[QoL] Pretty print - main package version

linkml/generators/pythongen.py

@@ -60,6 +60,16 @@ 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:
         self.sourcefile = self.schema
@@ -395,7 +405,7 @@ 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)}"

tests/test_compliance/test_core_compliance.py

@@ -97,7 +97,7 @@ def test_attributes(framework, description, object, is_valid):
             },
             "_mappings": {
                 PYDANTIC: f"class C({PYDANTIC_ROOT_CLASS}):",
-                PYTHON_DATACLASSES: f"@dataclass\nclass C({PYTHON_DATACLASSES_ROOT_CLASS}):",
+                PYTHON_DATACLASSES: f"@dataclass(repr=False)\nclass C({PYTHON_DATACLASSES_ROOT_CLASS}):",
                 JSON_SCHEMA: {
                     "$defs": {
                         "C": {

tests/test_compliance/test_inheritance_compliance.py

@@ -139,7 +139,7 @@ def test_basic_class_inheritance(framework, description, cls: str, object, is_va
             },
             "_mappings": {
                 PYDANTIC: "class C(D):",
-                PYTHON_DATACLASSES: "@dataclass\nclass C(D):",
+                PYTHON_DATACLASSES: "@dataclass(repr=False)\nclass C(D):",
                 JSON_SCHEMA: {"$defs": json_schema_defs},
             },
         },
@@ -279,7 +279,7 @@ def test_mixins(framework, description, cls, object, is_valid):
             },
             "_mappings": {
                 PYDANTIC: "class C(MC2, MC1):",
-                PYTHON_DATACLASSES: "@dataclass\nclass C(YAMLRoot):",  # DC rolls up
+                PYTHON_DATACLASSES: "@dataclass(repr=False)\nclass C(YAMLRoot):",  # DC rolls up
                 JSON_SCHEMA: json_schema_defs,
             },
         },

tests/test_enhancements/test_enumeration.py

@@ -151,22 +151,22 @@ def test_notebook_model_1(self):
         module = compile_python(env.expected_path(python_name))
         c1 = module.PositionalRecord("my location", "a")
         self.assertEqual(
-            "PositionalRecord(id='my location', position=(text='a', description='top'))",
-            str(c1),
+            module.PositionalRecord(id='my location', position=module.OpenEnum('a')),
+            c1,
         )
         self.assertEqual("a", str(c1.position))
-        self.assertEqual("(text='a', description='top')", repr(c1.position))
+        self.assertEqual("OpenEnum(text='a', description='top')", repr(c1.position))
         try:
             module.PositionalRecord("your location", "z")
         except ValueError as e:
             self.assertEqual("Unknown OpenEnum enumeration code: z", str(e))
         x = module.PositionalRecord("117493", "c")
         self.assertEqual("c", str(x.position))
         self.assertEqual(
-            "PositionalRecord(id='117493', position=(text='c', description='bottom'))",
+            "PositionalRecord({'id': '117493', 'position': OpenEnum(text='c', description='bottom')})",
             repr(x),
         )
-        self.assertEqual("(text='c', description='bottom')", repr(x.position))
+        self.assertEqual("OpenEnum(text='c', description='bottom')", repr(x.position))
 
     def test_notebook_model_2(self):
         file = "notebook_model_2"

tests/test_enhancements/test_pattern.py

@@ -36,8 +36,10 @@ def test_pattern_1(self):
         d1 = yaml.load(StringIO(d1_test), yaml.loader.SafeLoader)
         dev1 = module.DiskDevice(**d1)
         self.assertEqual(
-            "DiskDevice(label='AbCd0123-1111-FF10-AAF1-A1B2C3D4A1B2C3D4A1B2C3D4', "
-            "device='/dev/tty.Bluetooth-Incoming-Port')",
+            """DiskDevice({
+  'label': 'AbCd0123-1111-FF10-AAF1-A1B2C3D4A1B2C3D4A1B2C3D4',
+  'device': '/dev/tty.Bluetooth-Incoming-Port'
+})""",
             str(dev1),
         )
 

tests/test_enhancements/test_python_output.py

@@ -22,28 +22,42 @@ def __str__(self) -> str:
         [
             ("s1", "s2", "s3", "s4"),
             {},
-            "Strings(mand_string='s1', mand_multi_string=['s2'], opt_string='s3', opt_multi_string=['s4'])",
+            """Strings({
+  'mand_string': 's1',
+  'mand_multi_string': ['s2'],
+  'opt_string': 's3',
+  'opt_multi_string': ['s4']
+})""",
             None,
         ],
         [
             ("s1", ["s21", "s22"], "s3", ["s41", "s42"]),
             {},
             (
-                "Strings(mand_string='s1', mand_multi_string=['s21', 's22'], "
-                "opt_string='s3', opt_multi_string=['s41', 's42'])"
+                """Strings({
+  'mand_string': 's1',
+  'mand_multi_string': ['s21', 's22'],
+  'opt_string': 's3',
+  'opt_multi_string': ['s41', 's42']
+})"""
             ),
             None,
         ],
         [
             ("s1", ["s21", "s22"], None, None),
             {},
-            "Strings(mand_string='s1', mand_multi_string=['s21', 's22'], opt_string=None, opt_multi_string=[])",
+            "Strings({'mand_string': 's1', 'mand_multi_string': ['s21', 's22']})",
             None,
         ],
         [
             (NonStr("s1"), NonStr("s2"), NonStr("s3"), NonStr("s4")),
             {},
-            "Strings(mand_string='s1', mand_multi_string=['s2'], opt_string='s3', opt_multi_string=['s4'])",
+            """Strings({
+  'mand_string': 's1',
+  'mand_multi_string': ['s2'],
+  'opt_string': 's3',
+  'opt_multi_string': ['s4']
+})""",
             None,
         ],
         [
@@ -55,8 +69,12 @@ def __str__(self) -> str:
             ),
             {},
             (
-                "Strings(mand_string='s1', mand_multi_string=['s21', 's22'], "
-                "opt_string='s3', opt_multi_string=['s41', 's42'])"
+                """Strings({
+  'mand_string': 's1',
+  'mand_multi_string': ['s21', 's22'],
+  'opt_string': 's3',
+  'opt_multi_string': ['s41', 's42']
+})"""
             ),
             None,
         ],
@@ -69,8 +87,12 @@ def __str__(self) -> str:
             ("True", "false", 1, [1, 0, True, False]),
             {},
             (
-                "Booleans(mand_boolean=True, mand_multi_boolean=[False], opt_boolean=True, "
-                "opt_multi_boolean=[True, False, True, False])"
+            """Booleans({
+  'mand_boolean': True,
+  'mand_multi_boolean': [False],
+  'opt_boolean': True,
+  'opt_multi_boolean': [True, False, True, False]
+})"""
             ),
             None,
         ]
@@ -79,7 +101,12 @@ def __str__(self) -> str:
         [
             ("17", -2, 12 + 3, [42, "17"]),
             {},
-            "Integers(mand_integer=17, mand_multi_integer=[-2], opt_integer=15, opt_multi_integer=[42, 17])",
+            """Integers({
+  'mand_integer': 17,
+  'mand_multi_integer': [-2],
+  'opt_integer': 15,
+  'opt_multi_integer': [42, 17]
+})""",
             None,
         ],
         [

tests/test_generators/test_pythongen.py

@@ -1,3 +1,4 @@
+import re
 from types import ModuleType
 
 from linkml_runtime.loaders import json_loader
@@ -16,12 +17,9 @@ def test_pythongen(kitchen_sink_path):
     """python"""
     kitchen_module = make_python(kitchen_sink_path)
     c = kitchen_module.Company("ROR:1")
-    assert str(c) == "Company(id='ROR:1', name=None, aliases=[], ceo=None)"
+    assert str(c) == "Company({'id': 'ROR:1'})"
     h = kitchen_module.EmploymentEvent(employed_at=c.id)
-    assert str(h) == (
-        "EmploymentEvent(started_at_time=None, ended_at_time=None, is_current=None, "
-        "metadata=None, employed_at='ROR:1', type=None)"
-    )
+    assert str(h) == "EmploymentEvent({'employed_at': 'ROR:1'})"
     p = kitchen_module.Person("P:1", has_employment_history=[h])
     assert p.id == "P:1"
     assert p.has_employment_history[0] is not None
@@ -37,26 +35,21 @@ def test_pythongen(kitchen_sink_path):
     # however, inline in a non-list context does not
     p2dict = {"id": "P:2", "has_birth_event": {"started_at_time": "1981-01-01"}}
     json_loader.loads(p2dict, kitchen_module.Person)
-    assert str(p) == (
-        "Person(id='P:1', name=None, has_employment_history=[EmploymentEvent(started_at_time=None, "
-        "ended_at_time=None, is_current=None, metadata=None, employed_at='ROR:1', type=None)], "
-        "has_familial_relationships=[], has_medical_history=[], age_in_years=None, addresses=[], "
-        "has_birth_event=None, species_name=None, stomach_count=None, is_living=None, aliases=[])"
-    )
+    assert str(p) == "Person({'id': 'P:1', 'has_employment_history': [EmploymentEvent({'employed_at': 'ROR:1'})]})"
 
     f = kitchen_module.FamilialRelationship(related_to="me", type="SIBLING_OF", cordialness="heartfelt")
-    assert str(f) == (
-        "FamilialRelationship(started_at_time=None, ended_at_time=None, related_to='me', "
-        "type='SIBLING_OF', cordialness=(text='heartfelt', description='warm and hearty friendliness'))"
-    )
+    assert str(f) == """FamilialRelationship({
+  'related_to': 'me',
+  'type': 'SIBLING_OF',
+  'cordialness': CordialnessEnum(text='heartfelt', description='warm and hearty friendliness')
+})"""
 
     diagnosis = kitchen_module.DiagnosisConcept(id="CODE:D0001", name="headache")
     event = kitchen_module.MedicalEvent(in_location="GEO:1234", diagnosis=diagnosis)
-    assert str(event) == (
-        "MedicalEvent(started_at_time=None, ended_at_time=None, is_current=None, "
-        "metadata=None, in_location='GEO:1234', diagnosis=DiagnosisConcept(id='CODE:D0001', "
-        "name='headache', in_code_system=None), procedure=None)"
-    )
+    assert str(event) == """MedicalEvent({
+  'in_location': 'GEO:1234',
+  'diagnosis': DiagnosisConcept({'id': 'CODE:D0001', 'name': 'headache'})
+})"""
 
 
 def test_multiline_stuff(input_path):
@@ -96,3 +89,36 @@ def test_head():
 
     output = PythonGenerator(yaml, format="py", metadata=False).serialize()
     assert output.startswith("\n# id: https://w3id.org/biolink/metamodel")
+
+
+def test_repr(kitchen_sink_path):
+    """
+    Be default, don't create __repr__ for dataclasses, but do if requested!
+    """
+    parentclass = """
+class ParentClass:
+    def __repr__(self):
+        return "overridden"
+
+    def __post_init__(self, *args, **kwargs):
+        pass
+"""
+
+
+    pstr = str(PythonGenerator(kitchen_sink_path).serialize())
+    pstr = parentclass + pstr
+    pstr = re.sub(r'\(YAMLRoot\)', '(ParentClass)', pstr)
+    kitchen_module = compile_python(pstr)
+
+    # if a dataclass has `repr=False`, it shouldn't override the parent class's
+    friend = kitchen_module.Friend(name='bestie')
+    assert repr(friend) == 'overridden'
+
+    # but we should be able to make pythongenerator do `repr=True`, where the dataclasses _do_ override
+    pstr = str(PythonGenerator(kitchen_sink_path, dataclass_repr=True).serialize())
+    pstr = parentclass + pstr
+    pstr = re.sub(r'\(YAMLRoot\)', '(ParentClass)', pstr)
+    kitchen_module = compile_python(pstr)
+    friend = kitchen_module.Friend(name='bestie')
+    assert repr(friend) != 'overridden'
+

tests/test_issues/__snapshots__/issue_106.py

@@ -48,7 +48,7 @@ class String(str):
 
 
 
-@dataclass
+@dataclass(repr=False)
 class C1(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -70,7 +70,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class C2(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 

tests/test_issues/__snapshots__/issue_113.py

@@ -50,7 +50,7 @@ class NamedThing(YAMLRoot):
     class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/NamedThing")
 
 
-@dataclass
+@dataclass(repr=False)
 class TestClass(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 

tests/test_issues/__snapshots__/issue_120.py

@@ -49,7 +49,7 @@ class String(str):
 
 
 
-@dataclass
+@dataclass(repr=False)
 class Student(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -71,7 +71,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class Course(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 

tests/test_issues/__snapshots__/issue_121.py

@@ -41,7 +41,7 @@
 
 
 
-@dataclass
+@dataclass(repr=False)
 class Biosample(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 

tests/test_issues/__snapshots__/issue_134.py

@@ -68,7 +68,7 @@ class EId(D1Id):
     pass
 
 
-@dataclass
+@dataclass(repr=False)
 class A(YAMLRoot):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -88,7 +88,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class B(A):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -112,7 +112,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class C(B):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -136,7 +136,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class D1(C):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -160,7 +160,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class D2(C):
     _inherited_slots: ClassVar[List[str]] = []
 
@@ -180,7 +180,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
-@dataclass
+@dataclass(repr=False)
 class E(D1):
     _inherited_slots: ClassVar[List[str]] = []