Small formatting changes to make them more consistent

src/aiida_lammps/parsers/base.py

@@ -7,7 +7,7 @@
 import glob
 import os
 import time
-from typing import Union
+from typing import Any, Dict, List, Union
 
 from aiida import orm
 from aiida.common import exceptions
@@ -178,8 +178,8 @@ def parse(self, **kwargs):
 
     def parse_restartfile(
         self,
-        parameters: dict,
-        list_of_files: list,
+        parameters: Dict[str, Any],
+        list_of_files: List[str],
         temp_folder: Union[os.PathLike, str, None],
     ) -> str:
         """
@@ -247,8 +247,8 @@ def parse_restartfile(
                 self.out("restartfile", restart_file)
         return restart_filename
 
-    def check_convergence(self, global_data: dict):
-        """Check for the convergence of the calculaiton in the case of a minimization run"""
+    def check_convergence(self, global_data: Dict[str, Any]):
+        """Check for the convergence of the calculation in the case of a minimization run"""
         _etol = global_data.get("minimization", {}).get(
             "energy_relative_difference", None
         )

src/aiida_lammps/parsers/inputfile.py

@@ -14,7 +14,7 @@
 import json
 import os
 import re
-from typing import Any, Dict, Optional, Union
+from typing import Any, Dict, List, Optional, Union
 
 from aiida import orm
 import numpy as np
@@ -173,7 +173,7 @@ def generate_input_file(
     return input_file
 
 
-def write_control_block(parameters_control: dict) -> str:
+def write_control_block(parameters_control: Dict[str, Any]) -> str:
     """
     Generate the input block with global control options.
 
@@ -214,7 +214,7 @@ def write_control_block(parameters_control: dict) -> str:
 def write_potential_block(
     potential: LammpsPotentialData,
     structure: orm.StructureData,
-    parameters_potential: dict,
+    parameters_potential: Dict[str, Any],
     potential_file: str,
 ) -> str:
     """
@@ -341,7 +341,7 @@ def write_structure_block(
     return structure_block, group_names
 
 
-def write_minimize_block(parameters_minimize: dict) -> str:
+def write_minimize_block(parameters_minimize: Dict[str, Union[str, float, int]]) -> str:
     """
     Generate the input block with the minimization options.
 
@@ -367,7 +367,7 @@ def write_minimize_block(parameters_minimize: dict) -> str:
     return minimize_block
 
 
-def write_md_block(parameters_md: dict) -> str:
+def write_md_block(parameters_md: Dict[str, Any]) -> str:
     """
     Generate the input block with the MD options.
 
@@ -416,7 +416,7 @@ def write_md_block(parameters_md: dict) -> str:
 
 
 def write_final_variables_block(
-    fixed_thermo: list,
+    fixed_thermo: List[str],
     final_file: str = "aiida_lammps.yaml",
 ) -> str:
     """
@@ -455,7 +455,7 @@ def write_final_variables_block(
     return variables_block
 
 
-def generate_velocity_string(parameters_velocity: dict) -> str:
+def generate_velocity_string(parameters_velocity: Dict[str, Any]) -> str:
     """
     Generate the velocity string for the MD block.
 
@@ -497,7 +497,7 @@ def generate_velocity_string(parameters_velocity: dict) -> str:
     return options
 
 
-def generate_velocity_options(options_velocity: dict) -> str:
+def generate_velocity_options(options_velocity: Dict[str, Any]) -> str:
     """
     Generate the options string for every velocity.
 
@@ -520,7 +520,7 @@ def generate_velocity_options(options_velocity: dict) -> str:
 
 def generate_integration_options(
     style: str,
-    integration_parameters: dict,
+    integration_parameters: Dict[str, Any],
 ) -> str:
     """
     Create a string with the integration options.
@@ -639,8 +639,8 @@ def generate_integration_options(
 
 
 def write_fix_block(
-    parameters_fix: dict,
-    group_names: list = None,
+    parameters_fix: Dict[str, Any],
+    group_names: Optional[List[str]] = None,
 ) -> str:
     """
     Generate the input block with the fix options.
@@ -683,8 +683,8 @@ def write_fix_block(
 
 
 def write_compute_block(
-    parameters_compute: dict,
-    group_names: list = None,
+    parameters_compute: Dict[str, Any],
+    group_names: Optional[List[str]] = None,
 ) -> str:
     """
     Generate the input block with the compute options.
@@ -719,11 +719,11 @@ def write_compute_block(
 
 
 def write_dump_block(
-    parameters_dump: dict,
+    parameters_dump: Dict[str, Any],
     trajectory_filename: str,
     atom_style: str,
-    parameters_compute: dict = None,
-    kind_symbols: list = None,
+    parameters_compute: Optional[Dict[str, Any]] = None,
+    kind_symbols: Optional[List[str]] = None,
 ) -> str:
     """Generate the block with dumps commands.
 
@@ -785,9 +785,9 @@ def write_dump_block(
 
 
 def write_thermo_block(
-    parameters_thermo: dict,
-    parameters_compute: dict = None,
-) -> Union[str, list]:
+    parameters_thermo: Dict[str, Any],
+    parameters_compute: Optional[Dict[str, Any]] = None,
+) -> Union[str, List[str]]:
     """Generate the block with the thermo command.
 
     This will take all the global computes which were generated during the calculation
@@ -858,8 +858,8 @@ def write_thermo_block(
 
 
 def write_restart_block(
-    parameters_restart: dict, restart_filename: str, max_number_steps: int
-) -> dict:
+    parameters_restart: Dict[str, Any], restart_filename: str, max_number_steps: int
+) -> Dict[str, Any]:
     """Generate the block to write the restart file.
 
     :param parameters_restart: set of parameters controlling the printing of the restartfile
@@ -978,7 +978,7 @@ def generate_printing_string(
     return " ".join(_string)
 
 
-def generate_id_tag(name: str = None, group: str = None) -> str:
+def generate_id_tag(name: Optional[str] = None, group: Optional[str] = None) -> str:
     """Generate an id tag for fixes and/or computes.
 
     To standardize the naming of computes and/or fixes and to ensure that one
@@ -998,7 +998,7 @@ def generate_id_tag(name: str = None, group: str = None) -> str:
     return f"{name.replace('/','_')}_{group}_aiida"
 
 
-def join_keywords(value: list) -> str:
+def join_keywords(value: List[Any]) -> str:
     """
     Generate a string for the compute/fix options.