[Feature] Adding typing annotations

biobb_common/configuration/settings.py

@@ -36,7 +36,7 @@
 import logging
 from pathlib import Path
 from biobb_common.tools import file_utils as fu
-from typing import Optional
+from typing import Dict, Any, Optional
 
 GALAXY_CHARACTER_MAP = {
     "__gt__": ">",
@@ -50,7 +50,7 @@
     "__cn__": "\n",
     "__cr__": "\r",
     "__tc__": "\t",
-    "__pd__": "#",
+    "__pd__": "#"
 }
 
 
@@ -114,9 +114,7 @@ def get_working_dir_path(self) -> str:
 
         return self.properties.get("working_dir_path")
 
-    def get_prop_dic(
-        self, prefix: Optional[str] = None, global_log: Optional[logging.Logger] = None
-    ) -> dict:
+    def get_prop_dic(self, prefix: Optional[str] = None, global_log: Optional[logging.Logger] = None) -> Dict[str, Any]:
         """get_prop_dic() returns the properties dictionary where keys are the
         step names in the configuration YAML file and every value contains another
         nested dictionary containing the keys and values of each step properties section.
@@ -136,7 +134,8 @@ def get_prop_dic(
         Returns:
             dict: Dictionary of properties.
         """
-        prop_dic = dict()
+
+        prop_dic: Dict[str, Any] = dict()
         prefix = "" if prefix is None else prefix.strip()
 
         # There is no step
@@ -311,7 +310,7 @@ def get_paths_dic(self, prefix: Optional[str] = None) -> dict:
                         prop_dic[key2] = str(
                             Path(
                                 self.properties[self.system]["working_dir_path"]
-                            ).joinpath(prefix, key, value)
+                            ).joinpath(prefix, key2, value)
                         )
                     else:
                         prop_dic[key2] = str(
@@ -322,9 +321,11 @@ def get_paths_dic(self, prefix: Optional[str] = None) -> dict:
 
         # Properties with step name
         else:
+
             for key in prop_dic:
                 for key2, value in prop_dic[key].items():
                     if isinstance(value, str) and value.startswith("dependency"):
+                        dependency_step = value.split("/")[1]
                         while isinstance(value, str) and value.startswith("dependency"):
                             dependency_step = value.split("/")[1]
                             value = prop_dic[value.split("/")[1]][value.split("/")[2]]

biobb_common/generic/biobb_object.py

@@ -3,14 +3,15 @@
 import importlib
 import difflib
 import typing
-from typing import Optional, Mapping, Set, Union, Dict, List
+from typing import Optional, Mapping, Set, Union, Dict, List, Any
 import warnings
 from pathlib import Path
 from sys import platform
 import shutil
 from pydoc import locate
 from biobb_common.tools import file_utils as fu
 from biobb_common.command_wrapper import cmd_wrapper
+from logging import Logger
 
 
 class BiobbObject:
@@ -36,59 +37,57 @@ class BiobbObject:
             * **container_generic_command** (*str*) - ("run") Which command typically run or exec will be used to execute your image.
     """
 
-    def __init__(self, properties: Optional[dict] = None, **kwargs) -> None:
+    def __init__(self, properties=None, **kwargs) -> None:  # type: ignore
         properties = properties or {}
 
         # Input/Output files
-        self.io_dict: Dict[str, Union[str, Dict[str, Union[str, Path]]]] = {"in": {}, "out": {}}
+        self.io_dict: Dict[str, Dict] = {"in": {}, "out": {}}
 
         # container Specific
-        self.container_path = properties.get("container_path")
+        self.container_path: Optional[str] = properties.get("container_path")
         self.container_image: str = properties.get("container_image", '')
-        self.container_volume_path = properties.get(
+        self.container_volume_path: str = properties.get(
             "container_volume_path", "/data")
-        self.container_working_dir = properties.get("container_working_dir")
-        self.container_user_id = properties.get("container_user_id")
-        self.container_shell_path = properties.get(
+        self.container_working_dir: Optional[str] = properties.get("container_working_dir")
+        self.container_user_id: Optional[str] = properties.get("container_user_id")
+        self.container_shell_path: str = properties.get(
             "container_shell_path", "/bin/bash -c"
         )
-        self.container_generic_command = properties.get(
+        self.container_generic_command: str = properties.get(
             "container_generic_command", "run"
         )
 
         # stage
-        self.stage_io_dict: Dict[str, Union[str, Dict[str, Union[str, Path]]]] = {"in": {}, "out": {}}
+        self.stage_io_dict: Dict[str, Any] = {"in": {}, "out": {}}
 
         # Properties common in all BB
         self.disable_sandbox: bool = properties.get("disable_sandbox", False)
         self.chdir_sandbox: bool = properties.get("chdir_sandbox", False)
-        self.binary_path = properties.get("binary_path")
-        self.can_write_console_log = properties.get(
+        self.binary_path: Optional[str] = properties.get("binary_path")
+        self.can_write_console_log: bool = properties.get(
             "can_write_console_log", True)
-        self.global_log = properties.get("global_log", None)
-        self.out_log = None
-        self.err_log = None
-        self.prefix = properties.get("prefix", None)
-        self.step = properties.get("step", None)
-        self.path = properties.get("path", "")
-        self.remove_tmp = properties.get("remove_tmp", True)
-        self.restart = properties.get("restart", False)
+        self.global_log: Optional[Logger] = properties.get("global_log", None)
+        self.out_log: Optional[Logger] = None
+        self.err_log: Optional[Logger] = None
+        self.prefix: Optional[str] = properties.get("prefix", None)
+        self.step: Optional[str] = properties.get("step", None)
+        self.path: str = properties.get("path", "")
+        self.remove_tmp: bool = properties.get("remove_tmp", True)
+        self.restart: bool = properties.get("restart", False)
         self.cmd: List[str] = []
-        self.return_code = None
+        self.return_code: Optional[int] = None
         self.tmp_files: List[Union[str, Path]] = []
-        self.env_vars_dict: typing.Mapping = properties.get(
+        self.env_vars_dict: typing.Dict = properties.get(
             "env_vars_dict", {})
         self.shell_path: typing.Union[str, Path] = properties.get(
             "shell_path", os.getenv("SHELL", "/bin/bash")
         )
 
-        self.dev = properties.get("dev", None)
-        self.check_extensions = properties.get("check_extensions", True)
-        self.check_var_typing = properties.get("check_var_typing", True)
+        self.dev: Optional[str] = properties.get("dev", None)
+        self.check_extensions: bool = properties.get("check_extensions", True)
+        self.check_var_typing: bool = properties.get("check_var_typing", True)
         self.locals_var_dict: Mapping[str, str] = dict()
-        self.doc_arguments_dict, self.doc_properties_dict = fu.get_doc_dicts(
-            self.__doc__
-        )
+        self.doc_arguments_dict, self.doc_properties_dict = fu.get_doc_dicts(self.__doc__)
 
         try:
             self.version = importlib.import_module(
@@ -135,7 +134,10 @@ def check_properties(
             for prop, value in properties.items():
                 if self.doc_properties_dict.get(prop):
                     property_type = self.doc_properties_dict[prop].get("type")
-                    if not isinstance(value, locate(property_type)):
+                    classinfo: object = locate(property_type).__class__
+                    if classinfo == type:
+                        classinfo = locate(property_type)
+                    if not isinstance(value, classinfo):  # type: ignore
                         warnings.warn(
                             f"Warning: {prop} property type not recognized. Got {type(value)} Expected {locate(property_type)}"
                         )
@@ -163,7 +165,7 @@ def check_restart(self) -> bool:
             )
 
         if self.restart:
-            if fu.check_complete_files(self.io_dict["out"].values()):
+            if fu.check_complete_files(self.io_dict["out"].values()):  # type: ignore
                 fu.log(
                     "Restart is enabled, this step: %s will the skipped" % self.step,
                     self.out_log,

biobb_common/tools/test_fixtures.py

@@ -139,6 +139,9 @@ def equal(file_a: str, file_b: str, ignore_list: Optional[typing.List[typing.Uni
 
 
 def compare_line_by_line(file_a: str, file_b: str, ignore_list: typing.List[typing.Union[str, int]]) -> bool:
+    print(f"Comparing ignoring lines containing this words: {ignore_list}")
+    print("     FILE_A: "+file_a)
+    print("     FILE_B: "+file_b)
     with open(file_a) as fa, open(file_b) as fb:
         for index, (line_a, line_b) in enumerate(zip(fa, fb)):
             if index in ignore_list or any(word in line_a for word in ignore_list if isinstance(word, str)):

setup.py

@@ -18,6 +18,7 @@
         "Bioexcel": "https://bioexcel.eu/",
     },
     packages=setuptools.find_packages(exclude=["docs"]),
+    package_data={'biobb_common': ['py.typed']},
     install_requires=["pyyaml", "requests", "biopython"],
     python_requires='>=3.8',
     classifiers=[
@@ -28,6 +29,6 @@
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",
-        "Operating System :: Unix",
+        "Operating System :: Unix"
     ],
 )