[FIX] Fix type Hinting

biobb_gromacs/gromacs/editconf.py

@@ -131,7 +131,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(str(self.stage_io_dict.get("unique_dir")))
+        self.tmp_files.append(str(self.stage_io_dict.get("unique_dir", "")))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_gromacs/gromacs/genion.py

@@ -117,7 +117,7 @@ def launch(self) -> int:
         top_dir = str(Path(top_file).parent)
 
         if self.container_path:
-            shutil.copytree(top_dir, Path(str(self.stage_io_dict.get("unique_dir"))).joinpath(Path(top_dir).name))
+            shutil.copytree(top_dir, Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(Path(top_dir).name))
             top_file = str(Path(self.container_volume_path).joinpath(Path(top_dir).name, Path(top_file).name))
 
         self.cmd = [str(self.binary_path), 'genion',
@@ -156,15 +156,15 @@ def launch(self) -> int:
         self.copy_to_host()
 
         if self.container_path:
-            top_file = str(Path(str(self.stage_io_dict.get("unique_dir"))).joinpath(Path(top_dir).name, Path(top_file).name))
+            top_file = str(Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(Path(top_dir).name, Path(top_file).name))
 
         # zip topology
         fu.log('Compressing topology to: %s' % self.stage_io_dict["out"]["output_top_zip_path"],
                self.out_log, self.global_log)
         fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=top_file, out_log=self.out_log)
 
         # Remove temporal files
-        self.tmp_files.extend([str(self.stage_io_dict.get("unique_dir")), top_dir, str(self.io_dict['in'].get("stdin_file_path"))])
+        self.tmp_files.extend([str(self.stage_io_dict.get("unique_dir", "")), top_dir, str(self.io_dict['in'].get("stdin_file_path"))])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=True)

biobb_gromacs/gromacs/genrestr.py

@@ -128,7 +128,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([str(self.stage_io_dict.get("unique_dir")), str(self.io_dict['in'].get("stdin_file_path"))])
+        self.tmp_files.extend([str(self.stage_io_dict.get("unique_dir", "")), str(self.io_dict['in'].get("stdin_file_path"))])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_gromacs/gromacs/gmxselect.py

@@ -3,6 +3,7 @@
 """Module containing the Select class and the command line interface."""
 import argparse
 from pathlib import Path
+from typing import Optional, Dict
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
@@ -53,8 +54,8 @@ class Gmxselect(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: str = None,
-                 properties: dict = None, **kwargs) -> None:
+    def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None,
+                 properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -123,20 +124,20 @@ def launch(self) -> int:
                 fu.log(f"Appending {self.io_dict['in'].get('input_ndx_path')} to {self.io_dict['out']['output_ndx_path']}", self.out_log, self.global_log)
                 with open(self.io_dict["out"]["output_ndx_path"], 'a') as out_ndx_file:
                     out_ndx_file.write('\n')
-                    with open(self.io_dict["in"].get("input_ndx_path")) as in_ndx_file:
+                    with open(self.io_dict["in"].get("input_ndx_path", '')) as in_ndx_file:
                         for line in in_ndx_file:
                             out_ndx_file.write(line)
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
+        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ''))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
         return self.return_code
 
 
 def gmxselect(input_structure_path: str, output_ndx_path: str,
-              input_ndx_path: str = None, properties: 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

@@ -3,7 +3,7 @@
 """Module containing the Grompp class and the command line interface."""
 import argparse
 import shutil
-from typing import Optional
+from typing import Optional, Dict
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -69,7 +69,7 @@ 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: dict = None, **kwargs) -> None:
+                 properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -120,12 +120,12 @@ def launch(self) -> int:
         self.stage_files()
 
         # Unzip topology to topology_out
-        top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log, unique_dir=self.stage_io_dict.get("unique_dir"))
+        top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log, unique_dir=self.stage_io_dict.get("unique_dir", ""))
 
         # Create MDP file
-        self.output_mdp_path = create_mdp(output_mdp_path=str(Path(self.stage_io_dict.get("unique_dir")).joinpath(self.output_mdp_path)),
+        self.output_mdp_path = create_mdp(output_mdp_path=str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(self.output_mdp_path)),
                                           input_mdp_path=self.io_dict["in"]["input_mdp_path"],
-                                          preset_dict=mdp_preset(self.simulation_type),
+                                          preset_dict=mdp_preset(str(self.simulation_type)),
                                           mdp_properties_dict=self.mdp)
 
         # Copy extra files to container: MDP file and topology folder
@@ -145,15 +145,15 @@ def launch(self) -> int:
         if self.stage_io_dict["in"].get("input_cpt_path") and Path(self.stage_io_dict["in"]["input_cpt_path"]).exists():
             self.cmd.append('-t')
             if self.container_path:
-                shutil.copy2(self.stage_io_dict["in"]["input_cpt_path"], self.stage_io_dict.get("unique_dir"))
+                shutil.copy2(self.stage_io_dict["in"]["input_cpt_path"], self.stage_io_dict.get("unique_dir", ""))
                 self.cmd.append(str(Path(self.container_volume_path).joinpath(Path(self.stage_io_dict["in"]["input_cpt_path"]).name)))
             else:
                 self.cmd.append(self.stage_io_dict["in"]["input_cpt_path"])
         if self.stage_io_dict["in"].get("input_ndx_path") and Path(self.stage_io_dict["in"]["input_ndx_path"]).exists():
             self.cmd.append('-n')
             if self.container_path:
-                shutil.copy2(self.stage_io_dict["in"]["input_ndx_path"], self.stage_io_dict.get("unique_dir"))
-                self.cmd.append(Path(self.container_volume_path).joinpath(Path(self.stage_io_dict["in"]["input_ndx_path"]).name))
+                shutil.copy2(self.stage_io_dict["in"]["input_ndx_path"], self.stage_io_dict.get("unique_dir", ""))
+                self.cmd.append(str(Path(self.container_volume_path).joinpath(Path(self.stage_io_dict["in"]["input_ndx_path"]).name)))
             else:
                 self.cmd.append(self.stage_io_dict["in"]["input_ndx_path"])
 
@@ -167,7 +167,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), 'mdout.mdp'])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ''), 'mdout.mdp'])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_gromacs/gromacs/grompp_mdrun.py

@@ -2,7 +2,7 @@
 
 """Module containing the GromppMDrun class and the command line interface."""
 import argparse
-from typing import Optional
+from typing import Optional, Dict
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -137,14 +137,14 @@ def launch(self) -> int:
 
         fu.log('Calling Grompp class', self.out_log, self.global_log)
         grompp_return_code = grompp(input_gro_path=self.input_gro_path, input_top_zip_path=self.input_top_zip_path,
-                                    output_tpr_path=self.output_tpr_path, input_cpt_path=self.input_cpt_path,
+                                    output_tpr_path=self.output_tpr_path, input_cpt_path=self.input_cpt_path,  # type: ignore
                                     input_ndx_path=self.input_ndx_path, input_mdp_path=self.input_mdp_path,
                                     properties=self.properties_grompp)
         fu.log(f'Grompp return code: {grompp_return_code}', self.out_log, self.global_log)
 
         if not grompp_return_code:
             fu.log('Grompp return code is correct. Calling MDRun class', self.out_log, self.global_log)
-            mdrun_return_code = mdrun(input_tpr_path=self.output_tpr_path, output_trr_path=self.output_trr_path,
+            mdrun_return_code = mdrun(input_tpr_path=self.output_tpr_path, output_trr_path=self.output_trr_path,  # type: ignore
                                       output_gro_path=self.output_gro_path, output_edr_path=self.output_edr_path,
                                       output_log_path=self.output_log_path, output_xtc_path=self.output_xtc_path,
                                       output_cpt_path=self.output_cpt_path, output_dhdl_path=self.output_dhdl_path,
@@ -154,7 +154,7 @@ def launch(self) -> int:
             return 1
 
         # Remove temporal files
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), Path(self.output_tpr_path).parent])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ''), Path(str(self.output_tpr_path)).parent])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -165,7 +165,7 @@ 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: 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

@@ -3,6 +3,7 @@
 """Module containing the MakeNdx class and the command line interface."""
 import argparse
 from pathlib import Path
+from typing import Optional, Dict
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
@@ -52,8 +53,8 @@ class MakeNdx(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: str = None,
-                 properties: dict = None, **kwargs) -> None:
+    def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None,
+                 properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -122,15 +123,15 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), self.io_dict['in'].get("stdin_file_path")])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), self.io_dict['in'].get("stdin_file_path", '')])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
         return self.return_code
 
 
 def make_ndx(input_structure_path: str, output_ndx_path: str,
-             input_ndx_path: str = None, properties: 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

@@ -215,7 +215,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
+        self.tmp_files.append(self.stage_io_dict.get("unique_dir", ""))
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)

biobb_gromacs/gromacs/pdb2gmx.py

@@ -3,12 +3,12 @@
 """Module containing the Pdb2gmx class and the command line interface."""
 import os
 import argparse
+from typing import Optional, Dict
 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
 
 
 class Pdb2gmx(BiobbObject):
@@ -141,23 +141,23 @@ def launch(self) -> int:
         self.copy_to_host()
 
         if self.container_path:
-            internal_top_name = os.path.join(self.stage_io_dict.get("unique_dir"), internal_top_name)
+            internal_top_name = os.path.join(self.stage_io_dict.get("unique_dir", ""), internal_top_name)
 
         # zip topology
         fu.log('Compressing topology to: %s' % self.io_dict["out"]["output_top_zip_path"], self.out_log,
                self.global_log)
         fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=internal_top_name, out_log=self.out_log)
 
         # Remove temporal files
-        self.tmp_files.extend([self.internal_top_name, self.internal_itp_name, self.stage_io_dict.get("unique_dir"), self.io_dict['in'].get("stdin_file_path")])
+        self.tmp_files.extend([self.internal_top_name, self.internal_itp_name, self.stage_io_dict.get("unique_dir", ""), self.io_dict['in'].get("stdin_file_path", "")])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
         return self.return_code
 
 
 def pdb2gmx(input_pdb_path: str, output_gro_path: str, output_top_zip_path: str,
-            properties: 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

@@ -4,6 +4,7 @@
 import shutil
 import argparse
 from pathlib import Path
+from typing import Optional, Dict
 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 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: str = None, properties: 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
@@ -110,7 +111,7 @@ def launch(self) -> int:
         top_dir = str(Path(top_file).parent)
 
         if self.container_path:
-            shutil.copytree(top_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(top_dir).name)))
+            shutil.copytree(top_dir, str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(top_dir).name)))
             top_file = str(Path(self.container_volume_path).joinpath(Path(top_dir).name, Path(top_file).name))
 
         self.cmd = [self.binary_path, 'solvate',
@@ -133,23 +134,23 @@ def launch(self) -> int:
         self.copy_to_host()
 
         if self.container_path:
-            top_file = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(top_dir).name, Path(top_file).name))
+            top_file = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(top_dir).name, Path(top_file).name))
 
         # zip topology
         fu.log('Compressing topology to: %s' % self.stage_io_dict["out"]["output_top_zip_path"], self.out_log,
                self.global_log)
         fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=top_file, out_log=self.out_log)
 
         # Remove temporal files
-        self.tmp_files.extend([self.stage_io_dict.get("unique_dir"), top_dir])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), top_dir])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
         return self.return_code
 
 
 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: str = None, properties: 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."""