-0.3.54}/nerdd_module/config/merged_configuration.py

@@ -1,4 +1,5 @@
 from collections import Counter
+from typing import Any
 
 from .configuration import Configuration
 from .dict_configuration import DictConfiguration
@@ -6,27 +7,32 @@ from .dict_configuration import DictConfiguration
 __all__ = ["MergedConfiguration"]
 
 
-def merge(*args: dict) -> dict:
+def merge(*args: Any) -> Any:
     assert len(args) > 0
 
-    first_entry = args[0]
-    assert all(isinstance(d, type(first_entry)) for d in args)
+    if all(arg is None for arg in args):
+        return None
 
-    if isinstance(first_entry, list):
-        return [e for d in args for e in d]
-    if isinstance(first_entry, dict):
-        count_fields = Counter([k for d in args for k in d.keys()])
+    valid_args = [arg for arg in args if arg is not None]
+
+    first_valid_entry = valid_args[0]
+    assert all(isinstance(d, type(first_valid_entry)) for d in valid_args)
+
+    if isinstance(first_valid_entry, list):
+        return [e for d in valid_args for e in d]
+    if isinstance(first_valid_entry, dict):
+        count_fields = Counter([k for d in valid_args for k in d.keys()])
 
         # merge fields that occur in multiple dicts
         overlapping_fields = [k for k, v in count_fields.items() if v > 1]
         merged_overlapping_fields = {
-            k: merge(*[d[k] for d in args if k in d]) for k in overlapping_fields
+            k: merge(*[d[k] for d in valid_args if k in d]) for k in overlapping_fields
         }
 
         # collect fields that occur in only one dict
         non_overlapping_fields = [k for k, v in count_fields.items() if v == 1]
         merged_non_overlapping_fields = {
-            k: v for d in args for k, v in d.items() if k in non_overlapping_fields
+            k: v for d in valid_args for k, v in d.items() if k in non_overlapping_fields
         }
 
         return {
@@ -36,7 +42,7 @@ def merge(*args: dict) -> dict:
     else:
         # merge all configurations starting from the first one
         # --> last configuration has the highest priority
-        return args[-1]
+        return valid_args[-1]
 
 
 class MergedConfiguration(DictConfiguration):

{nerdd_module-0.3.52 → nerdd_module-0.3.54}/nerdd_module/model/prediction_step.py

@@ -94,7 +94,9 @@ class PredictionStep(Step):
         # 3. the list of predictions has as many records as the batch (and we assume
         #    that the order of the molecules stayed the same)
         if all("mol_id" in record for record in predictions):
-            pass
+            # convert mol_id to int (or raise an error if it is not possible)
+            for record in predictions:
+                record["mol_id"] = int(record["mol_id"])
         elif all("mol" in record for record in predictions):
             # check that molecule names contain only valid ids
             for record in predictions:

{nerdd_module-0.3.52 → nerdd_module-0.3.54}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.52
+Version: 0.3.54
 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-0.3.52 → nerdd_module-0.3.54}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.52"
+version = "0.3.54"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = "BSD-3-Clause"
@@ -88,6 +88,8 @@ Repository = "https://github.com/molinfo-vienna/nerdd-module"
 #
 # TOOLS
 #
+
+
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["nerdd_module*"]