ci ʘ‿ʘ

.github/workflows/code_quality.yaml

@@ -58,8 +58,8 @@ jobs:
         with:
           os: ${{ job.os }}
           python-version: '3.11'
-          poetry-install-options: "--only=types --no-root"
-          poetry-export-options: "--only=types"
+          poetry-install-options: "--only=main --only=types --no-root"
+          poetry-export-options: "--only=main --only=types"
 
       - name: Check types
         run: poetry run mypy tesk/

mypy.ini

@@ -1,6 +1,7 @@
 # Global options:
 
 [mypy]
+plugins = pydantic.mypy
 warn_return_any = True
 warn_unused_configs = True
 
@@ -12,3 +13,8 @@ ignore_missing_imports = True
 
 [mypy-foca]
 ignore_missing_imports = True
+
+[pydantic-mypy]
+init_forbid_extra = True
+init_typed = True
+warn_required_dynamic_aliases = True

pyproject.toml

@@ -69,6 +69,7 @@ types-botocore = "^1.0.2"
 types-requests = "^2.31.0.20240406"
 types-urllib3 = "^1.26.25.14"
 types-werkzeug = "^1.0.9"
+types-pyyaml = "^6.0.12.20240311"
 
 [tool.poetry.scripts]
 api = 'tesk.app:main'

tesk/api/ga4gh/tes/base/base_tesk_request.py

@@ -41,5 +41,6 @@ def response(self) -> dict:
 			dict: Serialized response for the specific endpoint.
 		"""
 		_response = self.api_response()
-		assert isinstance(_response, BaseModel)
+		if not isinstance(_response, BaseModel):
+			raise TypeError('API response must be a Pydantic model.')
 		return _response.dict()

tesk/api/ga4gh/tes/service_info/base/base_service_info_request.py

@@ -115,9 +115,8 @@ def _hash_service_info_config(self) -> str:
 		Returns:
 			str: Hash of the service info configuration.
 		"""
-		if not self._service_info_present_in_config():
-			return ''
 		_service_info = self._get_service_info_present_in_config()
-		assert _service_info is not None
+		if _service_info is None:
+			return ''
 		_config_to_hash = _service_info.json().encode('utf-8')
 		return sha256(_config_to_hash).hexdigest()

tesk/tesk_app.py

@@ -19,10 +19,12 @@
 
 
 # TODO: Maybe TeskApp should be a singleton, and extend the Foca class, so that
-# 			we can have a single instance of the app, and we can access the configuration
-# 			and other attributes from the instance itself. This way we can avoid passing
-# 			the configuration file path to the Foca class, and we can have a single point
-# 			of access to the configuration and other attributes.
+# 			we can have a single instance of the app, and we can access the
+# 			configuration and other attributes from the instance itself.
+# 			This way we can avoid passing the configuration file path to the Foca class,
+# 			and we can have a single point of access to the configuration and
+# 			other attributes.
+
 
 class TeskApp:
 	"""TESK API class."""