Converting the "issue" tests to pytest in preparation for rehoming the specific tests under the tests for the modules that they are testing. In some cases, the quality of the test was improved by adding in extra checks."

Author: ialarmedalien

linkml_runtime/loaders/loader_root.py

@@ -75,7 +75,7 @@ def load(self, *args, **kwargs) -> Union[BaseModel, YAMLRoot]:
         :return: instance of target_class
         """
         results = self.load_any(*args, **kwargs)
-        if isinstance(results, BaseModel) or isinstance(results, YAMLRoot):
+        if isinstance(results, (BaseModel, YAMLRoot)):
             return results
         else:
             raise ValueError(f"Result is not an instance of BaseModel or YAMLRoot: {type(results)}")
@@ -145,9 +145,9 @@ def _construct_target_class(
             elif isinstance(data_as_dict, dict):
                 if issubclass(target_class, BaseModel):
                     return target_class.model_validate(data_as_dict)
-                else:
-                    return target_class(**data_as_dict)
-            elif isinstance(data_as_dict, JsonObj):
+                return target_class(**data_as_dict)
+
+            if isinstance(data_as_dict, JsonObj):
                 return [target_class(**as_dict(x)) for x in data_as_dict]
             else:
                 raise ValueError(f"Unexpected type {data_as_dict}")
@@ -170,7 +170,7 @@ def _read_source(
         if not isinstance(source, dict):
             # Try to get local version of schema, if one is known to exist
             try:
-                if str(source) in URI_TO_LOCAL.keys():
+                if str(source) in URI_TO_LOCAL:
                     source = str(URI_TO_LOCAL[str(source)])
             except (TypeError, KeyError) as e:
                 # Fine, use original `source` value

tests/test_issues/input/linkml_issue_478.yaml

@@ -9,7 +9,7 @@ classes:
       - id
       - preferred label
       - SOURCE
-  biosample processing:
+  biosample_processing:
     is_a: named thing
     attributes:
       processingMethod:
@@ -23,4 +23,4 @@ classes:
 slots:
   id:
   preferred label:
-  SOURCE:
+  SOURCE:

tests/test_issues/test_dataclass_extensions_376.py

@@ -1,19 +1,19 @@
-import sys
-import pytest
-import importlib.util
 import dataclasses
+import importlib.util
+
+import pytest
 
 
 def import_patch_module():
-    """Fresh import to ensure warning is triggered"""
+    """Fresh import to ensure warning is triggered."""
     spec = importlib.util.find_spec("linkml_runtime.utils.dataclass_extensions_376")
     mod = importlib.util.module_from_spec(spec)
     spec.loader.exec_module(mod)
     return mod
 
 
-def test_patch_module_emits_deprecation_warning():
-    """All Python versions: emits DeprecationWarning and defines compatibility symbols"""
+def test_patch_module_emits_deprecation_warning() -> None:
+    """All Python versions: emits DeprecationWarning and defines compatibility symbols."""
     with pytest.warns(DeprecationWarning):
         mod = import_patch_module()
 

tests/test_issues/test_issue_1040.py

@@ -1,22 +1,13 @@
-from unittest import TestCase
-
+import pytest
 import yaml.constructor
 
 from linkml_runtime.linkml_model import SchemaDefinition
 from linkml_runtime.loaders import yaml_loader
 from tests.test_issues.environment import env
 
 
-class Issue1040TestCase(TestCase):
-    """
-    https://github.com/linkml/linkml/issues/1040
-    """
-
-    env = env
-
-    def test_issue_1040_file_name(self):
-        """issue_1040.yaml has a parsing error is confusing as all getout when accompanied by a stack
-        trace.  We use this to make sure that the file name gets in correctly."""
-        with self.assertRaises(yaml.constructor.ConstructorError) as e:
-            yaml_loader.load(env.input_path("issue_1040.yaml"), SchemaDefinition)
-        self.assertIn('"issue_1040.yaml"', str(e.exception))
+def test_issue_1040_file_name() -> None:
+    """issue_1040.yaml has a parsing error is confusing as all getout when accompanied by a stack
+    trace.  We use this to make sure that the file name gets in correctly."""
+    with pytest.raises(yaml.constructor.ConstructorError, match='"issue_1040.yaml"'):
+        yaml_loader.load(env.input_path("issue_1040.yaml"), SchemaDefinition)

tests/test_issues/test_issue_1355.py

@@ -1,29 +1,14 @@
-"""
-Created on 2023-03-24
+import pytest
 
-@author: wf
-"""
-
-from unittest import TestCase
 from linkml_runtime.utils.metamodelcore import URI
 
 
-class Issue1355TestCase(TestCase):
-    """
-    https://github.com/linkml/linkml/issues/1355
-    improve invalid URL message
-    """
+def test_issue_1355_invalid_url_message() -> None:
+    """Check that quotes are used when referencing invalid urls to improve troubleshooting UX.
 
-    def test_issue_1355_invalid_url_message(self):
-        """
-        check that quotes are used when referencing invalid urls so that
-        the visiblity of the problem gets better
-        """
-        #  note the trailing blank
-        url = "https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf "
-        try:
-            _uri = URI(url)
-        except ValueError as vex:
-            msg = str(vex)
-            # 'https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf ': is not a valid URI
-            self.assertTrue(".pdf '" in msg)
+    See https://github.com/linkml/linkml/issues/1355, improve invalid URL message
+    """
+    #  note the trailing blank
+    url = "https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf "
+    with pytest.raises(ValueError, match="'https://ceur-ws.org/Vol-2931/ICBO_2019_paper_20.pdf ': is not a valid URI"):
+        URI(url)

tests/test_issues/test_issue_163.py

@@ -1,40 +1,31 @@
-import unittest
-from typing import Callable
+from collections.abc import Callable
 
-from linkml_runtime.dumpers import json_dumper, yaml_dumper, rdf_dumper
-from tests.test_issues.environment import env
-from tests.test_loaders_dumpers.loaderdumpertestcase import LoaderDumperTestCase
+from linkml_runtime.dumpers import json_dumper, rdf_dumper, yaml_dumper
 from linkml_runtime.utils.compile_python import compile_python
+from tests.test_issues.environment import env
 
 
-class Issue368TestCase(LoaderDumperTestCase):
-    env = env
-
-    def header(self, txt: str) -> str:
-        return "\n" + ("=" * 20) + f" {txt} " + ("=" * 20)
-
-    def test_issue_368_enums(self):
-        """Test Enum generation"""
-
-        module = compile_python(env.input_path("issue_368.py"))
+def header(txt: str) -> str:
+    return "\n" + ("=" * 20) + f" {txt} " + ("=" * 20)
 
-        enum_inst = module.SampleEnum("pva")  # EnumInstanceImpl
-        example = module.SampleClass(slot_1="pva")
-        assert hasattr(example, "slot_1")
-        assert example.slot_1.code.text == enum_inst.code.text
-        assert str(example.slot_1) == "pva"
 
-        def dump_and_load(dumper: Callable, sfx: str) -> None:
-            fname = env.actual_path(f"issue_368_1.{sfx}")
-            dumper(example, fname)
-            with open(fname) as f:
-                print(f"\n----- {sfx} -----")
-                print(f.read())
+def test_issue_368_enums() -> None:
+    """Test Enum generation."""
+    module = compile_python(env.input_path("issue_368.py"))
 
-        dump_and_load(json_dumper.dump, "json")
-        dump_and_load(yaml_dumper.dump, "yaml")
-        dump_and_load(lambda obj, fname: rdf_dumper.dump(obj, fname, env.input_path("issue_368.context.jsonld")), "ttl")
+    enum_inst = module.SampleEnum("pva")  # EnumInstanceImpl
+    example = module.SampleClass(slot_1="pva")
+    assert hasattr(example, "slot_1")
+    assert example.slot_1.code.text == enum_inst.code.text
+    assert str(example.slot_1) == "pva"
 
+    def dump_and_load(dumper: Callable, sfx: str) -> None:
+        fname = env.actual_path(f"issue_368_1.{sfx}")
+        dumper(example, fname)
+        with open(fname) as f:
+            print(f"\n----- {sfx} -----")
+            print(f.read())
 
-if __name__ == "__main__":
-    unittest.main()
+    dump_and_load(json_dumper.dump, "json")
+    dump_and_load(yaml_dumper.dump, "yaml")
+    dump_and_load(lambda obj, fname: rdf_dumper.dump(obj, fname, env.input_path("issue_368.context.jsonld")), "ttl")

tests/test_issues/test_issue_368_enums.py

@@ -1,6 +1,5 @@
-import unittest
-
 import hbreader
+import pytest
 import yaml
 
 from linkml_runtime.utils.yamlutils import DupCheckYamlLoader, TypedNode
@@ -13,26 +12,29 @@
 """
 
 
-class Issue6TestCase(unittest.TestCase):
-    def test_loc_function(self):
-        inp = yaml.load(hbreader.hbread(inp_yaml), DupCheckYamlLoader)
-        self.assertEqual('File "<unicode string>", line 3, col 8: ', TypedNode.yaml_loc(inp["foo"]["x"]))
-        self.assertEqual('File "<unicode string>", line 3, col 8', TypedNode.yaml_loc(inp["foo"]["x"], suffix=""))
-        self.assertEqual('File "<unicode string>", line 4, col 8: ', TypedNode.yaml_loc(inp["foo"]["y"]))
-        self.assertEqual(
-            'File "<unicode string>", line 4, col 8I yam that I yam',
-            TypedNode.yaml_loc(inp["foo"]["y"], suffix=inp["foo"]["y"]),
-        )
-        self.assertEqual('File "<unicode string>", line 5, col 8: ', TypedNode.yaml_loc(inp["foo"]["z"]))
-
-        with self.assertWarns(DeprecationWarning) as cm:
-            self.assertEqual('File "<unicode string>", line 3, col 8', TypedNode.loc(inp["foo"]["x"]))
-        self.assertEqual("Call to deprecated method loc. (Use yaml_loc instead)", cm.warning.args[0])
-
-        self.assertEqual("", TypedNode.yaml_loc(None))
-        self.assertEqual("", TypedNode.yaml_loc("abc"))
-        self.assertEqual("", TypedNode.yaml_loc(["a", "b"]))
-
-
-if __name__ == "__main__":
-    unittest.main()
+def test_loc_function() -> None:
+    """Test the TypedNode.yaml_loc function."""
+    inp = yaml.load(hbreader.hbread(inp_yaml), DupCheckYamlLoader)
+    assert TypedNode.yaml_loc(inp["foo"]["x"]) == 'File "<unicode string>", line 3, col 8: '
+    assert TypedNode.yaml_loc(inp["foo"]["x"], suffix="") == 'File "<unicode string>", line 3, col 8'
+    assert TypedNode.yaml_loc(inp["foo"]["y"]) == 'File "<unicode string>", line 4, col 8: '
+    assert (
+        TypedNode.yaml_loc(inp["foo"]["y"], suffix=inp["foo"]["y"])
+        == 'File "<unicode string>", line 4, col 8I yam that I yam'
+    )
+    assert TypedNode.yaml_loc(inp["foo"]["z"]) == 'File "<unicode string>", line 5, col 8: '
+
+
+def test_yaml_loc_warning() -> None:
+    """Test that a warning is emitted when using the `loc` method."""
+    inp = yaml.load(hbreader.hbread(inp_yaml), DupCheckYamlLoader)
+    with pytest.warns(DeprecationWarning) as warning_list:
+        assert TypedNode.loc(inp["foo"]["x"]) == 'File "<unicode string>", line 3, col 8'
+    assert len(warning_list) == 1
+    assert str(warning_list[0].message) == "Call to deprecated method loc. (Use yaml_loc instead)"
+
+
+@pytest.mark.parametrize("loc", [None, "abc", ["a", "b"]])
+def test_yaml_loc_empty_str(loc) -> None:
+    """Test yaml_loc values that translate to an empty string."""
+    assert TypedNode.yaml_loc(loc) == ""

tests/test_issues/test_issue_6.py

@@ -1,5 +1,3 @@
-import unittest
-
 from linkml_runtime.linkml_model import SchemaDefinition
 from linkml_runtime.utils.yamlutils import from_yaml
 
@@ -12,22 +10,17 @@
   string:
     base: str
     uri: xsd:string
-    
+
 slots:
   name:
 """
 
 
-class IsolatedNameTestCase(unittest.TestCase):
-    def test_it(self):
-        """Dangling name should not throw a type error"""
-        error_thrown = False
-        try:
-            from_yaml(model_txt, SchemaDefinition)
-        except TypeError as e:
-            error_thrown = True
-        self.assertFalse(error_thrown, msg="Type error should not be thrown")
-
-
-if __name__ == "__main__":
-    unittest.main()
+def test_read_dangling_name() -> None:
+    """Dangling name should not throw a type error."""
+    error_thrown = False
+    try:
+        from_yaml(model_txt, SchemaDefinition)
+    except TypeError:
+        error_thrown = True
+    assert error_thrown is False

tests/test_issues/test_issue_626.py

@@ -1,14 +1,16 @@
-import pytest
+from __future__ import annotations
+
 from dataclasses import dataclass
-from typing import Optional, ClassVar
+from typing import ClassVar
 
+import pytest
 import yaml
 
-from linkml_runtime.utils.yamlutils import YAMLRoot, DupCheckYamlLoader
+from linkml_runtime.utils.yamlutils import DupCheckYamlLoader, YAMLRoot
 
 
 @pytest.mark.xfail(reason="Reporting line numbers should happen at load time not when instantiating dataclasses")
-def test_issue_38():
+def test_issue_38() -> None:
     # The goal is to provide line numbers on error messages.   We've tweaked the parser so that it returns augmented
     # str's and int's with the line numbers on them.  The problem we are trying to address now is that the dataclass
     # constructor doesn't support **argv out of the box.  We can certainly tweak the generator to emit the __init__
@@ -18,8 +20,8 @@ def test_issue_38():
     class FesterBesterTester(YAMLRoot):
         cv: ClassVar[int] = 42
 
-        a: Optional[int] = 0
-        b: Optional[str] = None
+        a: int | None = 0
+        b: str | None = None
 
     with pytest.raises(TypeError, match="unexpected keyword argument 'c'"):
         FesterBesterTester(a=12, b="Sell", c="buy")