nerdd-module 0.3.51__tar.gz → 0.3.53__tar.gz

{nerdd_module-0.3.51 → nerdd_module-0.3.53}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.51
+Version: 0.3.53
 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-0.3.51 → nerdd_module-0.3.53}/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-0.3.51 → nerdd_module-0.3.53}/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-0.3.51 → nerdd_module-0.3.53}/nerdd_module/config/models.py

@@ -1,3 +1,5 @@
+"""Pydantic models describing module metadata, schema, and parameters."""
+
 from typing import Any, List, Optional, Union
 
 from pydantic import BaseModel, computed_field, model_validator
@@ -7,6 +9,8 @@ from ..polyfills import Literal
 
 
 class Partner(BaseModel):
+    """Partner organization metadata for module marketing/attribution."""
+
     name: str
     logo: str
     url: Optional[str] = None
@@ -31,14 +35,18 @@ class Author(BaseModel):
 
 
 class Publication(BaseModel):
-    title: str
-    authors: List[Author] = []
-    journal: str
-    year: int
+    """Reference to a publication related to the module or model."""
+
+    title: Optional[str] = None
+    authors: Optional[List[Author]] = None
+    journal: Optional[str] = None
+    year: Optional[int] = None
     doi: Optional[str]
 
 
 class ColorPalette(BaseModel):
+    """Optional color mapping for visualizing categorical or numeric outputs."""
+
     type: Optional[str] = None
     name: Optional[str] = None
     domain: Optional[Union[List[str], List[float], List[int], List[bool]]] = None
@@ -47,6 +55,8 @@ class ColorPalette(BaseModel):
 
 
 class Choice(BaseModel):
+    """Select options for job parameters or categorical result properties."""
+
     value: Union[str, int, float, bool]
     label: Optional[str] = None
 
@@ -55,6 +65,8 @@ JobType = Literal["int", "integer", "float", "bool", "boolean", "str", "string"]
 
 
 class JobParameter(BaseModel):
+    """Definition of a user-configurable parameter for a job run."""
+
     name: str
     type: JobType
     visible_name: Optional[str] = None
@@ -64,6 +76,7 @@ class JobParameter(BaseModel):
     choices: Optional[List[Choice]] = None
 
     def validate_value(self, value: Any) -> None:
+        """Validate a provided value against type and choices."""
         if self.type == ["int", "integer"]:
             if not isinstance(value, int):
                 raise ValueError(
@@ -107,11 +120,15 @@ FormatSpec = Union[List[str], str]
 
 
 class IncludeExcludeFormatSpec(BaseModel):
+    """Visibility filter for result properties per output format."""
+
     include: Optional[FormatSpec]
     exclude: Optional[FormatSpec]
 
 
 class ResultProperty(BaseModel):
+    """Schema entry for a model output property."""
+
     name: str
     type: str
     visible_name: Optional[str] = None
@@ -129,6 +146,7 @@ class ResultProperty(BaseModel):
     color_palette: Optional[ColorPalette] = None
 
     def is_visible(self, output_format: str) -> bool:
+        """Return True if property should be shown for the given format."""
         formats = self.formats
 
         if formats is None:
@@ -144,6 +162,8 @@ class ResultProperty(BaseModel):
 
 
 class Module(BaseModel):
+    """Full module configuration: metadata, schema, parameters, and validation."""
+
     @computed_field  # type: ignore[prop-decorator]
     @property
     def id(self) -> str:
@@ -194,6 +214,7 @@ class Module(BaseModel):
     @model_validator(mode="after")
     @classmethod
     def validate_model(cls, values: Any) -> Any:
+        """Enforce consistency between task type and declared result properties."""
         assert isinstance(values, Module)
 
         num_atom_properties = len(values.get_property_columns_of_type("atom"))
@@ -244,10 +265,7 @@ class Module(BaseModel):
         return values
 
     def validate_job_parameters(self, params: dict) -> None:
-        """
-        Validate the job parameters against the module's job parameters.
-        Raises an error if a parameter is missing or has an invalid type.
-        """
+        """Validate provided job parameters against the module declaration."""
         # make sure that all job parameters are present
         for param in self.job_parameters:
             if param.name not in params and param.required:

{nerdd_module-0.3.51 → nerdd_module-0.3.53}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.51
+Version: 0.3.53
 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-0.3.51 → nerdd_module-0.3.53}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.51"
+version = "0.3.53"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = "BSD-3-Clause"
@@ -88,6 +88,7 @@ Repository = "https://github.com/molinfo-vienna/nerdd-module"
 #
 # TOOLS
 #
+
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["nerdd_module*"]