[FIX] Fix all type hints of the project

biobb_haddock/haddock/__init__.py

@@ -5,6 +5,7 @@
 from . import rigid_body
 from . import sele_top
 from . import topology
+from . import sele_top_clusts
 
 name = "haddock"
 __all__ = ["capri_eval", "clust_fcc", "em_ref", "flex_ref", "rigid_body", "sele_top_clusts", "sele_top", "topology"]

biobb_haddock/haddock/capri_eval.py

@@ -4,6 +4,7 @@
 import argparse
 import shutil
 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
@@ -58,8 +59,8 @@ class CapriEval(BiobbObject):
     """
 
     def __init__(self, input_haddock_wf_data_zip: str, output_evaluation_zip_path: str,
-                 reference_pdb_path: str = None, output_haddock_wf_data_zip: str = None,
-                 haddock_config_path: str = None, properties: dict = None, **kwargs) -> None:
+                 reference_pdb_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+                 haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -118,11 +119,11 @@ def launch(self) -> int:
         if self.container_path:
             fu.log('Container execution enabled', self.out_log)
 
-            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir"))
+            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir", ''))
             self.output_cfg_path = str(Path(self.container_volume_path).joinpath(Path(self.output_cfg_path).name))
 
-            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name)))
-            run_dir = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name))
+            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir", '')).joinpath(Path(run_dir).name)))
+            run_dir = str(Path(self.stage_io_dict.get("unique_dir", '')).joinpath(Path(run_dir).name))
 
         self.cmd = [self.binary_path, self.output_cfg_path, '--extend-run', run_dir]
 
@@ -151,9 +152,9 @@ def launch(self) -> int:
 
 
 def capri_eval(input_haddock_wf_data_zip: str, output_evaluation_zip_path: str,
-               reference_pdb_path: str = None, output_haddock_wf_data_zip: str = None,
-               haddock_config_path: str = None,
-               properties: dict = None, **kwargs) -> int:
+               reference_pdb_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+               haddock_config_path: Optional[str] = None,
+               properties: Optional[Dict] = None, **kwargs) -> int:
     """Create :class:`haddock <haddock.haddock.haddock>` class and
     execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
 

biobb_haddock/haddock/clust_fcc.py

@@ -4,6 +4,7 @@
 import argparse
 import shutil
 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
@@ -57,8 +58,8 @@ class ClustFCC(BiobbObject):
     """
 
     def __init__(self, input_haddock_wf_data_zip: str, output_cluster_zip_path: str,
-                 output_haddock_wf_data_zip: str = None, haddock_config_path: str = None,
-                 properties: dict = None, **kwargs) -> None:
+                 output_haddock_wf_data_zip: Optional[str] = None, haddock_config_path: Optional[str] = None,
+                 properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -111,11 +112,11 @@ def launch(self) -> int:
         if self.container_path:
             fu.log('Container execution enabled', self.out_log)
 
-            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir"))
+            shutil.copy2(self.output_cfg_path, str(self.stage_io_dict.get("unique_dir", "")))
             self.output_cfg_path = str(Path(self.container_volume_path).joinpath(Path(self.output_cfg_path).name))
 
-            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name)))
-            run_dir = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name))
+            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir", '')).joinpath(Path(run_dir).name)))
+            run_dir = str(Path(self.stage_io_dict.get("unique_dir", '')).joinpath(Path(run_dir).name))
 
         self.cmd = [self.binary_path, self.output_cfg_path, '--extend-run', run_dir]
 
@@ -144,8 +145,8 @@ def launch(self) -> int:
 
 
 def clust_fcc(input_haddock_wf_data_zip: str, output_cluster_zip_path: str,
-              output_haddock_wf_data_zip: str = None, haddock_config_path: str = None,
-              properties: dict = None, **kwargs) -> int:
+              output_haddock_wf_data_zip: Optional[str] = None, haddock_config_path: Optional[str] = None,
+              properties: Optional[Dict] = None, **kwargs) -> int:
     """Create :class:`haddock <haddock.haddock.haddock>` class and
     execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
 

biobb_haddock/haddock/common.py

@@ -1,17 +1,15 @@
 """ Common functions for package biobb_haddock.haddock """
 import re
-# import uuid
-# import json
 import logging
-# from pathlib import Path
-from typing import List, Dict, Mapping  # , Union, Tuple, Sequence
+from typing import List, Dict, Optional, Any
 import biobb_common.tools.file_utils as fu
 
 
-def create_cfg(output_cfg_path: str, workflow_dict: Mapping[str, str], input_cfg_path: str = None, preset_dict: Mapping[str, str] = None,
-               cfg_properties_dict: Mapping[str, str] = None) -> str:
+def create_cfg(output_cfg_path: str, workflow_dict: Dict[str, Any],
+               input_cfg_path: Optional[str] = None, preset_dict: Optional[Dict[str, str]] = None,
+               cfg_properties_dict: Optional[Dict[str, str]] = None) -> str:
     """Creates an CFG file using the following hierarchy  cfg_properties_dict > input_cfg_path > preset_dict"""
-    cfg_dict: Mapping[str, str] = {}
+    cfg_dict: Dict[str, str] = {}
 
     if preset_dict:
         for k, v in preset_dict.items():
@@ -29,7 +27,7 @@ def create_cfg(output_cfg_path: str, workflow_dict: Mapping[str, str], input_cfg
     return write_cfg(output_cfg_path, workflow_dict, cfg_dict)
 
 
-def write_cfg(output_cfg_path: str, workflow_dict: Mapping[str, str], cfg_dict: Mapping[str, str]):
+def write_cfg(output_cfg_path: str, workflow_dict: Dict[str, str], cfg_dict: Dict[str, str]):
     cfg_list: List[str] = []
     if workflow_dict.get('run_dir'):
         cfg_list.append(f"run_dir = '{workflow_dict['run_dir']}'")
@@ -70,8 +68,8 @@ def read_cfg(input_mdp_path: str) -> Dict[str, str]:
     return cfg_dict
 
 
-def cfg_preset(haddock_step_name: str) -> Dict[str, str]:
-    cfg_dict = {}
+def cfg_preset(haddock_step_name: str) -> Dict[str, Any]:
+    cfg_dict: Dict[str, Any] = {}
     if not haddock_step_name:
         return cfg_dict
 
@@ -104,7 +102,7 @@ def cfg_preset(haddock_step_name: str) -> Dict[str, str]:
     return cfg_dict
 
 
-def unzip_workflow_data(zip_file: str, out_log: logging.Logger = None) -> str:
+def unzip_workflow_data(zip_file: str, out_log: Optional[logging.Logger] = None) -> str:
     """ Extract all files in the zip_file and return the directory.
 
     Args:

biobb_haddock/haddock/em_ref.py

@@ -5,6 +5,7 @@
 import argparse
 import shutil
 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
@@ -59,8 +60,8 @@ class EMRef(BiobbObject):
     """
 
     def __init__(self, input_haddock_wf_data_zip: str, refinement_output_zip_path: str,
-                 restraints_table_path: str = None, output_haddock_wf_data_zip: str = None,
-                 haddock_config_path: str = None, properties: dict = None, **kwargs) -> None:
+                 restraints_table_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+                 haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -118,11 +119,11 @@ def launch(self) -> int:
         if self.container_path:
             fu.log('Container execution enabled', self.out_log)
 
-            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir"))
+            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir", ""))
             self.output_cfg_path = str(Path(self.container_volume_path).joinpath(Path(self.output_cfg_path).name))
 
-            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name)))
-            run_dir = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name))
+            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name)))
+            run_dir = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name))
 
         self.cmd = [self.binary_path, self.output_cfg_path, '--extend-run', run_dir]
 
@@ -152,8 +153,8 @@ def launch(self) -> int:
 
 
 def em_ref(input_haddock_wf_data_zip: str, refinement_output_zip_path: str,
-           restraints_table_path: str = None, output_haddock_wf_data_zip: str = None,
-           haddock_config_path: str = None, properties: dict = None, **kwargs) -> int:
+           restraints_table_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+           haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> int:
     """Create :class:`haddock <haddock.haddock.haddock>` class and
     execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
 

biobb_haddock/haddock/flex_ref.py

@@ -5,6 +5,7 @@
 import argparse
 import shutil
 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
@@ -59,8 +60,8 @@ class FlexRef(BiobbObject):
     """
 
     def __init__(self, input_haddock_wf_data_zip: str, refinement_output_zip_path: str,
-                 restraints_table_path: str = None, output_haddock_wf_data_zip: str = None,
-                 haddock_config_path: str = None, properties: dict = None, **kwargs) -> None:
+                 restraints_table_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+                 haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -118,11 +119,11 @@ def launch(self) -> int:
         if self.container_path:
             fu.log('Container execution enabled', self.out_log)
 
-            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir"))
+            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir", ""))
             self.output_cfg_path = str(Path(self.container_volume_path).joinpath(Path(self.output_cfg_path).name))
 
-            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name)))
-            run_dir = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name))
+            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name)))
+            run_dir = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name))
 
         self.cmd = [self.binary_path, self.output_cfg_path, '--extend-run', run_dir]
 
@@ -152,8 +153,8 @@ def launch(self) -> int:
 
 
 def flex_ref(input_haddock_wf_data_zip: str, refinement_output_zip_path: str,
-             restraints_table_path: str = None, output_haddock_wf_data_zip: str = None,
-             haddock_config_path: str = None, properties: dict = None, **kwargs) -> int:
+             restraints_table_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+             haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> int:
     """Create :class:`haddock <haddock.haddock.haddock>` class and
     execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
 

biobb_haddock/haddock/rigid_body.py

@@ -6,6 +6,7 @@
 import argparse
 import shutil
 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
@@ -62,9 +63,9 @@ class RigidBody(BiobbObject):
     """
 
     def __init__(self, input_haddock_wf_data_zip: str, docking_output_zip_path: str,
-                 ambig_restraints_table_path: str = None, unambig_restraints_table_path: str = None,
-                 hb_restraints_table_path: str = None, output_haddock_wf_data_zip: str = None,
-                 haddock_config_path: str = None, properties: dict = None, **kwargs) -> None:
+                 ambig_restraints_table_path: Optional[str] = None, unambig_restraints_table_path: Optional[str] = None,
+                 hb_restraints_table_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+                 haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -131,11 +132,11 @@ def launch(self) -> int:
         if self.container_path:
             fu.log('Container execution enabled', self.out_log)
 
-            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir"))
+            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir", ""))
             self.output_cfg_path = str(Path(self.container_volume_path).joinpath(Path(self.output_cfg_path).name))
 
-            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name)))
-            run_dir = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name))
+            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name)))
+            run_dir = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name))
 
         self.cmd = [self.binary_path, self.output_cfg_path, '--extend-run', run_dir]
 
@@ -165,10 +166,10 @@ def launch(self) -> int:
 
 
 def rigid_body(input_haddock_wf_data_zip: str, docking_output_zip_path: str,
-               ambig_restraints_table_path: str = None, unambig_restraints_table_path: str = None,
-               hb_restraints_table_path: str = None, output_haddock_wf_data_zip: str = None,
-               haddock_config_path: str = None,
-               properties: dict = None, **kwargs) -> int:
+               ambig_restraints_table_path: Optional[str] = None, unambig_restraints_table_path: Optional[str] = None,
+               hb_restraints_table_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+               haddock_config_path: Optional[str] = None,
+               properties: Optional[Dict] = None, **kwargs) -> int:
     """Create :class:`haddock <haddock.haddock.haddock>` class and
     execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""
 

biobb_haddock/haddock/sele_top.py

@@ -4,6 +4,7 @@
 import argparse
 import shutil
 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
@@ -57,8 +58,8 @@ class SeleTop(BiobbObject):
     """
 
     def __init__(self, input_haddock_wf_data_zip: str, output_selection_zip_path: str,
-                 reference_pdb_path: str = None, output_haddock_wf_data_zip: str = None,
-                 haddock_config_path: str = None, properties: dict = None, **kwargs) -> None:
+                 reference_pdb_path: Optional[str] = None, output_haddock_wf_data_zip: Optional[str] = None,
+                 haddock_config_path: Optional[str] = None, properties: Optional[Dict] = None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -111,11 +112,11 @@ def launch(self) -> int:
         if self.container_path:
             fu.log('Container execution enabled', self.out_log)
 
-            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir"))
+            shutil.copy2(self.output_cfg_path, self.stage_io_dict.get("unique_dir", ""))
             self.output_cfg_path = str(Path(self.container_volume_path).joinpath(Path(self.output_cfg_path).name))
 
-            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name)))
-            run_dir = str(Path(self.stage_io_dict.get("unique_dir")).joinpath(Path(run_dir).name))
+            shutil.copytree(run_dir, str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name)))
+            run_dir = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(run_dir).name))
 
         self.cmd = [self.binary_path, self.output_cfg_path, '--extend-run', run_dir]
 
@@ -144,8 +145,8 @@ def launch(self) -> int:
 
 
 def sele_top(input_haddock_wf_data_zip: str, output_selection_zip_path: str,
-             output_haddock_wf_data_zip: str = None, haddock_config_path: str = None,
-             properties: dict = None, **kwargs) -> int:
+             output_haddock_wf_data_zip: Optional[str] = None, haddock_config_path: Optional[str] = None,
+             properties: Optional[Dict] = None, **kwargs) -> int:
     """Create :class:`haddock <haddock.haddock.haddock>` class and
     execute the :meth:`launch() <haddock.haddock.haddock.launch>` method."""