build: upgrade Pydantic to 2.7 (#241)

Author: uniqueg

foca/api/register_openapi.py

@@ -90,7 +90,7 @@ def register_openapi(
         spec.connexion = {} if spec.connexion is None else spec.connexion
         app.add_api(
             specification=spec_parsed,
-            **spec.dict().get('connexion', {}),
+            **spec.model_dump().get('connexion', {}),
         )
         logger.info(f"API endpoints added from spec: {spec.path_out}")
 

foca/config/config_parser.py

@@ -68,14 +68,14 @@ def __init__(
             )
         if format_logs:
             self._configure_logging()
-        logger.debug(f"Parsed config: {self.config.dict(by_alias=True)}")
+        logger.debug(f"Parsed config: {self.config.model_dump(by_alias=True)}")
 
     def _configure_logging(self) -> None:
         """Configure logging."""
         try:
-            dictConfig(self.config.log.dict(by_alias=True))
+            dictConfig(self.config.log.model_dump(by_alias=True))
         except Exception as e:
-            dictConfig(LogConfig().dict(by_alias=True))
+            dictConfig(LogConfig().model_dump(by_alias=True))
             logger.warning(
                 f"Failed to configure logging. Falling back to default "
                 f"settings. Original error: {type(e).__name__}: {e}"

foca/models/config.py

@@ -134,7 +134,7 @@ def register_permission_specs(
 
     app.add_api(
         specification=spec.path[0],  # type: ignore[index]
-        **spec.dict().get("connexion", {}),
+        **spec.model_dump().get("connexion", {}),
     )
     return app
 

foca/security/access_control/register_access_control.py

@@ -6,7 +6,7 @@ Flask~=2.2
 flask-authz~=2.5
 Flask-Cors~=4.0
 Flask-PyMongo~=2.3
-pydantic~=1.10
+pydantic~=2.7
 PyJWT~=2.4
 pymongo~=4.7
 PyYAML~=6.0

requirements.txt

@@ -5,8 +5,9 @@ mypy>=0.991
 mypy-extensions>=0.4.4
 pylint>=3.2
 pytest>=7.4
-python-semantic-release>=7.34,<8.2
+python-semantic-release>=9.7
 types-PyYAML
 types-requests
 types-setuptools
 types-urllib3
+typing_extensions>=4.11

requirements_dev.txt

@@ -31,35 +31,35 @@
 
 def test_config_parser_valid_config_file():
     """Test valid YAML parsing."""
-    conf = ConfigParser(TEST_FILE)
-    assert type(conf.config.dict()) == type(TEST_DICT)
+    conf = ConfigParser(Path(TEST_FILE))
+    assert type(conf.config.model_dump()) == type(TEST_DICT)
     assert isinstance(conf.config, type(TEST_CONFIG_INSTANCE))
 
 
 def test_config_parser_invalid_config_file():
     """Test invalid YAML parsing."""
     with pytest.raises(ValidationError):
-        ConfigParser(TEST_FILE_INVALID)
+        ConfigParser(Path(TEST_FILE_INVALID))
 
 
 def test_config_parser_invalid_file_path():
     """Test invalid file path."""
-    conf = ConfigParser(TEST_FILE)
+    conf = ConfigParser(Path(TEST_FILE))
     with pytest.raises(OSError):
-        assert conf.parse_yaml("") is not None
+        assert conf.parse_yaml(Path("")) is not None
 
 
 def test_config_parser_invalid_log_config():
     """Test invalid log config YAML."""
-    conf = ConfigParser(TEST_FILE_INVALID_LOG)
-    assert type(conf.config.dict()) == type(TEST_DICT)
+    conf = ConfigParser(Path(TEST_FILE_INVALID_LOG))
+    assert type(conf.config.model_dump()) == type(TEST_DICT)
     assert isinstance(conf.config, type(TEST_CONFIG_INSTANCE))
 
 
 def test_config_parser_with_custom_config_model():
     """Test with valid custom config model class."""
     conf = ConfigParser(
-        config_file=TEST_FILE,
+        config_file=Path(TEST_FILE),
         custom_config_model=TEST_CONFIG_MODEL,
     )
     assert isinstance(conf.config.custom.param, str)
@@ -68,22 +68,22 @@ def test_config_parser_with_custom_config_model():
 
 def test_process_yaml_valid_config_file():
     """Test process_yaml with valid YAML file."""
-    result = ConfigParser.parse_yaml(TEST_FILE)
+    result = ConfigParser.parse_yaml(Path(TEST_FILE))
     assert isinstance(result, dict)
 
 
 def test_process_yaml_invalid_config_file():
     """Test process_yaml with invalid YAML file."""
     with pytest.raises(ValueError):
-        ConfigParser.parse_yaml(TEST_FILE_INVALID_YAML)
+        ConfigParser.parse_yaml(Path(TEST_FILE_INVALID_YAML))
 
 
 def test_process_yaml_missing_file():
     """Test process_yaml when file cannot be opened."""
     with mock.patch("foca.config.config_parser.open") as mock_open:
         mock_open.side_effect = OSError
         with pytest.raises(OSError):
-            ConfigParser.parse_yaml(TEST_FILE)
+            ConfigParser.parse_yaml(Path(TEST_FILE))
 
 
 def test_merge_yaml_with_no_args():
@@ -95,14 +95,14 @@ def test_merge_yaml_with_no_args():
 
 def test_merge_yaml_with_two_args():
     """Test merge_yaml with no arguments."""
-    yaml_list = [PATH, PATH_ADDITION]
+    yaml_list = [Path(PATH), Path(PATH_ADDITION)]
     res = ConfigParser.merge_yaml(*yaml_list)
     assert 'put' in res['paths']['/pets/{petId}']
 
 
 def test_parse_custom_config_valid_model():
     """Test ``.parse_custom_config()`` with a valid model class."""
-    conf = ConfigParser(config_file=TEST_FILE)
+    conf = ConfigParser(config_file=Path(TEST_FILE))
     result = conf.parse_custom_config(model=TEST_CONFIG_MODEL)
     assert isinstance(result, BaseModel)
     assert isinstance(result.param, str)
@@ -111,20 +111,20 @@ def test_parse_custom_config_valid_model():
 
 def test_parse_custom_config_model_module_not_exists():
     """Test ``.parse_custom_config()`` when module does not exist."""
-    conf = ConfigParser(config_file=TEST_FILE)
+    conf = ConfigParser(config_file=Path(TEST_FILE))
     with pytest.raises(ValueError):
         conf.parse_custom_config(model=TEST_CONFIG_MODEL_MODULE_NOT_EXISTS)
 
 
 def test_parse_custom_config_model_not_exists():
     """Test ``.parse_custom_config()`` when model class does not exist."""
-    conf = ConfigParser(config_file=TEST_FILE)
+    conf = ConfigParser(config_file=Path(TEST_FILE))
     with pytest.raises(ValueError):
         conf.parse_custom_config(model=TEST_CONFIG_MODEL_NOT_EXISTS)
 
 
 def test_parse_custom_config_invalid():
     """Test ``.parse_custom_config()`` when model class does not exist."""
-    conf = ConfigParser(config_file=TEST_FILE_CUSTOM_INVALID)
+    conf = ConfigParser(config_file=Path(TEST_FILE_CUSTOM_INVALID))
     with pytest.raises(ValueError):
         conf.parse_custom_config(model=TEST_CONFIG_MODEL)

tests/config/test_config_parser.py

@@ -18,7 +18,7 @@
 
 DIR = Path(__file__).parent / "test_files"
 EXCEPTIONS_NO_DICT = []
-EXCEPTIONS_NOT_NESTED = {'a': 'b'}
+EXCEPTIONS_NOT_NESTED = {Exception: 'b'}
 EXCEPTIONS_NOT_EXC = {'a': {'status': 400, 'title': 'Bad Request'}}
 REQUIRED_MEMBERS = [['title'], ['status']]
 MEMBER_TITLE = ['title']