[TYPING](ALL): Fix typing problems

biobb_analysis/ambertools/common.py

@@ -468,8 +468,8 @@ def copy_instructions_file_to_container(instructions_file, unique_dir):
 def remove_tmp_files(list, remove_tmp, out_log, input_top_path_orig=None, input_top_path=None):
     """ Removes temporal files generated by the wrapper """
     tmp_files = list
-    if zipfile.is_zipfile(input_top_path_orig):
-        tmp_files.append(PurePath(input_top_path).parent)
+    if zipfile.is_zipfile(str(input_top_path_orig)):
+        tmp_files.append(PurePath(str(input_top_path)).parent)
 
     if remove_tmp:
         removed_files = [f for f in tmp_files if fu.rm(f)]

biobb_analysis/ambertools/cpptraj_average.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Average class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -167,8 +168,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(str(self.instructions_file)).parent)
         ])
         self.remove_tmp_files()
 
@@ -177,7 +178,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_average(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_average(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajAverage <ambertools.cpptraj_average.CpptrajAverage>` class and
     execute the :meth:`launch() <ambertools.cpptraj_average.CpptrajAverage.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_bfactor.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Bfactor class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -174,8 +175,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(str(PurePath(self.instructions_file).parent))
         ])
         self.remove_tmp_files()
 
@@ -184,7 +185,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_bfactor(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str = None, properties: dict = None, **kwargs) -> int:
+def cpptraj_bfactor(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajBfactor <ambertools.cpptraj_bfactor.CpptrajBfactor>` class and
     execute the :meth:`launch() <ambertools.cpptraj_bfactor.CpptrajBfactor.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_convert.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Convert class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -164,8 +165,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -174,7 +175,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_convert(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_convert(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajConvert <ambertools.cpptraj_convert.CpptrajConvert>` class and
     execute the :meth:`launch() <ambertools.cpptraj_convert.CpptrajConvert.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_dry.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Dry class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -170,8 +171,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -180,7 +181,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_dry(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_dry(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajDry <ambertools.cpptraj_dry.CpptrajDry>` class and
     execute the :meth:`launch() <ambertools.cpptraj_dry.CpptrajDry.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_image.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Image class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -170,8 +171,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -180,7 +181,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_image(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_image(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajImage <ambertools.cpptraj_image.CpptrajImage>` class and
     execute the :meth:`launch() <ambertools.cpptraj_image.CpptrajImage.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_input.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Input class and the command line interface."""
 import argparse
+from typing import Optional
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
@@ -65,9 +66,9 @@ def create_instrucions_file(self):
         instructions_list = []
         output_instructions_path = fu.create_name(prefix=self.prefix, step=self.step, name=get_default_value("instructions_file"))
 
-        instructions_list.append('parm ' + self.input_top_path)
-        instructions_list.append('trajin ' + self.input_traj_path)
-        instructions_list.append('trajout ' + self.output_cpptraj_path + ' ' + get_default_value("format"))
+        instructions_list.append('parm ' + str(self.input_top_path))
+        instructions_list.append('trajin ' + str(self.input_traj_path))
+        instructions_list.append('trajout ' + str(self.output_cpptraj_path) + ' ' + get_default_value("format"))
 
         with open(output_instructions_path, 'w') as mdp:
             for line in instructions_list:
@@ -101,7 +102,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_input(input_instructions_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_input(input_instructions_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajInput <ambertools.cpptraj_input.CpptrajInput>` class and
     execute the :meth:`launch() <ambertools.cpptraj_input.CpptrajInput.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_mask.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Mask class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -169,8 +170,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -179,7 +180,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_mask(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_mask(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajMask <ambertools.cpptraj_mask.CpptrajMask>` class and
     execute the :meth:`launch() <ambertools.cpptraj_mask.CpptrajMask.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_rgyr.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Rgyr class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -162,8 +163,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -172,7 +173,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_rgyr(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_rgyr(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajRgyr <ambertools.cpptraj_rgyr.CpptrajRgyr>` class and
     execute the :meth:`launch() <ambertools.cpptraj_rgyr.CpptrajRgyr.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_rms.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Rms class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -188,8 +189,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -198,7 +199,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_rms(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str = None, output_traj_path: str = None, properties: dict = None, **kwargs) -> int:
+def cpptraj_rms(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: Optional[str] = None, output_traj_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajRms <ambertools.cpptraj_rms.CpptrajRms>` class and
     execute the :meth:`launch() <ambertools.cpptraj_rms.CpptrajRms.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_rmsf.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Rmsf class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -174,8 +175,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -184,7 +185,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_rmsf(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str = None, properties: dict = None, **kwargs) -> int:
+def cpptraj_rmsf(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajRmsf <ambertools.cpptraj_rmsf.CpptrajRmsf>` class and
     execute the :meth:`launch() <ambertools.cpptraj_rmsf.CpptrajRmsf.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_slice.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Slice class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -164,8 +165,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -174,7 +175,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_slice(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_slice(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajSlice <ambertools.cpptraj_slice.CpptrajSlice>` class and
     execute the :meth:`launch() <ambertools.cpptraj_slice.CpptrajSlice.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_snapshot.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Snapshot class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -158,8 +159,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -168,7 +169,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_snapshot(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_snapshot(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajSnapshot <ambertools.cpptraj_snapshot.CpptrajSnapshot>` class and
     execute the :meth:`launch() <ambertools.cpptraj_snapshot.CpptrajSnapshot.launch>` method."""
 

biobb_analysis/ambertools/cpptraj_strip.py

@@ -2,6 +2,7 @@
 
 """Module containing the Cpptraj Strip class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import PurePath
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -169,8 +170,8 @@ def launch(self) -> int:
 
         # remove temporary folder(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            PurePath(self.instructions_file).parent
+            self.stage_io_dict.get("unique_dir", ""),
+            str(PurePath(self.instructions_file).parent)
         ])
         self.remove_tmp_files()
 
@@ -179,7 +180,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def cpptraj_strip(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
+def cpptraj_strip(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`CpptrajStrip <ambertools.cpptraj_strip.CpptrajStrip>` class and
     execute the :meth:`launch() <ambertools.cpptraj_strip.CpptrajStrip.launch>` method."""