[Typing](ALL): Update typing from python 3.8 style to python 3.9

.github/env.yaml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==4.2.0
+  - biobb_common ==5.0.0
   - mdanalysis >=2.0.0
-  - biobb_structure_checking ==3.13.4
+  - biobb_structure_checking ==3.13.5
   - cmip ==2.7.0

biobb_cmip/cmip/cmip_ignore_residues.py

@@ -96,7 +96,7 @@ def launch(self) -> int:
                     chain, resnum = residue_code_list
                 self.residue_list[i] = chain.strip().upper()+":"+str(resnum).strip()
 
-        mark_residues(residue_list=self.residue_list, input_cmip_pdb_path=self.io_dict["in"]["input_cmip_pdb_path"], output_cmip_pdb_path=self.io_dict["out"]["output_cmip_pdb_path"], out_log=self.out_log, global_log=self.global_log)
+        mark_residues(residue_list=self.residue_list or [], input_cmip_pdb_path=self.io_dict["in"]["input_cmip_pdb_path"], output_cmip_pdb_path=self.io_dict["out"]["output_cmip_pdb_path"], out_log=self.out_log, global_log=self.global_log)
 
         # remove temporary
         self.remove_tmp_files()

biobb_cmip/cmip/cmip_prepare_pdb.py

@@ -111,7 +111,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir")])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_cmip/cmip/cmip_run.py

@@ -5,6 +5,7 @@
 import json
 import argparse
 from typing import Optional
+from typing import Any
 import shutil
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
@@ -130,7 +131,7 @@ def launch(self) -> int:
                 raise ValueError(f"ERROR: output_pdb_path ({self.io_dict['out']['output_pdb_path']})"
                                  f"name must end in .pdb and not contain underscores")
 
-        params_preset_dict = params_preset(execution_type=self.execution_type)
+        params_preset_dict: dict[str, Any] = params_preset(execution_type=self.execution_type)
         if self.io_dict['in']["input_json_external_box_path"]:
             params_preset_dict["readgrid0"] = 0
             origin, size, grid_params = get_grid(self.io_dict['in']["input_json_external_box_path"])
@@ -159,7 +160,7 @@ def launch(self) -> int:
 
         # Restart OUT
         if self.io_dict["out"].get("output_rst_path"):
-            params_preset_dict['FULLRST'] = 1
+            params_preset_dict['FULLRST'] = 1  # type: ignore
             params_preset_dict['OREST'] = 1
 
         # Restart IN
@@ -187,7 +188,7 @@ def launch(self) -> int:
                     '-hs', self.stage_io_dict['in']['input_pdb_path']]
 
         if self.stage_io_dict["in"].get("input_probe_pdb_path") and Path(
-                self.io_dict["in"].get("input_probe_pdb_path")).exists():
+                self.io_dict["in"].get("input_probe_pdb_path", "")).exists():
             self.cmd.append('-pr')
             self.cmd.append(self.stage_io_dict["in"].get("input_probe_pdb_path"))
 
@@ -225,17 +226,17 @@ def launch(self) -> int:
         # CMIP removes or adds a .pdb extension from pdb output name
         # manual copy_to_host or unstage
         if self.io_dict['out'].get('output_pdb_path'):
-            output_pdb_path = str(Path(self.stage_io_dict["unique_dir"]).joinpath(Path(self.io_dict['out'].get('output_pdb_path')).name))
+            output_pdb_path = str(Path(self.stage_io_dict["unique_dir"]).joinpath(Path(self.io_dict['out'].get('output_pdb_path', '')).name))
             if Path(output_pdb_path[:-4]).exists():
-                shutil.move(output_pdb_path[:-4], self.io_dict['out'].get('output_pdb_path'))
+                shutil.move(output_pdb_path[:-4], self.io_dict['out'].get('output_pdb_path', ''))
             elif Path(output_pdb_path + ".pdb").exists():
-                shutil.move(output_pdb_path + ".pdb", self.io_dict['out'].get('output_pdb_path'))
+                shutil.move(output_pdb_path + ".pdb", self.io_dict['out'].get('output_pdb_path', ''))
             elif not Path(output_pdb_path).exists():
                 fu.log(f"WARNING: File not found output_pdb_path: {output_pdb_path}", self.out_log, self.global_log)
 
         # Replace "ATOMTM" tag for "ATOM  "
 
-        output_pdb_path = self.io_dict['out'].get('output_pdb_path')
+        output_pdb_path = self.io_dict['out'].get('output_pdb_path', '')
         if output_pdb_path:
             if Path(output_pdb_path).exists():
                 with open(output_pdb_path) as pdb_file:
@@ -261,7 +262,7 @@ def launch(self) -> int:
             grid_dict = {'origin': origin_dict,
                          'size': size_dict,
                          'params': grid_params}
-            with open(self.io_dict['out'].get('output_json_box_path'), 'w') as json_file:
+            with open(self.io_dict['out'].get('output_json_box_path', ''), 'w') as json_file:
                 json_file.write(json.dumps(grid_dict, indent=4))
 
         # Create external_json_box_path file from CMIP log file
@@ -279,14 +280,14 @@ def launch(self) -> int:
             grid_dict = {'origin': origin_dict,
                          'size': size_dict,
                          'params': grid_params}
-            with open(self.io_dict['out'].get('output_json_external_box_path'), 'w') as json_file:
+            with open(self.io_dict['out'].get('output_json_external_box_path', ''), 'w') as json_file:
                 json_file.write(json.dumps(grid_dict, indent=4))
 
         # Copy files to host
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), combined_params_dir])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), combined_params_dir])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_cmip/cmip/cmip_titration.py

@@ -4,6 +4,7 @@
 import os
 import argparse
 from typing import Optional
+from typing import Any
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -88,7 +89,7 @@ def __init__(self, input_pdb_path: str, output_pdb_path: str,
         self.output_params_path = properties.get('output_params_path', 'params')
         if not self.io_dict['in'].get('input_vdw_params_path'):
             self.io_dict['in']['input_vdw_params_path'] = f"{os.environ.get('CONDA_PREFIX')}/share/cmip/dat/vdwprm"
-        self.params = {k: str(v) for k, v in properties.get('params', dict()).items()}
+        self.params: dict[str, Any] = {k: str(v) for k, v in properties.get('params', dict()).items()}
         self.energy_cutoff = properties.get('energy_cutoff', 9999.9)
 
         # Check the properties
@@ -155,7 +156,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), combined_params_dir])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), combined_params_dir])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_cmip/cmip/common.py

@@ -146,7 +146,7 @@ def get_topology_cmip_elements_canonical(input_topology_filename: str) -> list:
     # mda_charges = [round(val, 4) for val in u.atoms.charges]
     # mda_atom_types = list(guess_types(u.atoms.names))
     mda_atom_types = []
-    for atom in u.atoms:
+    for atom in u.atoms:  # type: ignore
         atom_element = guess_atom_element(atom.name)
         if atom_element == 'H':
             bonded_atom_element = guess_atom_element(atom.bonded_atoms[0].name)
@@ -178,7 +178,7 @@ def get_topology_charges(input_topology_filename: str) -> list:
         os.unlink(top_file)
     else:
         u = mda.Universe(input_topology_filename)
-    return [round(val, 4) for val in u.atoms.charges]
+    return [round(val, 4) for val in u.atoms.charges]  # type: ignore
 
 
 class Residue:
@@ -241,7 +241,7 @@ def get_pdb_charges(input_pdb_filename: str, residue_library_path: Optional[str]
                 print(f"WARNING replacing {nomr[:-1]}:{line[23:27]} by {nomr}")
             ######################################################
             parms = aaLib.getParams(nomr, nomat)
-            charges_list.append(parms.charg)
+            charges_list.append(parms.charg)  # type: ignore
         return charges_list
 
 
@@ -278,7 +278,7 @@ def get_pdb_cmip_elements_canonical(input_pdb_filename: str, residue_library_pat
                 print(f"WARNING replacing {nomr[:-1]}:{line[23:27]} by {nomr}")
             ######################################################
             parms = aaLib.getParams(nomr, nomat)
-            elements_list.append(parms.atType)
+            elements_list.append(parms.atType)  # type: ignore
         return elements_list