[TYPING](ALL): Fix typing errors

bioexcel · Oct 17, 2024 · 4e60e7c · 4e60e7c
1 parent 79bd550
commit 4e60e7c
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/biobb_godmd/godmd/godmd_prep.py b/biobb_godmd/godmd/godmd_prep.py
@@ -2,6 +2,7 @@
 
 """Module containing the GOdMDPrep class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -53,9 +54,10 @@ class GOdMDPrep(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
 
     """
+
     def __init__(self, input_pdb_orig_path: str, input_pdb_target_path: str,
                  output_aln_orig_path: str, output_aln_target_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -313,7 +315,7 @@ def launch(self):
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -324,7 +326,7 @@ def launch(self):
 
 def godmd_prep(input_pdb_orig_path: str, input_pdb_target_path: str,
                output_aln_orig_path: str, output_aln_target_path: str,
-               properties: dict = None, **kwargs) -> int:
+               properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`GOdMDPrep <godmd.godmd_prep.GOdMDPrep>`godmd.godmd_prep.GOdMDPrep class and
     execute :meth:`launch() <godmd.godmd_prep.GOdMDPrep.launch>` method"""
 

diff --git a/biobb_godmd/godmd/godmd_run.py b/biobb_godmd/godmd/godmd_run.py
@@ -2,6 +2,7 @@
 
 """Module containing the GOdMDRun class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from pathlib import Path
 from pathlib import PurePath
@@ -61,10 +62,11 @@ class GOdMDRun(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
 
     """
+
     def __init__(self, input_pdb_orig_path: str, input_pdb_target_path: str,
                  input_aln_orig_path: str, input_aln_target_path: str, input_config_path: str,
                  output_log_path: str, output_ene_path: str, output_trj_path: str, output_pdb_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -196,7 +198,7 @@ def launch(self):
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
+            self.stage_io_dict.get("unique_dir", ""),
         ])
         self.remove_tmp_files()
 
@@ -208,7 +210,7 @@ def launch(self):
 def godmd_run(input_pdb_orig_path: str, input_pdb_target_path: str,
               input_aln_orig_path: str, input_aln_target_path: str,
               output_log_path: str, output_ene_path: str, output_trj_path: str, output_pdb_path: str,
-              input_config_path: str = None, properties: dict = None, **kwargs) -> int:
+              input_config_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`GOdMDRun <godmd.godmd_run.GOdMDRun>`godmd.godmd_run.GOdMDRun class and
     execute :meth:`launch() <godmd.godmd_run.GOdMDRun.launch>` method"""