[QoL] Pretty print - main package version (linkml#2032)

* make pythongen add repr=False by default

* add test for repr override in python generator

* update frozen strings in other tests

* update snapshots

* update code to match new pprint format

* update snapshots

* lint

* use latest linkml-runtime with linkml/linkml-runtime#314 merged

* regenerate snapshots

---------

Co-authored-by: Chris Mungall <[email protected]>

Author: 2 people

linkml/generators/pythongen.py

@@ -54,6 +54,16 @@ class PythonGenerator(Generator):
     gen_slots: bool = True
     genmeta: bool = False
     emit_metadata: bool = True
+    dataclass_repr: bool = False
+    """
+    Whether generated dataclasses should also generate a default __repr__ method.
+    
+    Default ``False`` so that the parent :class:`linkml_runtime.utils.yamlutils.YAMLRoot` 's
+    ``__repr__`` method is inherited for model pretty printing.
+    
+    References:
+        - https://docs.python.org/3/library/dataclasses.html#dataclasses.dataclass
+    """
 
     def __post_init__(self) -> None:
         if isinstance(self.schema, Path):
@@ -388,7 +398,7 @@ def gen_classdef(self, cls: ClassDefinition) -> str:
             return f"\n{self.class_or_type_name(cls.name)} = Any"
 
         cd_str = (
-            ("\n@dataclass" if slotdefs else "")
+            (f"\n@dataclass(repr={self.dataclass_repr})" if slotdefs else "")
             + f"\nclass {self.class_or_type_name(cls.name)}{parentref}:{wrapped_description}"
             + f"{self.gen_inherited_slots(cls)}"
             + f"{self.gen_class_meta(cls)}"

poetry.lock

@@ -107,7 +107,7 @@ jinja2 = ">= 3.1.0"
 jsonasobj2 = "==1.*,>=1.0.0,>=1.0.3"
 jsonschema = {extras = ["format"], version = ">=4.0.0"}
 linkml-dataops = "*"
-linkml-runtime = "1.8.0"
+linkml-runtime = "^1.8.1"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"

pyproject.toml

@@ -44,7 +44,7 @@ class AnnotationTag(ExtensionTag):
     pass
 
 
-@dataclass
+@dataclass(repr=False)
 class Annotatable(YAMLRoot):
     """
     mixin for classes that support annotations
@@ -64,7 +64,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Annotation(Extension):
     """
     a tag/value pair with the semantics of OWL Annotation

tests/test_base/__snapshots__/annotations.py

@@ -45,7 +45,7 @@ class ExtensionTag(URIorCURIE):
 
 AnyValue = Any
 
-@dataclass
+@dataclass(repr=False)
 class Extension(YAMLRoot):
     """
     a tag/value pair used to add non-model information to an entry
@@ -72,7 +72,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Extensible(YAMLRoot):
     """
     mixin for classes that support extension

tests/test_base/__snapshots__/extensions.py

@@ -48,7 +48,7 @@ URI: [linkml:status](https://w3id.org/linkml/status)
 | --- | --- | --- |
 | **Aliases:** | | workflow status |
 | **Mappings:** | | bibo:status |
-| **Examples:** | | Example(value='bibo:draft', description=None, object=None) |
+| **Examples:** | | Example({'value': 'bibo:draft'}) |
 | **In Subsets:** | | BasicSubset |
 | **See also:** | | [https://www.hl7.org/fhir/valueset-publication-status.html](https://www.hl7.org/fhir/valueset-publication-status.html) |
 |  | | [https://www.hl7.org/fhir/versions.html#std-process](https://www.hl7.org/fhir/versions.html#std-process) |

tests/test_base/__snapshots__/markdown/meta/status.md

@@ -27,5 +27,5 @@ URI: [linkml:structured_alias_categories](https://w3id.org/linkml/structured_ali
 | --- | --- | --- |
 | **Mappings:** | | dcterms:subject |
 | **Comments:** | | if you wish to use uncontrolled terms or terms that lack identifiers then use the keywords element |
-| **Examples:** | | Example(value='https://w3id.org/mod#acronym', description='An acronym', object=None) |
+| **Examples:** | | Example({'value': 'https://w3id.org/mod#acronym', 'description': 'An acronym'}) |
 | **In Subsets:** | | BasicSubset |

tests/test_base/__snapshots__/markdown/meta/structured_alias_categories.md

@@ -25,4 +25,14 @@ URI: [linkml:subproperty_of](https://w3id.org/linkml/subproperty_of)
 |  |  |  |
 | --- | --- | --- |
 | **Mappings:** | | rdfs:subPropertyOf |
-| **Examples:** | | Example(value='RO:HOM0000001', description='this is the RO term for "in homology relationship with", and used as a value of subproperty of this means that any ontological child (related to RO:HOM0000001 via an is_a relationship), is a valid value for the slot that declares this with the subproperty_of tag.  This differs from the \'values_from\' meta model component in that \'values_from\' requires the id of a value set (said another way, if an entire ontology had a curie/identifier that was the identifier for the entire ontology, then that identifier would be used in \'values_from.\')', object=None) |
+| **Examples:** | | Example({
+  'value': 'RO:HOM0000001',
+  'description': ('this is the RO term for "in homology relationship with", and used as a value '
+     'of subproperty of this means that any ontological child (related to '
+     'RO:HOM0000001 via an is_a relationship), is a valid value for the slot that '
+     'declares this with the subproperty_of tag.  This differs from the '
+     "'values_from' meta model component in that 'values_from' requires the id of "
+     'a value set (said another way, if an entire ontology had a curie/identifier '
+     'that was the identifier for the entire ontology, then that identifier would '
+     "be used in 'values_from.')")
+}) |