[TYPING](ALL): Fix typing errors

biobb_flexserv/flexserv/bd_run.py

@@ -2,6 +2,7 @@
 
 """Module containing the bd_run 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
@@ -51,7 +52,7 @@ class BDRun(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, output_log_path: str,
-                 output_crd_path: str, properties: dict = None, **kwargs) -> None:
+                 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -120,7 +121,7 @@ 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()
 
@@ -131,7 +132,7 @@ def launch(self):
 
 def bd_run(input_pdb_path: str,
            output_log_path: str, output_crd_path: str,
-           properties: dict = None, **kwargs) -> int:
+           properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`BDRun <flexserv.bd_run.BDRun>`flexserv.bd_run.BDRun class and
     execute :meth:`launch() <flexserv.bd_run.BDRun.launch>` method"""
 

biobb_flexserv/flexserv/dmd_run.py

@@ -2,6 +2,7 @@
 
 """Module containing the dmd_run 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
@@ -51,7 +52,7 @@ class DMDRun(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, output_log_path: str,
-                 output_crd_path: str, properties: dict = None, **kwargs) -> None:
+                 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -131,7 +132,7 @@ 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()
 
@@ -142,7 +143,7 @@ def launch(self):
 
 def dmd_run(input_pdb_path: str,
             output_log_path: str, output_crd_path: str,
-            properties: dict = None, **kwargs) -> int:
+            properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`DMDRun <flexserv.dmd_run.DMDRun>`flexserv.dmd_run.DMDRun class and
     execute :meth:`launch() <flexserv.dmd_run.DMDRun.launch>` method"""
 

biobb_flexserv/flexserv/nma_run.py

@@ -2,6 +2,7 @@
 
 """Module containing the nma_run class and the command line interface."""
 import argparse
+from typing import Optional
 import os
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
@@ -51,7 +52,7 @@ class NMARun(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, output_log_path: str,
-                 output_crd_path: str, properties: dict = None, **kwargs) -> None:
+                 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -132,7 +133,7 @@ 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()
 
@@ -143,7 +144,7 @@ def launch(self):
 
 def nma_run(input_pdb_path: str,
             output_log_path: str, output_crd_path: str,
-            properties: dict = None, **kwargs) -> int:
+            properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`NMARun <flexserv.nma_run.NMARun>`flexserv.nma_run.NMARun class and
     execute :meth:`launch() <flexserv.nma_run.NMARun.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_animate.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZanimate 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 PCZanimate(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_crd_path: str, properties: dict = None, **kwargs) -> None:
+                 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -146,7 +147,7 @@ def launch(self):
 
 
 def pcz_animate(input_pcz_path: str, output_crd_path: str,
-                properties: dict = None, **kwargs) -> int:
+                properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZanimate <flexserv.pcasuite.pcz_animate>`flexserv.pcasuite.PCZanimate class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_animate.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_bfactor.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZbfactor 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
@@ -53,7 +54,7 @@ class PCZbfactor(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str, output_dat_path: str,
-                 output_pdb_path: str, properties: dict = None, **kwargs) -> None:
+                 output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -176,7 +177,7 @@ def launch(self):
 
 
 def pcz_bfactor(input_pcz_path: str, output_dat_path: str, output_pdb_path: str,
-                properties: dict = None, **kwargs) -> int:
+                properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZbfactor <flexserv.pcasuite.pcz_bfactor>`flexserv.pcasuite.PCZbfactor class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_bfactor.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_collectivity.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZcollectivity 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 PCZcollectivity(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_json_path: str, properties: dict = None, **kwargs) -> None:
+                 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -162,7 +163,7 @@ def launch(self):
 
 
 def pcz_collectivity(input_pcz_path: str, output_json_path: str,
-                     properties: dict = None, **kwargs) -> int:
+                     properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZcollectivity <flexserv.pcasuite.pcz_collectivity>`flexserv.pcasuite.PCZcollectivity class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_collectivity.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_evecs.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZevecs class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 import json
 import math
@@ -53,7 +54,7 @@ class PCZevecs(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_json_path: str, properties: dict = None, **kwargs) -> None:
+                 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -180,7 +181,7 @@ def launch(self):
 
 
 def pcz_evecs(input_pcz_path: str, output_json_path: str,
-              properties: dict = None, **kwargs) -> int:
+              properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZevecs <flexserv.pcasuite.pcz_evecs>`flexserv.pcasuite.PCZevecs class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_evecs.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_hinges.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZhinges class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 import json
 import re
@@ -53,7 +54,7 @@ class PCZhinges(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str, output_json_path: str,
-                 properties: dict = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -244,7 +245,7 @@ def launch(self):
 
 
 def pcz_hinges(input_pcz_path: str, output_json_path: str,
-               properties: dict = None, **kwargs) -> int:
+               properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZhinges <flexserv.pcasuite.pcz_hinges>`flexserv.pcasuite.PCZhinges class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_hinges.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_info.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZinfo class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 import json
 from pathlib import PurePath
@@ -46,7 +47,7 @@ class PCZinfo(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_json_path: str, properties: dict = None, **kwargs) -> None:
+                 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -192,7 +193,7 @@ def launch(self):
 
 
 def pcz_info(input_pcz_path: str, output_json_path: str,
-             properties: dict = None, **kwargs) -> int:
+             properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZinfo <flexserv.pcasuite.pcz_info>`flexserv.pcasuite.PCZinfo class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_info.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_lindemann.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZlindemann class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 import json
 from pathlib import PurePath
@@ -50,7 +51,7 @@ class PCZlindemann(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_json_path: str, properties: dict = None, **kwargs) -> None:
+                 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -160,7 +161,7 @@ def launch(self):
 
 
 def pcz_lindemann(input_pcz_path: str, output_json_path: str,
-                  properties: dict = None, **kwargs) -> int:
+                  properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZlindemann <flexserv.pcasuite.pcz_lindemann>`flexserv.pcasuite.PCZlindemann class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_lindemann.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_similarity.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZsimilarity class and the command line interface."""
 import argparse
+from typing import Optional
 import json
 import numpy as np
 import shutil
@@ -52,7 +53,7 @@ class PCZsimilarity(BiobbObject):
     """
 
     def __init__(self, input_pcz_path1: str, input_pcz_path2: str,
-                 output_json_path: str, properties: dict = None, **kwargs) -> None:
+                 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -470,7 +471,7 @@ def launch(self):
 
 
 def pcz_similarity(input_pcz_path1: str, input_pcz_path2: str, output_json_path: str,
-                   properties: dict = None, **kwargs) -> int:
+                   properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZsimilarity <flexserv.pcasuite.pcz_similarity>`flexserv.pcasuite.PCZsimilarity class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_similarity.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_stiffness.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZstiffness class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
 import json
 import math
@@ -54,7 +55,7 @@ class PCZstiffness(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_json_path: str, properties: dict = None, **kwargs) -> None:
+                 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -180,7 +181,7 @@ def launch(self):
 
 
 def pcz_stiffness(input_pcz_path: str, output_json_path: str,
-                  properties: dict = None, **kwargs) -> int:
+                  properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZstiffness <flexserv.pcasuite.pcz_stiffness>`flexserv.pcasuite.PCZstiffness class and
     execute :meth:`launch() <flexserv.pcasuite.pcz_stiffness.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_unzip.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCZunzip 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
@@ -50,7 +51,7 @@ class PCZunzip(BiobbObject):
     """
 
     def __init__(self, input_pcz_path: str,
-                 output_crd_path: str, properties: dict = None, **kwargs) -> None:
+                 output_crd_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -147,7 +148,7 @@ def launch(self):
 
 def pcz_unzip(input_pcz_path: str,
               output_crd_path: str,
-              properties: dict = None, **kwargs) -> int:
+              properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZunzip <flexserv.pcasuite.PCZunzip>`flexserv.pcasuite.PCZunzip class and
     execute :meth:`launch() <flexserv.pcasuite.PCZunzip.launch>` method"""
 

biobb_flexserv/pcasuite/pcz_zip.py

@@ -2,6 +2,7 @@
 
 """Module containing the PCAzip 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
@@ -54,7 +55,7 @@ class PCZzip(BiobbObject):
     """
 
     def __init__(self, input_pdb_path: str, input_crd_path: str,
-                 output_pcz_path: str, properties: dict = None, **kwargs) -> None:
+                 output_pcz_path: str, properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -168,7 +169,7 @@ def launch(self):
 
 def pcz_zip(input_pdb_path: str, input_crd_path: str,
             output_pcz_path: str,
-            properties: dict = None, **kwargs) -> int:
+            properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`PCZzip <flexserv.pcasuite.PCZzip>`flexserv.pcasuite.PCZzip class and
     execute :meth:`launch() <flexserv.pcasuite.PCZzip.launch>` method"""