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

.github/env.yaml

@@ -4,5 +4,5 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==4.2.0
+  - biobb_common ==5.0.0
   - cp2k ==7.1.0

biobb_cp2k/cp2k/cp2k_prep.py

@@ -3,6 +3,7 @@
 """Module containing the Cp2kPrep class and the command line interface."""
 import argparse
 from typing import Optional
+from typing import Any
 import os
 import collections.abc
 from pathlib import Path
@@ -127,9 +128,9 @@ def iterdict(self, d, depth, fileout_h):
                     print(' ' * depth, k.upper(), v, file=fileout_h)
 
     # global dict3 = {}
-    def parse_rec_def(self, cp2k_in_array, index, stop):
-        dict = {}
-        dict2 = {}
+    def parse_rec_def(self, cp2k_in_array: list[Any], index: int, stop: str) -> dict[Any, Any]:
+        dict_var: dict[Any, Any] = {}
+        dict_var2: dict[Any, Any] = {}
         depth = 0
         rec = False
         for line in cp2k_in_array[index:]:
@@ -142,49 +143,49 @@ def parse_rec_def(self, cp2k_in_array, index, stop):
                 vals = line.lstrip().split()
 
                 if depth < 0:
-                    return dict
+                    return dict_var
             elif '&' in line:
                 depth = depth + 1
                 if depth == 1:
                     vals = line.lstrip().split()
                     key = vals[0].replace('&', '')
                     if (key == 'KIND'):
                         key_name = key + "-" + vals[1]
-                        if dict.get(key):
-                            dict[key].append(self.parse_rec_def(cp2k_in_array, index, key_name))
+                        if dict_var.get(key):
+                            dict_var[key].append(self.parse_rec_def(cp2k_in_array, index, key_name))
                         else:
-                            dict[key] = []
-                            dict[key].append(self.parse_rec_def(cp2k_in_array, index, key_name))
+                            dict_var[key] = []
+                            dict_var[key].append(self.parse_rec_def(cp2k_in_array, index, key_name))
                     else:
                         rec = True
-                        dict[key] = self.parse_rec_def(cp2k_in_array, index, key)
+                        dict_var[key] = self.parse_rec_def(cp2k_in_array, index, key)
                         if len(vals) > 1 and key != 'KIND':
-                            # print(stop + " Add dict[key]['name'] = " + str(vals[1].strip()))
-                            dict[key]['name'] = vals[1].strip()
+                            # print(stop + " Add dict_var[key]['name'] = " + str(vals[1].strip()))
+                            dict_var[key]['name'] = vals[1].strip()
 
             elif not rec:
                 vals = line.lstrip().split()
-                # print(stop + " Add dict[" + str(vals[0]) + "] = " + str(vals[1].strip()))
+                # print(stop + " Add dict_var[" + str(vals[0]) + "] = " + str(vals[1].strip()))
                 if (stop == 'COORD'):
-                    if dict2.get('coords_list'):
-                        dict2['coords_list'].append({vals[0]: vals[1:]})
+                    if dict_var2.get('coords_list'):
+                        dict_var2['coords_list'].append({vals[0]: vals[1:]})
                     else:
-                        dict2['coords_list'] = []
-                        dict2['coords_list'].append({vals[0]: vals[1:]})
+                        dict_var2['coords_list'] = []
+                        dict_var2['coords_list'].append({vals[0]: vals[1:]})
 
-                    dict = dict2['coords_list']
+                    dict_var = dict_var2['coords_list']  # type: ignore
                 elif (len(vals) == 2):
                     if (stop.startswith('KIND-')):
                         key2, name = stop.split('-')
-                        dict['name'] = name
-                    dict[vals[0]] = vals[1].strip()
+                        dict_var['name'] = name
+                    dict_var[vals[0]] = vals[1].strip()
                 else:
-                    dict[vals[0]] = vals[1:]
+                    dict_var[vals[0]] = vals[1:]
 
-        return dict
+        return dict_var
 
     def parse_pdb(self, pdb_file):
-        dict = {}
+        dict_var = {}
         # coord = {}
         coord = []
         cell = {}
@@ -237,11 +238,11 @@ def parse_pdb(self, pdb_file):
 
         cell['ABC'] = [str(box_x), str(box_y), str(box_z)]
 
-        dict['coord'] = coord
-        # dict['coords'] = coords
-        dict['cell'] = cell
+        dict_var['coord'] = coord
+        # dict_var['coords'] = coords
+        dict_var['cell'] = cell
 
-        return dict
+        return dict_var
 
     def merge(self, a, b):
         for key_b in b:
@@ -273,7 +274,7 @@ def merge(self, a, b):
         return a
 
     def replace_coords(self, a, b):
-        # dict['force_eval'] = {'subsys' : {'coord' : coord } }
+        # dict_var['force_eval'] = {'subsys' : {'coord' : coord } }
         print("BioBB_CP2K, replacing coordinates...")
         for key in a:
             if key.upper() == 'FORCE_EVAL':
@@ -364,7 +365,7 @@ def launch(self):
             print("Will take just the input_inp_path.")
         elif (self.simulation_type):
             # path_cp2k_in = PurePath(myself.__file__).parent
-            path_cp2k_in = Path(os.getenv("CONDA_PREFIX")).joinpath('cp2k_aux')
+            path_cp2k_in = Path(os.getenv("CONDA_PREFIX", "")).joinpath('cp2k_aux')
             if (self.simulation_type == 'energy'):
                 self.io_dict["in"]["input_inp_path"] = str(Path(path_cp2k_in).joinpath("cp2k_in/cp2k_energy.inp"))
             elif (self.simulation_type == 'geom_opt'):

biobb_cp2k/cp2k/cp2k_run.py

@@ -123,7 +123,7 @@ def launch(self):
         # set path to the CP2K parameter data files
         if not self.param_path:
             # os.environ["CP2K_DATA_DIR"] = str(PurePath(myself.__file__).parent.joinpath('cp2k_data'))
-            os.environ["CP2K_DATA_DIR"] = str(Path(os.getenv("CONDA_PREFIX")).joinpath('cp2k_aux').joinpath('cp2k_data'))
+            os.environ["CP2K_DATA_DIR"] = str(Path(os.getenv("CONDA_PREFIX", "")).joinpath('cp2k_aux').joinpath('cp2k_data'))
         else:
             if not Path(PurePath(self.param_path)).exists():
                 fu.log(self.__class__.__name__ + ': Unexisting  %s folder, exiting' % self.param_path, self.out_log)
@@ -167,7 +167,7 @@ def launch(self):
                 else:
                     out_files.append(self.tmp_folder + '/' + file)
 
-        fu.zip_list(self.output, out_files, self.out_log)
+        fu.zip_list(str(self.output), out_files, self.out_log)
 
         # Copy outputs from temporary folder to output path
         shutil.copy2(self.output, PurePath(self.io_dict["out"]["output_outzip_path"]))

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_cp2k",
-    version="4.2.0",
+    version="5.0.0",
     author="Biobb developers",
     author_email="[email protected]",
     description="Biobb_cp2k is a BioBB category for CP2K QM package.",
@@ -20,21 +20,19 @@
     packages=setuptools.find_packages(exclude=['docs', 'test']),
     package_data={'biobb_cp2k': ['py.typed']},
     include_package_data=True,
-    install_requires=['biobb_common==4.2.0'],
-    python_requires='>=3.8',
+    install_requires=['biobb_common==5.0.0'],
+    python_requires='>=3.9',
     entry_points={
         "console_scripts": [
             "cp2k_run = biobb_cp2k.cp2k.cp2k_run:main",
             "cp2k_prep = biobb_cp2k.cp2k.cp2k_prep:main"
         ]
     },
-    classifiers=(
-        "Development Status :: 3 - Alpha",
-        "Programming Language :: Python :: 3.8",
+    classifiers=[
+        "Development Status :: 5 - Production/Stable",
         "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
-        "Operating System :: POSIX",
-    ),
+        "Operating System :: POSIX"
+    ],
 )