🔧Add more QA tools for parts of glotaran (#739)

* 🔧 Allowed mypy to run on a subset of glotaran

modules that will be checked are:
- utils
- plugin_system
- deprecation

* 🔧 Partially activated docstring QA tools and fixed issues

modules that will be checked are:
- utils
- plugin_system
- deprecation

.pre-commit-config.yaml

@@ -57,34 +57,48 @@ repos:
         args: [--strip-empty-cells]
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 0.13.0
+    rev: 0.13.1
     hooks:
       - id: nbqa-black
-        additional_dependencies: [black==20.8b1]
+        additional_dependencies: [black==21.6b0]
         args: [--nbqa-mutate]
       - id: nbqa-pyupgrade
-        additional_dependencies: [pyupgrade==2.9.0]
+        additional_dependencies: [pyupgrade==2.19.4]
         args: [--nbqa-mutate, --py38-plus]
       - id: nbqa-flake8
       - id: nbqa-check-ast
       - id: nbqa-isort
-        additional_dependencies: [isort==5.7.0]
+        additional_dependencies: [isort==5.9.1]
         args: [--nbqa-mutate]
 
   # Linters
 
-  # - repo: https://github.com/PyCQA/pydocstyle
-  #   rev: 5.1.1
-  #   hooks:
-  #     - id: pydocstyle
-  #       exclude: "docs|tests"
-  #       # this is needed due to the following issue:
-  #       # https://github.com/PyCQA/pydocstyle/issues/368
-  #       args: [--ignore-decorators=wrap_func_as_method]
-  # - repo: https://github.com/terrencepreilly/darglint
-  #   rev: v1.5.5
-  #   hooks:
-  #     - id: darglint
+  - repo: https://github.com/PyCQA/pydocstyle
+    rev: 6.1.1
+    hooks:
+      - id: pydocstyle
+        files: "^glotaran/(plugin_system|utils|deprecation)"
+        exclude: "docs|tests?"
+        # this is needed due to the following issue:
+        # https://github.com/PyCQA/pydocstyle/issues/368
+        args: [--ignore-decorators=wrap_func_as_method]
+
+  - repo: https://github.com/terrencepreilly/darglint
+    rev: v1.8.0
+    hooks:
+      - id: darglint
+        files: "^glotaran/(plugin_system|utils|deprecation)"
+        exclude: "docs|tests?"
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.910
+    hooks:
+      - id: mypy
+        files: "^glotaran/(plugin_system|utils|deprecation)"
+        exclude: "docs"
+        args: [glotaran]
+        pass_filenames: false
+        additional_dependencies: [types-all]
 
   - repo: https://github.com/econchick/interrogate
     rev: 1.4.0

glotaran/deprecation/deprecation_utils.py

@@ -321,17 +321,17 @@ def inner_wrapper(*args: Any, **kwargs: Any) -> DecoratedCallable:
 
     def outer_wrapper(deprecated_object: DecoratedCallable) -> DecoratedCallable:
         """Wrap deprecated_object of all callable kinds."""
-        if type(deprecated_object) is not type:
+        if not isinstance(deprecated_object, type):
             return cast(DecoratedCallable, inject_warn_into_call(deprecated_object))
 
         setattr(
             deprecated_object,
             "__new__",
             inject_warn_into_call(deprecated_object.__new__),  # type: ignore [arg-type]
         )
-        return deprecated_object
+        return deprecated_object  # type: ignore[return-value]
 
-    return outer_wrapper
+    return cast(Callable[[DecoratedCallable], DecoratedCallable], outer_wrapper)
 
 
 def module_attribute(module_qual_name: str, attribute_name: str) -> Any:
@@ -488,7 +488,7 @@ def deprecate_submodule(
     def warn_getattr(attribute_name: str):
 
         if attribute_name == "__file__":
-            return module_attribute(new_module, attribute_name)
+            return new_module.__file__
 
         elif attribute_name in dir(new_module):
             return deprecate_module_attribute(

glotaran/plugin_system/data_io_registration.py

@@ -302,7 +302,7 @@ def data_io_plugin_table(*, plugin_names: bool = False, full_names: bool = False
 
     Returns
     -------
-    str
+    MarkdownStr
         Markdown table of data io plugins.
     """
     table_data = methods_differ_from_baseclass_table(

glotaran/plugin_system/model_registration.py

@@ -134,7 +134,7 @@ def model_plugin_table(*, plugin_names: bool = False, full_names: bool = False)
 
     Returns
     -------
-    str
+    MarkdownStr
         Markdown table of modelnames.
     """
     table_data = []

glotaran/plugin_system/project_io_registration.py

@@ -488,7 +488,7 @@ def project_io_plugin_table(
 
     Returns
     -------
-    str
+    MarkdownStr
         Markdown table of project io plugins.
     """
     table_data = methods_differ_from_baseclass_table(

glotaran/utils/ipython.py

@@ -9,8 +9,7 @@ class MarkdownStr(UserString):
     """String wrapper class for rich display integration of markdown in ipython."""
 
     def __init__(self, wrapped_str: str, *, syntax: str = None):
-        """String class automatically displayed as markdown by ipython.
-
+        """Initialize string class that is automatically displayed as markdown by ``ipython``.
 
         Parameters
         ----------
@@ -23,13 +22,16 @@ def __init__(self, wrapped_str: str, *, syntax: str = None):
         ----
         Possible syntax highlighting values can e.g. be found here:
         https://support.codebasehq.com/articles/tips-tricks/syntax-highlighting-in-markdown
+
+
+        .. # noqa: DAR101
         """
         # This needs to be called data since ipython is looking for this attr
         self.data = str(wrapped_str)
         self.syntax = syntax
 
     def _repr_markdown_(self) -> str:
-        """Special method used by ``ipython`` to render markdown.
+        """Render markdown automatically when in a ``ipython`` context.
 
         See:
         https://ipython.readthedocs.io/en/latest/config/integrating.html?highlight=_repr_markdown_#rich-display
@@ -64,7 +66,7 @@ def display_file(path: str | PathLike[str], *, syntax: str = None) -> MarkdownSt
     ----------
     path : str | PathLike[str]
         Paths to the file
-    syntax : str, optional
+    syntax : str
         Syntax highlighting which should be applied, by default None
 
     Returns

glotaran/utils/test/test_ipython.py

@@ -39,5 +39,6 @@ def test_display_file(tmp_path: Path):
     expected = MarkdownStr(file_content, syntax="yaml")
     tmp_file = tmp_path / "test.yml"
     tmp_file.write_text(file_content)
-    for path in (tmp_file, str(tmp_file)):
-        assert display_file(path, syntax="yaml") == expected
+
+    assert display_file(tmp_file, syntax="yaml") == expected
+    assert display_file(str(tmp_file), syntax="yaml") == expected

setup.cfg

@@ -75,7 +75,7 @@ ignore_messages = xarraydoc
 
 [darglint]
 docstring_style = numpy
-ignore_regex = test_.+|.*wrapper.*|inject_warn_into_call|.*dummy.*
+ignore_regex = test_.+|.*wrapper.*|inject_warn_into_call|.*dummy.*|__(str|eq)__
 
 [pydocstyle]
 convention = numpy
@@ -84,3 +84,15 @@ convention = numpy
 ignore_missing_imports = True
 scripts_are_modules = True
 show_error_codes = True
+
+[mypy-glotaran.*]
+ignore_errors = True
+
+[mypy-glotaran.plugin_system.*]
+ignore_errors = False
+
+[mypy-glotaran.utils.*]
+ignore_errors = False
+
+[mypy-glotaran.deprecation.*]
+ignore_errors = False