[TYPING](ALL): Fix typing errors

Author: PauAndrio

biobb_structure_utils/utils/cat_pdb.py

@@ -2,6 +2,7 @@
 
 """Module containing the CatPDB class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
@@ -114,7 +115,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cat_pdb(input_structure1: str, input_structure2: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
+def cat_pdb(input_structure1: str, input_structure2: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CatPDB <utils.cat_pdb.CatPDB>` class and
     execute the :meth:`launch() <utils.cat_pdb.CatPDB.launch>` method."""
 

biobb_structure_utils/utils/closest_residues.py

@@ -2,6 +2,7 @@
 
 """Module containing the ClosestResidues class and the command line interface."""
 import argparse
+from typing import Optional
 import Bio.PDB
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
@@ -171,7 +172,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def closest_residues(input_structure_path: str, output_residues_path: str, properties: dict = None, **kwargs) -> int:
+def closest_residues(input_structure_path: str, output_residues_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ClosestResidues <utils.closest_residues.ClosestResidues>` class and
     execute the :meth:`launch() <utils.closest_residues.ClosestResidues.launch>` method."""
 

biobb_structure_utils/utils/extract_atoms.py

@@ -2,6 +2,7 @@
 
 """Module containing the ExtractAtoms class and the command line interface."""
 import argparse
+from typing import Optional
 import re
 from pathlib import Path
 from biobb_common.configuration import settings
@@ -124,7 +125,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def extract_atoms(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
+def extract_atoms(input_structure_path: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ExtractAtoms <utils.extract_atoms.ExtractAtoms>` class and
     execute the :meth:`launch() <utils.extract_atoms.ExtractAtoms.launch>` method."""
 

biobb_structure_utils/utils/extract_chain.py

@@ -2,6 +2,7 @@
 
 """Module containing the ExtractChain class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
@@ -137,7 +138,7 @@ def check_format_chains(chains, out_log):
     return ','.join(chains)
 
 
-def extract_chain(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
+def extract_chain(input_structure_path: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ExtractChain <utils.extract_chain.ExtractChain>` class and
     execute the :meth:`launch() <utils.extract_chain.ExtractChain.launch>` method."""
 

biobb_structure_utils/utils/extract_heteroatoms.py

@@ -2,6 +2,7 @@
 
 """Module containing the ExtractHeteroAtoms class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
@@ -142,7 +143,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def extract_heteroatoms(input_structure_path: str, output_heteroatom_path: str, properties: dict = None, **kwargs) -> int:
+def extract_heteroatoms(input_structure_path: str, output_heteroatom_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` class and
     execute the :meth:`launch() <utils.extract_heteroatoms.ExtractHeteroAtoms.launch>` method."""
 

biobb_structure_utils/utils/extract_model.py

@@ -2,6 +2,7 @@
 
 """Module containing the ExtractModel class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
@@ -149,7 +150,7 @@ def check_format_models(models, out_log):
     return models
 
 
-def extract_model(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
+def extract_model(input_structure_path: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ExtractModel <utils.extract_model.ExtractModel>` class and
     execute the :meth:`launch() <utils.extract_model.ExtractModel.launch>` method."""
 

biobb_structure_utils/utils/extract_molecule.py

@@ -2,6 +2,7 @@
 
 """Module containing the ExtractMolecule class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
@@ -123,7 +124,7 @@ def launch(self) -> int:
 
         # Remove temporal files
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
+            self.stage_io_dict.get("unique_dir", ""),
             tmp_folder
         ])
         self.remove_tmp_files()
@@ -133,7 +134,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def extract_molecule(input_structure_path: str, output_molecule_path: str, properties: dict = None, **kwargs) -> int:
+def extract_molecule(input_structure_path: str, output_molecule_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ExtractMolecule <utils.extract_molecule.ExtractMolecule>` class and
     execute the :meth:`launch() <utils.extract_molecule.ExtractMolecule.launch>` method."""
 

biobb_structure_utils/utils/extract_residues.py

@@ -2,6 +2,7 @@
 
 """Module containing the ExtractResidues class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
@@ -133,7 +134,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def extract_residues(input_structure_path: str, output_residues_path: str, properties: dict = None, **kwargs) -> int:
+def extract_residues(input_structure_path: str, output_residues_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`ExtractResidues <utils.extract_residues.ExtractResidues>` class and
     execute the :meth:`launch() <utils.extract_residues.ExtractResidues.launch>` method."""
 

biobb_structure_utils/utils/remove_ligand.py

@@ -2,6 +2,7 @@
 
 """Module containing the RemoveLigand class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
@@ -110,7 +111,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def remove_ligand(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
+def remove_ligand(input_structure_path: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`RemoveLigand <utils.remove_ligand.RemoveLigand>` class and
     execute the :meth:`launch() <utils.remove_ligand.RemoveLigand.launch>` method."""
 

biobb_structure_utils/utils/remove_molecules.py

@@ -2,6 +2,7 @@
 
 """Module containing the RemoveMolecules class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
@@ -138,7 +139,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def remove_molecules(input_structure_path: str, output_molecules_path: str, properties: dict = None, **kwargs) -> int:
+def remove_molecules(input_structure_path: str, output_molecules_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`RemoveMolecules <utils.remove_molecules.RemoveMolecules>` class and
     execute the :meth:`launch() <utils.remove_molecules.RemoveMolecules.launch>` method."""
 

biobb_structure_utils/utils/remove_pdb_water.py

@@ -2,6 +2,7 @@
 
 """Module containing the RemovePdbWater class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
@@ -92,7 +93,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def remove_pdb_water(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int:
+def remove_pdb_water(input_pdb_path: str, output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` class and
     execute the :meth:`launch() <utils.remove_pdb_water.RemovePdbWater.launch>` method."""
 

biobb_structure_utils/utils/renumber_structure.py

@@ -3,6 +3,7 @@
 """Module containing the RenumberStructure class and the command line interface."""
 import json
 import argparse
+from typing import Optional
 from pathlib import Path
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
@@ -149,7 +150,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def renumber_structure(input_structure_path: str, output_structure_path: str, output_mapping_json_path: str, properties: dict = None, **kwargs) -> int:
+def renumber_structure(input_structure_path: str, output_structure_path: str, output_mapping_json_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`RenumberStructure <utils.renumber_structure.RenumberStructure>` class and
     execute the :meth:`launch() <utils.renumber_structure.RenumberStructure.launch>` method."""
 

biobb_structure_utils/utils/sort_gro_residues.py

@@ -2,6 +2,7 @@
 
 """Module containing the SortGroResidues class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
@@ -93,7 +94,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def sort_gro_residues(input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) -> int:
+def sort_gro_residues(input_gro_path: str, output_gro_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` class and
     execute the :meth:`launch() <utils.sort_gro_residues.SortGroResidues.launch>` method."""
 

biobb_structure_utils/utils/str_check_add_hydrogens.py

@@ -2,6 +2,7 @@
 
 """Module containing the StrCheckAddHydrogens class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
@@ -133,7 +134,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def str_check_add_hydrogens(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
+def str_check_add_hydrogens(input_structure_path: str, output_structure_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` class and
     execute the :meth:`launch() <utils.str_check_add_hydrogens.StrCheckAddHydrogens.launch>` method."""
 

biobb_structure_utils/utils/structure_check.py

@@ -2,6 +2,7 @@
 
 """Module containing the StructureCheck class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
@@ -124,7 +125,7 @@ def launch(self) -> int:
 
         # Remove temporal files
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
+            self.stage_io_dict.get("unique_dir", ""),
             tmp_folder
         ])
         self.remove_tmp_files()
@@ -134,7 +135,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def structure_check(input_structure_path: str, output_summary_path: str, properties: dict = None, **kwargs) -> int:
+def structure_check(input_structure_path: str, output_summary_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`StructureCheck <utils.structure_check.StructureCheck>` class and
     execute the :meth:`launch() <utils.structure_check.StructureCheck.launch>` method."""