Convert test_loaders_pydantic.py to pytest format

CONTRIBUTING.md

@@ -72,7 +72,7 @@ are correct and expected given the context of the PR.
 2. Install all the dependencies from your project, which are typically specified in a `uv.lock` file.
 
 ```
-uv sync --all-extras --dev  
+uv sync --all-extras --dev
 ```
 
 3. Run any python scripts or CLI commands by prefixing with `uv run`.

tests/test_loaders_dumpers/input/book_series_lotr_json.yaml

@@ -0,0 +1,20 @@
+id: S001
+name: Lord of the Rings
+genres:
+- fantasy
+creator:
+  name: JRR Tolkien
+  from_country: England
+books:
+- id: S001.1
+  name: Fellowship of the Ring
+  summary: Hobbits
+  price: 5.99
+- id: S001.2
+  name: The Two Towers
+  summary: More hobbits
+  price: 5.99
+- id: S001.3
+  name: Return of the King
+  summary: Yet more hobbits
+  price: 6.99

tests/test_loaders_dumpers/input/book_series_lotr_yaml.yaml

@@ -0,0 +1,20 @@
+id: S001
+name: Lord of the Rings
+genres:
+- fantasy
+creator:
+  name: JRR Tolkien
+  from_country: England
+books:
+- id: S001.1
+  name: Fellowship of the Ring
+  summary: Hobbits
+  price: 5.99
+- id: S001.2
+  name: The Two Towers
+  summary: More hobbits
+  price: 5.99
+- id: S001.3
+  name: Return of the King
+  summary: Yet more hobbits
+  price: 6.99

tests/test_loaders_dumpers/input/kitchen_sink_normalized_inst_01_json.yaml

@@ -0,0 +1,41 @@
+persons:
+- id: P:001
+  name: fred bloggs
+  age_in_years: 33
+- id: P:002
+  name: joe schmoe
+  has_employment_history:
+  - started_at_time: 2019-01-01
+    is_current: true
+    employed_at: ROR:1
+  has_familial_relationships:
+  - related_to: P:001
+    type: SIBLING_OF
+  has_medical_history:
+  - started_at_time: 2019-01-01
+    in_location: GEO:1234
+    diagnosis:
+      id: CODE:D0001
+      name: headache
+      in_code_system: DiseaseCodes
+    procedure:
+      id: CODE:P0001
+      name: trepanation
+      in_code_system: ProcedureCodes
+  addresses:
+  - street: 1 foo street
+    city: foo city
+companies:
+- id: ROR:1
+  name: foo
+activities:
+- id: A:1
+  started_at_time: 2019-01-01
+  was_associated_with: Agent:987
+code_systems:
+  DiseaseCodes:
+    id: DiseaseCodes
+    name: disease codes
+  ProcedureCodes:
+    id: ProcedureCodes
+    name: disease codes

tests/test_loaders_dumpers/input/kitchen_sink_normalized_inst_01_yaml.yaml

@@ -0,0 +1,41 @@
+persons:
+- id: P:001
+  name: fred bloggs
+  age_in_years: 33
+- id: P:002
+  name: joe schmoe
+  has_employment_history:
+  - started_at_time: 2019-01-01
+    is_current: true
+    employed_at: ROR:1
+  has_familial_relationships:
+  - related_to: P:001
+    type: SIBLING_OF
+  has_medical_history:
+  - started_at_time: 2019-01-01
+    in_location: GEO:1234
+    diagnosis:
+      id: CODE:D0001
+      name: headache
+      in_code_system: DiseaseCodes
+    procedure:
+      id: CODE:P0001
+      name: trepanation
+      in_code_system: ProcedureCodes
+  addresses:
+  - street: 1 foo street
+    city: foo city
+companies:
+- id: ROR:1
+  name: foo
+activities:
+- id: A:1
+  started_at_time: 2019-01-01
+  was_associated_with: Agent:987
+code_systems:
+  DiseaseCodes:
+    id: DiseaseCodes
+    name: disease codes
+  ProcedureCodes:
+    id: ProcedureCodes
+    name: disease codes

tests/test_loaders_dumpers/test_loaders_pydantic.py

@@ -1,29 +1,39 @@
-import unittest
+from pathlib import Path
 
+import pytest
+from hbreader import FileInfo
+from pydantic import BaseModel
+
+from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.loaders import json_loader, yaml_loader
 from tests.test_loaders_dumpers.environment import env
-from tests.test_loaders_dumpers.loaderdumpertestcase import LoaderDumperTestCase
 from tests.test_loaders_dumpers.models.books_normalized_pydantic import BookSeries
 from tests.test_loaders_dumpers.models.kitchen_sink_pydantic import Dataset
 
 
-class PydanticLoadersUnitTest(LoaderDumperTestCase):
-    env = env
-
-    def test_yaml_loader_single(self):
-        """Load obo_sample.yaml, emit obo_sample_yaml.yaml and compare to obo_sample_output.yaml"""
-        self.loader_test("book_series_lotr.yaml", BookSeries, yaml_loader)
-
-    def test_json_loader(self):
-        """Load obo_sample.json, emit obo_sample_json.yaml and check the results"""
-        self.loader_test("book_series_lotr.json", BookSeries, json_loader)
-
-    def test_yaml_loader_kitchen_sink(self):
-        self.loader_test("kitchen_sink_normalized_inst_01.yaml", Dataset, yaml_loader)
-
-    def test_json_loader_kitchen_sink(self):
-        self.loader_test("kitchen_sink_normalized_inst_01.json", Dataset, json_loader)
-
-
-if __name__ == "__main__":
-    unittest.main()
+@pytest.mark.parametrize(
+    "filename,model,loader",
+    [
+        ("book_series_lotr.yaml", BookSeries, yaml_loader),
+        ("book_series_lotr.json", BookSeries, json_loader),
+        ("kitchen_sink_normalized_inst_01.yaml", Dataset, yaml_loader),
+        ("kitchen_sink_normalized_inst_01.json", Dataset, json_loader),
+    ],
+)
+def test_loader_basemodel(filename, model, loader):
+    name = Path(filename).stem
+    type = Path(filename).suffix.lstrip(".")
+    expected_yaml_file = env.input_path(f"{name}_{type}.yaml")
+
+    metadata = FileInfo()
+
+    python_obj: BaseModel = loader.load(filename, model, metadata=metadata, base_dir=env.indir)
+
+    # Load expected output
+    with open(expected_yaml_file) as expf:
+        expected = expf.read()
+
+    got = yaml_dumper.dumps(python_obj)
+    expected_trimmed = expected.replace("\r\n", "\n").strip()
+    got_trimmed = got.replace("\r\n", "\n").strip()
+    assert expected_trimmed == got_trimmed