fix check-task issues

Author: seebi

.flake8

@@ -2,3 +2,4 @@
 [flake8]
 max-line-length = 88
 extend-ignore = E203
+

.pre-commit-config.yaml

@@ -21,3 +21,5 @@ repos:
     rev: 19.3b0
     hooks:
       - id: black
+        language_version: python3
+

cmem_plugin_base/dataintegration/description.py

@@ -1,5 +1,5 @@
 """Classes for describing plugins"""
-from typing import Optional, Sequence
+from typing import Optional, List
 
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin, TransformPlugin
 
@@ -11,11 +11,18 @@ class PluginParameter:
     :param label: A human-readable label of the parameter
     :param description: A human-readable description of the parameter
     :param default_value: The parameter default value (optional)
-    :param advanced: True, if this is an advanced parameter that should only be changed by experienced users
+    :param advanced: True, if this is an advanced parameter that should only be
+        changed by experienced users
     """
 
-    def __init__(self, name: str, label: str = "", description: str = "",
-                 default_value: Optional[str] = None, advanced: bool = False) -> None:
+    def __init__(
+        self,
+        name: str,
+        label: str = "",
+        description: str = "",
+        default_value: Optional[str] = None,
+        advanced: bool = False,
+    ) -> None:
         self.name = name
         self.label = label
         self.description = description
@@ -34,44 +41,75 @@ class PluginDescription:
     :param parameters: Available plugin parameters
     """
 
-    def __init__(self, plugin_class, label: str, description: str = "", documentation: str = "",
-                 categories: Sequence[str] = [], parameters: Sequence[PluginParameter] = []) -> None:
-        #  Set the type of the plugin. Same as the class name of the plugin base class, e.g., 'WorkflowPlugin'.
+    def __init__(
+        self,
+        plugin_class,
+        label: str,
+        description: str = "",
+        documentation: str = "",
+        categories: List[str] = None,
+        parameters: List[PluginParameter] = None,
+    ) -> None:
+        #  Set the type of the plugin. Same as the class name of the plugin
+        #  base class, e.g., 'WorkflowPlugin'.
         if issubclass(plugin_class, WorkflowPlugin):
             self.plugin_type = "WorkflowPlugin"
         elif issubclass(plugin_class, TransformPlugin):
             self.plugin_type = "TransformPlugin"
         else:
-            raise ValueError(f"Class {plugin_class.__name__} does not implement a supported plugin base class"
-                             f" (e.g., WorkflowPlugin).")
+            raise ValueError(
+                f"Class {plugin_class.__name__} does not implement a supported"
+                f"plugin base class (e.g., WorkflowPlugin)."
+            )
 
         self.plugin_class = plugin_class
         self.module_name = plugin_class.__module__
         self.class_name = plugin_class.__name__
-        self.categories = categories
+        if categories is None:
+            self.categories = []
+        else:
+            self.categories = categories
         self.label = label
         self.description = description
         self.documentation = documentation
-        self.parameters = parameters
+        if parameters is None:
+            self.parameters = []
+        else:
+            self.parameters = parameters
 
 
 class Plugin:
+    """Annotate classes with plugin descriptions."""
     plugins: list[PluginDescription] = []
 
-    def __init__(self, label: str, description: str = "", documentation: str = "",
-                 categories: Sequence[str] = [], parameters: Sequence[PluginParameter] = []):
+    def __init__(
+        self,
+        label: str,
+        description: str = "",
+        documentation: str = "",
+        categories: List[str] = None,
+        parameters: List[PluginParameter] = None,
+    ):
         self.label = label
         self.description = description
         self.documentation = documentation
-        self.categories = categories
-        self.parameters = parameters
+        if categories is None:
+            self.categories = []
+        else:
+            self.categories = categories
+        if parameters is None:
+            self.parameters = []
+        else:
+            self.parameters = parameters
 
     def __call__(self, func):
-        plugin_desc = PluginDescription(plugin_class=func,
-                                        label=self.label,
-                                        description=self.description,
-                                        documentation=self.documentation,
-                                        categories=self.categories,
-                                        parameters=self.parameters)
+        plugin_desc = PluginDescription(
+            plugin_class=func,
+            label=self.label,
+            description=self.description,
+            documentation=self.documentation,
+            categories=self.categories,
+            parameters=self.parameters,
+        )
         Plugin.plugins.append(plugin_desc)
         return func

cmem_plugin_base/dataintegration/discovery.py

@@ -3,37 +3,32 @@
 import importlib.util
 import json
 import pkgutil
-from subprocess import check_output
-from typing import Dict, List
+from subprocess import check_output  # nosec
 from typing import Sequence
 
 from cmem_plugin_base.dataintegration.description import PluginDescription, Plugin
 
 
-def get_packages() -> List[Dict]:
+def get_packages():
     """Get installed python packages.
 
     Returns a list of dict with the following keys:
      - name - package name
      - version - package version
     """
-    return json.loads(
-        check_output(
-            ["pip", "list", "--format", "json"],
-            shell=False
-        )
-    )
+    return json.loads(check_output(["pip", "list", "--format", "json"], shell=False))
 
 
 def discover_plugins(package_name: str = "cmem") -> Sequence[PluginDescription]:
     """Finds all plugins within a base package.
 
-    :param package_name: The base package. Will recurse into all submodules of this package.
+    :param package_name: The base package. Will recurse into all submodules
+        of this package.
     """
 
     def import_submodules(package):
-        for loader, name, is_pkg in pkgutil.walk_packages(package.__path__):
-            full_name = package.__name__ + '.' + name
+        for _loader, name, is_pkg in pkgutil.walk_packages(package.__path__):
+            full_name = package.__name__ + "." + name
             module = importlib.import_module(full_name)
             if is_pkg:
                 import_submodules(module)

cmem_plugin_base/dataintegration/plugins.py

@@ -28,8 +28,8 @@ class TransformPlugin:
     def transform(self, inputs: Sequence[Sequence[str]]) -> Sequence[str]:
         """
         Transforms a collection of values.
-        :param inputs: A sequence which contains as many elements as there are input operators for this transformation.
-                       For each input operator it contains a sequence of values.
+        :param inputs: A sequence which contains as many elements as there are input
+            operators for this transformation.
+            For each input operator it contains a sequence of values.
         :return: The transformed values.
         """
-        pass

pyproject.toml

@@ -39,6 +39,9 @@ defusedxml = "^0.7.1"
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
+[tool.isort]
+profile = "black"
+
 [tool.pylint.MASTER]
 load-plugins="pylint_junit"
 
@@ -55,10 +58,14 @@ disable = "C0330, C0326, R0903"
 
 [tool.pylint.format]
 max-line-length = "88"
+disable = "C0330, C0326"
+max-args = "8"
+max-attributes = "9"
 
 [tool.mypy]
 warn_return_any = true
 ignore_missing_imports = true
 
 [tool.pytest.ini_options]
 addopts = ""
+