[TYPING](ALL): Fix typing errors

biobb_pmx/docs/source/conf.py

@@ -14,7 +14,6 @@
 
 import sys
 from pathlib import Path
-from typing import List, Dict
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -92,9 +91,9 @@
 # Else, today_fmt is used as the format for a strftime call.
 # today_fmt = '%B %d, %Y'
 
-# List of patterns, relative to source directory, that match files and
+# list of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns: List[str] = []
+exclude_patterns: list[str] = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -120,7 +119,7 @@
 # If true, keep warnings as "system message" paragraphs in the built documents.
 # keep_warnings = False
 
-# If true, `todo` and `todoList` produce output, else they produce nothing.
+# If true, `todo` and `todolist` produce output, else they produce nothing.
 todo_include_todos = False
 
 
@@ -228,7 +227,7 @@ def setup(app):
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements: Dict[str, str] = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
 
@@ -242,7 +241,7 @@ def setup(app):
     # 'figure_align': 'htbp',
 }
 
-# Grouping the document tree into LaTeX files. List of tuples
+# Grouping the document tree into LaTeX files. list of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
@@ -273,7 +272,7 @@ def setup(app):
 
 # -- Options for manual page output ---------------------------------------
 
-# One entry per manual page. List of tuples
+# One entry per manual page. list of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
     (master_doc, 'biobb_pmx', u'biobb_pmx Documentation',
@@ -286,7 +285,7 @@ def setup(app):
 
 # -- Options for Texinfo output -------------------------------------------
 
-# Grouping the document tree into Texinfo files. List of tuples
+# Grouping the document tree into Texinfo files. list of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [

biobb_pmx/pmxbiobb/pmxanalyse.py

@@ -2,9 +2,10 @@
 
 """Module containing the PMX analyse class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
 import shutil
-from typing import Dict, 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
@@ -76,7 +77,7 @@ class Pmxanalyse(BiobbObject):
     """
 
     def __init__(self, input_a_xvg_zip_path: str, input_b_xvg_zip_path: str, output_result_path: str, output_work_plot_path: str,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -210,7 +211,7 @@ def launch(self) -> int:
 
 def pmxanalyse(input_a_xvg_zip_path: str, input_b_xvg_zip_path: str,
                output_result_path: str, output_work_plot_path: str,
-               properties: Optional[Dict] = None, **kwargs) -> int:
+               properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pmxanalyse <pmx.pmxanalyse.Pmxanalyse>` class and
     execute the :meth:`launch() <pmx.pmxanalyse.Pmxanalyse.launch> method."""
 

biobb_pmx/pmxbiobb/pmxatom_mapping.py

@@ -6,7 +6,8 @@
 from pathlib import Path
 import shutil
 import argparse
-from typing import Dict, Optional
+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.file_utils import launchlogger
@@ -83,7 +84,7 @@ class Pmxatom_mapping(BiobbObject):
     def __init__(self, input_structure1_path: str, input_structure2_path: str, output_pairs1_path: str, output_pairs2_path: str,
                  output_log_path: str, output_structure1_path: Optional[str] = None, output_structure2_path: Optional[str] = None, output_morph1_path: Optional[str] = None,
                  output_morph2_path: Optional[str] = None, output_scaffold1_path: Optional[str] = None, output_scaffold2_path: Optional[str] = None, output_score_path: Optional[str] = None,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -236,7 +237,7 @@ def launch(self) -> int:
 def pmxatom_mapping(input_structure1_path: str, input_structure2_path: str, output_pairs1_path: str, output_pairs2_path: str,
                     output_log_path: str, output_structure1_path: Optional[str] = None, output_structure2_path: Optional[str] = None, output_morph1_path: Optional[str] = None,
                     output_morph2_path: Optional[str] = None, output_scaffold1_path: Optional[str] = None, output_scaffold2_path: Optional[str] = None, output_score_path: Optional[str] = None,
-                    properties: Optional[Dict] = None, **kwargs) -> int:
+                    properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pmxatom_mapping <pmx.pmxmutate.Pmxatom_mapping>` class and
     execute the :meth:`launch() <pmx.pmxatom_mapping.Pmxatom_mapping.launch> method."""
 

biobb_pmx/pmxbiobb/pmxcreate_top.py

@@ -6,7 +6,8 @@
 from pathlib import Path, PurePath
 import shutil
 import argparse
-from typing import Dict, Optional
+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
@@ -63,7 +64,7 @@ class Pmxcreate_top(BiobbObject):
     """
 
     def __init__(self, input_topology1_path: str, input_topology2_path: str, output_topology_path: str,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -173,7 +174,7 @@ def launch(self) -> int:
 
 
 def pmxcreate_top(input_topology1_path: str, input_topology2_path: str, output_topology_path: str,
-                  properties: Optional[Dict] = None, **kwargs) -> int:
+                  properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pmxcreate_top <pmx.pmxcreate_top.Pmxcreate_top>` class and
     execute the :meth:`launch() <pmx.pmxmcreate_top.Pmxmcreate_top.launch> method."""
 

biobb_pmx/pmxbiobb/pmxgentop.py

@@ -4,9 +4,10 @@
 import os
 import sys
 import argparse
+from typing import Optional
 import shutil
 from pathlib import Path
-from typing import Dict, 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
@@ -62,7 +63,7 @@ class Pmxgentop(BiobbObject):
     """
 
     def __init__(self, input_top_zip_path: str, output_top_zip_path: str,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -179,7 +180,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def pmxgentop(input_top_zip_path: str, output_top_zip_path: str, properties: Optional[Dict] = None, **kwargs) -> int:
+def pmxgentop(input_top_zip_path: str, output_top_zip_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pmxgentop <pmx.pmxgentop.Pmxgentop>` class and
     execute the :meth:`launch() <pmx.pmxgentop.Pmxgentop.launch> method."""
 

biobb_pmx/pmxbiobb/pmxligand_hybrid.py

@@ -6,7 +6,8 @@
 from pathlib import Path
 import shutil
 import argparse
-from typing import Dict, Optional
+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.file_utils import launchlogger
@@ -84,7 +85,7 @@ class Pmxligand_hybrid(BiobbObject):
     def __init__(self, input_structure1_path: str, input_structure2_path: str, input_topology1_path: str, input_topology2_path: str,
                  output_log_path: str, output_structure1_path: str, output_structure2_path: str, output_topology_path: str, output_atomtypes_path: str,
                  input_scaffold1_path: Optional[str] = None, input_scaffold2_path: Optional[str] = None, input_pairs_path: Optional[str] = None,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
 
         properties = properties or {}
 
@@ -209,7 +210,7 @@ def launch(self) -> int:
 def pmxligand_hybrid(input_structure1_path: str, input_structure2_path: str, input_topology1_path: str, input_topology2_path: str,
                      output_log_path: str, output_structure1_path: str, output_structure2_path: str, output_topology_path: str, output_atomtypes_path: str,
                      input_scaffold1_path: Optional[str] = None, input_scaffold2_path: Optional[str] = None, input_pairs_path: Optional[str] = None,
-                     properties: Optional[Dict] = None, **kwargs) -> int:
+                     properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pmxligand_hybrid <pmx.pmxmutate.Pmxligand_hybrid>` class and
     execute the :meth:`launch() <pmx.pmxligand_hybrid.Pmxligand_hybrid.launch> method."""
 

biobb_pmx/pmxbiobb/pmxmerge_ff.py

@@ -6,8 +6,9 @@
 from pathlib import Path
 import glob
 import argparse
+from typing import Optional
 from pmx import ligand_alchemy  # type: ignore
-from typing import Dict, 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
@@ -57,7 +58,7 @@ class Pmxmerge_ff(BiobbObject):
 
     """
 
-    def __init__(self, input_topology_path: str, output_topology_path: str, properties: Optional[Dict] = None, **kwargs) -> None:
+    def __init__(self, input_topology_path: str, output_topology_path: str, properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -128,7 +129,7 @@ def launch(self) -> int:
         return self.return_code
 
 
-def pmxmerge_ff(input_topology_path: str, output_topology_path: str, properties: Optional[Dict] = None, **kwargs) -> int:
+def pmxmerge_ff(input_topology_path: str, output_topology_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pmxmerge_ff <pmx.pmxmerge_ff.Pmxmerge_ff>` class and
     execute the :meth:`launch() <pmx.pmxmerge_ff.Pmxmerge_ff.launch> method."""
 

biobb_pmx/pmxbiobb/pmxmutate.py

@@ -6,7 +6,8 @@
 import sys
 import shutil
 import argparse
-from typing import Dict, Optional
+from typing import Optional
+from typing import Optional
 from biobb_pmx.pmxbiobb.common import create_mutations_file, MUTATION_DICT
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -66,7 +67,7 @@ class Pmxmutate(BiobbObject):
     """
 
     def __init__(self, input_structure_path: str, output_structure_path: str, input_b_structure_path: Optional[str] = None,
-                 properties: Optional[Dict] = None, **kwargs) -> None:
+                 properties: Optional[dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -158,7 +159,7 @@ def launch(self) -> int:
 
 
 def pmxmutate(input_structure_path: str, output_structure_path: str,
-              input_b_structure_path: Optional[str] = None, properties: Optional[Dict] = None,
+              input_b_structure_path: Optional[str] = None, properties: Optional[dict] = None,
               **kwargs) -> int:
     """Execute the :class:`Pmxmutate <pmx.pmxmutate.Pmxmutate>` class and
     execute the :meth:`launch() <pmx.pmxmutate.Pmxmutate.launch> method."""