[TYPING](ALL): Fix typing errors

biobb_flexdyn/flexdyn/concoord_disco.py

@@ -2,6 +2,7 @@
 
 """Module containing the concoord_disco class and the command line interface."""
 import argparse
+from typing import Optional
 import os
 import shutil
 from pathlib import Path
@@ -74,7 +75,7 @@ class ConcoordDisco(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, input_dat_path: str, output_traj_path: str,
-                 output_rmsd_path: str, output_bfactor_path: str, properties: dict = None, **kwargs) -> None:
+                 output_rmsd_path: str, output_bfactor_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -242,7 +243,7 @@ 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()
 
@@ -253,7 +254,7 @@ def launch(self):
 
 def concoord_disco(input_pdb_path: str, input_dat_path: str,
                    output_traj_path: str, output_rmsd_path: str, output_bfactor_path: str,
-                   properties: dict = None, **kwargs) -> int:
+                   properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`ConcoordDisco <flexdyn.concoord_disco.ConcoordDisco>`flexdyn.concoord_disco.ConcoordDisco class and
     execute :meth:`launch() <flexdyn.concoord_disco.ConcoordDisco.launch>` method"""
 

biobb_flexdyn/flexdyn/concoord_dist.py

@@ -2,6 +2,7 @@
 
 """Module containing the concoord_dist class and the command line interface."""
 import argparse
+from typing import Optional
 import os
 import shutil
 from pathlib import Path
@@ -62,7 +63,7 @@ class ConcoordDist(BiobbObject):
     """
 
     def __init__(self, input_structure_path: str, output_pdb_path: str,
-                 output_gro_path: str, output_dat_path: str, properties: dict = None, **kwargs) -> None:
+                 output_gro_path: str, output_dat_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -191,7 +192,7 @@ 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.io_dict['in'].get("stdin_file_path")
         ])
         self.remove_tmp_files()
@@ -203,7 +204,7 @@ def launch(self):
 
 def concoord_dist(input_structure_path: str,
                   output_pdb_path: str, output_gro_path: str, output_dat_path: str,
-                  properties: dict = None, **kwargs) -> int:
+                  properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`ConcoordDist <flexdyn.concoord_dist.ConcoordDist>`flexdyn.concoord_dist.ConcoordDist class and
     execute :meth:`launch() <flexdyn.concoord_dist.ConcoordDist.launch>` method"""
 

biobb_flexdyn/flexdyn/imod_imc.py

@@ -2,6 +2,7 @@
 
 """Module containing the imode class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from pathlib import PurePath
 from biobb_common.tools import file_utils as fu
@@ -52,7 +53,7 @@ class ImodImc(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, input_dat_path: str, output_traj_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -159,7 +160,7 @@ def launch(self):
 
 
 def imod_imc(input_pdb_path: str, input_dat_path: str, output_traj_path: str,
-             properties: dict = None, **kwargs) -> int:
+             properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`ImodImc <flexdyn.imod_imc.ImodImc>`flexdyn.imod_imc.ImodImc class and
     execute :meth:`launch() <flexdyn.imod_imc.ImodImc.launch>` method"""
 

biobb_flexdyn/flexdyn/imod_imode.py

@@ -2,6 +2,7 @@
 
 """Module containing the imode class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from pathlib import PurePath
 from biobb_common.tools import file_utils as fu
@@ -48,7 +49,7 @@ class ImodImode(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, output_dat_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -139,7 +140,7 @@ def launch(self):
 
 
 def imod_imode(input_pdb_path: str, output_dat_path: str,
-               properties: dict = None, **kwargs) -> int:
+               properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`ImodImode <flexdyn.imod_imode.ImodImode>`flexdyn.imod_imode.ImodImode class and
     execute :meth:`launch() <flexdyn.imod_imode.ImodImode.launch>` method"""
 

biobb_flexdyn/flexdyn/imod_imove.py

@@ -2,6 +2,7 @@
 
 """Module containing the imode class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from pathlib import PurePath
 from biobb_common.tools import file_utils as fu
@@ -51,7 +52,7 @@ class ImodImove(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, input_dat_path: str, output_pdb_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -142,7 +143,7 @@ def launch(self):
 
 
 def imod_imove(input_pdb_path: str, input_dat_path: str, output_pdb_path: str,
-               properties: dict = None, **kwargs) -> int:
+               properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`ImodImove <flexdyn.imod_imove.ImodImove>`flexdyn.imod_imove.ImodImove class and
     execute :meth:`launch() <flexdyn.imod_imove.ImodImove.launch>` method"""
 

biobb_flexdyn/flexdyn/nolb_nma.py

@@ -2,6 +2,7 @@
 
 """Module containing the nolb class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
@@ -49,7 +50,7 @@ class Nolb_nma(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, output_pdb_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -130,7 +131,7 @@ 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()
 
@@ -140,7 +141,7 @@ def launch(self):
 
 
 def nolb_nma(input_pdb_path: str, output_pdb_path: str,
-             properties: dict = None, **kwargs) -> int:
+             properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Nolb_nma <flexdyn.nolb_nma.Nolb_nma>`flexdyn.nolb_nma.Nolb_nma class and
     execute :meth:`launch() <flexdyn.nolb_nma.Nolb_nma.launch>` method"""
 

biobb_flexdyn/flexdyn/prody_anm.py

@@ -2,6 +2,7 @@
 
 """Module containing the prody_anm class and the command line interface."""
 import argparse
+from typing import Optional
 import prody
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -51,7 +52,7 @@ class ProdyANM(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, output_pdb_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -112,7 +113,7 @@ 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()
 
@@ -122,7 +123,7 @@ def launch(self):
 
 
 def prody_anm(input_pdb_path: str, output_pdb_path: str,
-              properties: dict = None, **kwargs) -> int:
+              properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`ProdyANM <flexdyn.prody_anm.ProdyANM>`flexdyn.prody_anm.ProdyANM class and
     execute :meth:`launch() <flexdyn.prody_anm.ProdyANM.launch>` method"""