[TYPING](ALL): Fix typing errors

biobb_gromacs/gromacs/common.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from biobb_common.tools import file_utils as fu
 from biobb_common.command_wrapper import cmd_wrapper
-from typing import Dict, Mapping, Optional
+from typing import Mapping, Optional
 
 
 def get_gromacs_version(gmx: str = "gmx", minimum_version: int = 512) -> int:
@@ -108,7 +108,7 @@ def gmx_rms(file_a: str, file_b: str, file_tpr: str, gmx: str = 'gmx', tolerance
     return True
 
 
-def read_mdp(input_mdp_path: str) -> Dict[str, str]:
+def read_mdp(input_mdp_path: str) -> dict[str, str]:
     # Credit for these two reg exps to:
     # https://github.com/Becksteinlab/GromacsWrapper/blob/master/gromacs/fileformats/mdp.py
     parameter_re = re.compile(r"\s*(?P<parameter>[^=]+?)\s*=\s*(?P<value>[^;]*)(?P<comment>\s*;.*)?", re.VERBOSE)
@@ -125,8 +125,8 @@ def read_mdp(input_mdp_path: str) -> Dict[str, str]:
     return mdp_dict
 
 
-def mdp_preset(sim_type: str) -> Dict[str, str]:
-    mdp_dict: Dict[str, str] = {}
+def mdp_preset(sim_type: str) -> dict[str, str]:
+    mdp_dict: dict[str, str] = {}
     if not sim_type or sim_type == 'index':
         return mdp_dict
 

biobb_gromacs/gromacs/editconf.py

@@ -2,12 +2,13 @@
 
 """Module containing the Editconf 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
 from biobb_common.tools.file_utils import launchlogger
 from biobb_gromacs.gromacs.common import get_gromacs_version
-from typing import Optional, Dict
+from typing import Optional
 
 
 class Editconf(BiobbObject):
@@ -56,7 +57,7 @@ class Editconf(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_gro_path: str, output_gro_path: str, properties: Optional[Dict] = None, **kwargs) -> None:
+    def __init__(self, input_gro_path: str, output_gro_path: str, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -139,7 +140,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def editconf(input_gro_path: str, output_gro_path: str, properties: Optional[Dict] = None, **kwargs) -> int:
+def editconf(input_gro_path: str, output_gro_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Editconf <gromacs.editconf.Editconf>` class and
     execute the :meth:`launch() <gromacs.editconf.Editconf.launch>` method."""
 

biobb_gromacs/gromacs/genion.py

@@ -3,13 +3,14 @@
 """Module containing the Genion class and the command line interface."""
 import shutil
 import argparse
+from typing import Optional
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
 from biobb_gromacs.gromacs.common import get_gromacs_version
-from typing import Optional, Dict, Union
+from typing import Optional, Union
 
 
 class Genion(BiobbObject):
@@ -64,7 +65,7 @@ class Genion(BiobbObject):
     """
 
     def __init__(self, input_tpr_path: Union[str, Path], output_gro_path: Union[str, Path], input_top_zip_path: Union[str, Path],
-                 output_top_zip_path: Union[str, Path], input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[Dict] = None, **kwargs) -> None:
+                 output_top_zip_path: Union[str, Path], input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -173,7 +174,7 @@ def launch(self) -> int:
 
 
 def genion(input_tpr_path: Union[str, Path], output_gro_path: Union[str, Path], input_top_zip_path: Union[str, Path],
-           output_top_zip_path: Union[str, Path], input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[Dict] = None, **kwargs) -> int:
+           output_top_zip_path: Union[str, Path], input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Genion <gromacs.genion.Genion>` class and
         execute the :meth:`launch() <gromacs.genion.Genion.launch>` method."""
     return Genion(input_tpr_path=input_tpr_path, output_gro_path=output_gro_path,

biobb_gromacs/gromacs/genrestr.py

@@ -2,13 +2,14 @@
 
 """Module containing the Genrestr 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
 from biobb_common.tools.file_utils import launchlogger
 from biobb_gromacs.gromacs.common import get_gromacs_version
 from pathlib import Path
-from typing import Union, Optional, Dict
+from typing import Union, Optional
 
 
 class Genrestr(BiobbObject):
@@ -57,7 +58,7 @@ class Genrestr(BiobbObject):
     """
 
     def __init__(self, input_structure_path: Union[str, Path], output_itp_path: Union[str, Path],
-                 input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[Dict] = None, **kwargs) -> None:
+                 input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -137,7 +138,7 @@ def launch(self) -> int:
 
 
 def genrestr(input_structure_path: Union[str, Path], output_itp_path: Union[str, Path],
-             input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[Dict] = None, **kwargs) -> int:
+             input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Genrestr <gromacs.genrestr.Genrestr>` class and
     execute the :meth:`launch() <gromacs.genrestr.Genrestr.launch>` method."""
 

biobb_gromacs/gromacs/gmxselect.py

@@ -2,8 +2,9 @@
 
 """Module containing the Select class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
-from typing import Optional, Dict
+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
@@ -56,7 +57,7 @@ class Gmxselect(BiobbObject):
     """
 
     def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -138,7 +139,7 @@ def launch(self) -> int:
 
 
 def gmxselect(input_structure_path: str, output_ndx_path: str,
-              input_ndx_path: Optional[str] = None, properties: Optional[Dict] = None,
+              input_ndx_path: Optional[str] = None, properties: Optional[dict] = None,
               **kwargs) -> int:
     """Create :class:`Gmxselect <gromacs.gmxselect.Gmxselect>` class and
     execute the :meth:`launch() <gromacs.gmxselect.Gmxselect.launch>` method."""

biobb_gromacs/gromacs/grompp.py

@@ -2,8 +2,9 @@
 
 """Module containing the Grompp class and the command line interface."""
 import argparse
+from typing import Optional
 import shutil
-from typing import Optional, Dict
+from typing import Optional
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -70,7 +71,7 @@ class Grompp(BiobbObject):
 
     def __init__(self, input_gro_path: str, input_top_zip_path: str, output_tpr_path: str,
                  input_cpt_path: Optional[str] = None, input_ndx_path: Optional[str] = None, input_mdp_path: Optional[str] = None,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor

biobb_gromacs/gromacs/grompp_mdrun.py

@@ -2,7 +2,8 @@
 
 """Module containing the GromppMDrun class and the command line interface."""
 import argparse
-from typing import Optional, Dict
+from typing import Optional
+from typing import Optional
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -44,8 +45,8 @@ class GromppMdrun(BiobbObject):
             * **num_threads_omp** (*int*) - (0) [0-1000|1] Let GROMACS guess. The number of GROMACS OPENMP threads that are going to be used.
             * **num_threads_omp_pme** (*int*) - (0) [0-1000|1] Let GROMACS guess. The number of GROMACS OPENMP_PME threads that are going to be used.
             * **use_gpu** (*bool*) - (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu
-            * **gpu_id** (*str*) - (None) List of unique GPU device IDs available to use.
-            * **gpu_tasks** (*str*) - (None) List of GPU device IDs, mapping each PP task on each node to a device.
+            * **gpu_id** (*str*) - (None) list of unique GPU device IDs available to use.
+            * **gpu_tasks** (*str*) - (None) list of GPU device IDs, mapping each PP task on each node to a device.
             * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
             * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
@@ -166,7 +167,7 @@ def grompp_mdrun(input_gro_path: str, input_top_zip_path: str, output_trr_path:
                  output_gro_path: str, output_edr_path: str, output_log_path: str,
                  input_cpt_path: Optional[str] = None, input_ndx_path: Optional[str] = None, input_mdp_path: Optional[str] = None,
                  output_xtc_path: Optional[str] = None, output_cpt_path: Optional[str] = None, output_dhdl_path: Optional[str] = None,
-                 output_tpr_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> int:
+                 output_tpr_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     return GromppMdrun(input_gro_path=input_gro_path, input_top_zip_path=input_top_zip_path,
                        output_trr_path=output_trr_path, output_gro_path=output_gro_path,
                        output_edr_path=output_edr_path, output_log_path=output_log_path,

biobb_gromacs/gromacs/make_ndx.py

@@ -2,8 +2,9 @@
 
 """Module containing the MakeNdx class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
-from typing import Optional, Dict
+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
@@ -55,7 +56,7 @@ class MakeNdx(BiobbObject):
     """
 
     def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -132,7 +133,7 @@ def launch(self) -> int:
 
 
 def make_ndx(input_structure_path: str, output_ndx_path: str,
-             input_ndx_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> int:
+             input_ndx_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` class and
     execute the :meth:`launch() <gromacs.make_ndx.MakeNdx.launch>` method."""
     return MakeNdx(input_structure_path=input_structure_path,

biobb_gromacs/gromacs/mdrun.py

@@ -3,6 +3,7 @@
 """Module containing the MDrun class and the command line interface."""
 import argparse
 from typing import Optional
+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
@@ -36,8 +37,8 @@ class Mdrun(BiobbObject):
             * **num_threads_omp** (*int*) - (0) [0~1000|1] Let GROMACS guess. The number of GROMACS OPENMP threads that are going to be used.
             * **num_threads_omp_pme** (*int*) - (0) [0~1000|1] Let GROMACS guess. The number of GROMACS OPENMP_PME threads that are going to be used.
             * **use_gpu** (*bool*) - (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu
-            * **gpu_id** (*str*) - (None) List of unique GPU device IDs available to use.
-            * **gpu_tasks** (*str*) - (None) List of GPU device IDs, mapping each PP task on each node to a device.
+            * **gpu_id** (*str*) - (None) list of unique GPU device IDs available to use.
+            * **gpu_tasks** (*str*) - (None) list of GPU device IDs, mapping each PP task on each node to a device.
             * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
             * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
@@ -198,11 +199,11 @@ def launch(self) -> int:
             fu.log('Adding GPU specific settings adds: -nb gpu -pme gpu', self.out_log)
             self.cmd += ["-nb", "gpu", "-pme", "gpu"]
         if self.gpu_id:
-            fu.log(f'List of unique GPU device IDs available to use: {self.gpu_id}', self.out_log)
+            fu.log(f'list of unique GPU device IDs available to use: {self.gpu_id}', self.out_log)
             self.cmd.append('-gpu_id')
             self.cmd.append(self.gpu_id)
         if self.gpu_tasks:
-            fu.log(f'List of GPU device IDs, mapping each PP task on each node to a device: {self.gpu_tasks}', self.out_log)
+            fu.log(f'list of GPU device IDs, mapping each PP task on each node to a device: {self.gpu_tasks}', self.out_log)
             self.cmd.append('-gputasks')
             self.cmd.append(self.gpu_tasks)
 

biobb_gromacs/gromacs/pdb2gmx.py

@@ -3,7 +3,8 @@
 """Module containing the Pdb2gmx class and the command line interface."""
 import os
 import argparse
-from typing import Optional, Dict
+from typing import Optional
+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
@@ -59,7 +60,7 @@ class Pdb2gmx(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_pdb_path: str, output_gro_path: str, output_top_zip_path: str, properties: Optional[Dict] = None,
+    def __init__(self, input_pdb_path: str, output_gro_path: str, output_top_zip_path: str, properties: Optional[dict] = None,
                  **kwargs) -> None:
         properties = properties or {}
 
@@ -158,7 +159,7 @@ def launch(self) -> int:
 
 
 def pdb2gmx(input_pdb_path: str, output_gro_path: str, output_top_zip_path: str,
-            properties: Optional[Dict] = None, **kwargs) -> int:
+            properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx>` class and
     execute the :meth:`launch() <gromacs.pdb2gmx.Pdb2gmx.launch>` method."""
 

biobb_gromacs/gromacs/solvate.py

@@ -3,8 +3,9 @@
 """Module containing the Editconf class and the command line interface."""
 import shutil
 import argparse
+from typing import Optional
 from pathlib import Path
-from typing import Optional, Dict
+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
@@ -61,7 +62,7 @@ class Solvate(BiobbObject):
     """
 
     def __init__(self, input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
-                 output_top_zip_path: str, input_solvent_gro_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
+                 output_top_zip_path: str, input_solvent_gro_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -151,7 +152,7 @@ def launch(self) -> int:
 
 
 def solvate(input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
-            output_top_zip_path: str, input_solvent_gro_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> int:
+            output_top_zip_path: str, input_solvent_gro_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Solvate <gromacs.solvate.Solvate>` class and
     execute the :meth:`launch() <gromacs.solvate.Solvate.launch>` method."""
 

biobb_gromacs/gromacs/trjcat.py

@@ -1,11 +1,11 @@
 #!/usr/bin/env python3
 
 """Module containing the Trjcat class and the command line interface."""
-import typing
 import shutil
 import argparse
+from typing import Optional
 from pathlib import Path
-from typing import Optional, Dict
+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
@@ -55,7 +55,7 @@ class Trjcat(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_trj_zip_path: str, output_trj_path: str, properties: Optional[Dict] = None, **kwargs) -> None:
+    def __init__(self, input_trj_zip_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -101,7 +101,7 @@ def launch(self) -> int:
 
         # Unzip trajectory bundle
         trj_dir: str = fu.create_unique_dir()
-        trj_list: typing.List[str] = fu.unzip_list(self.input_trj_zip_path, trj_dir, self.out_log)
+        trj_list: list[str] = fu.unzip_list(self.input_trj_zip_path, trj_dir, self.out_log)
 
         # Copy trajectories to container
         if self.container_path:
@@ -135,7 +135,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def trjcat(input_trj_zip_path: str, output_trj_path: str, properties: Optional[Dict] = None, **kwargs) -> int:
+def trjcat(input_trj_zip_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Trjcat <gromacs.trjcat.Trjcat>` class and
     execute the :meth:`launch() <gromacs.trjcat.Trjcat.launch>` method."""
 

biobb_gromacs/gromacs_extra/append_ligand.py

@@ -3,9 +3,10 @@
 """Module containing the AppendLigand class and the command line interface."""
 import re
 import argparse
+from typing import Optional
 import shutil
 from pathlib import Path
-from typing import Optional, Dict
+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
@@ -49,7 +50,7 @@ class AppendLigand(BiobbObject):
     """
 
     def __init__(self, input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str,
-                 input_posres_itp_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
+                 input_posres_itp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -156,7 +157,7 @@ def launch(self) -> int:
 
 
 def append_ligand(input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str,
-                  input_posres_itp_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> int:
+                  input_posres_itp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` class and
     execute the :meth:`launch() <gromacs_extra.append_ligand.AppendLigand.launch>` method."""
     return AppendLigand(input_top_zip_path=input_top_zip_path,