added types

src/pyeed/tools/abstract_tool.py

@@ -2,6 +2,7 @@
 import tempfile
 from abc import ABC, abstractmethod
 from enum import Enum
+from typing import Any
 
 import httpx
 from pydantic import BaseModel, PrivateAttr
@@ -23,15 +24,15 @@ class AbstractTool(BaseModel, ABC):
     _service_url: str = PrivateAttr()
     _tempdir_path: str = PrivateAttr()
 
-    def model_post_init(self, __context) -> None:
+    def model_post_init(self, __context: Any) -> None:
         """Create temporary directory."""
         self._tempdir_path = tempfile.mkdtemp()
 
-    def _delete_temp_dir(self):
+    def _delete_temp_dir(self) -> None:
         """Deletes the temporary directory."""
         shutil.rmtree(self._tempdir_path)
 
     @abstractmethod
-    def run_service(self, data) -> httpx.Response:
+    def run_service(self, data: dict[str, Any]) -> httpx.Response:
         """Executes the service."""
         pass

src/pyeed/tools/clustalo.py

@@ -11,7 +11,7 @@ class ClustalOmega(AbstractTool):
     Class for ClustalOmega aligner running as a REST service.
     """
 
-    def __init__(self):
+    def __init__(self) -> None:
         super().__init__()
         self._service_url = ServiceURL.CLUSTALO.value
 
@@ -28,19 +28,19 @@ def create_file(self, multifasta: list[str]) -> dict[str, str]:
         data = "\n".join(multifasta)
         return {"file": data}
 
-    def extract_output_data(self, response) -> MultipleSeqAlignment:
+    def extract_output_data(self, response: str) -> MultipleSeqAlignment:
         """
         Extracts the output data from the ClustalOmega container.
 
         Returns:
             MultiSequenceAlignment: The alignment result.
         """
-        alignment = AlignIO.read(io.StringIO(response), "clustal")
+        alignment: MultipleSeqAlignment = AlignIO.read(io.StringIO(response), "clustal")  # type: ignore
         self._delete_temp_dir()
 
-        return alignment
+        return alignment  # type: ignore
 
-    def run_service(self, data) -> httpx.Response:
+    def run_service(self, data: list[str]) -> httpx.Response:
         """Executes the ClustalOmega service."""
         file = self.create_file(data)
         try:

src/pyeed/tools/test_services.py

@@ -0,0 +1,10 @@
+from pyeed import Pyeed
+from pyeed.model import Protein
+
+pyeed = Pyeed(
+    uri="bolt://localhost:7688",
+    user="neo4j",
+    password="12345678",
+)
+
+prots = Protein.nodes.all()