🔧♻️ Remove parameter.py from linter exceptions (#862)

* 🔧👌 Move up yesqa hook, to remove noqa's before linting

* 🔧♻️ Moved pydocstyle config to tox.ini

* 🔧 ♻️ Moved up flake8 hook directly after yesqa hook

* 🔧⬆️ Updated pre-commit config

* 🔧♻️ Run Doc linting tools via flake8

This allows a uniform usage of 'noqa's, which is also compatible with yesqa

* 🔧🩹 Remove parameter.py from linter exceptions

* 🔧 Fixed darglint version to 1.8.0 due to bug in 1.8.1

Ref: terrencepreilly/darglint#180

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
         args: [--remove]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.19.4
+    rev: v2.29.0
     hooks:
       - id: pyupgrade
         types: [file]
@@ -32,35 +32,35 @@ repos:
         types_or: [python, pyi]
 
   - repo: https://github.com/psf/black
-    rev: 21.6b0
+    rev: 21.9b0
     hooks:
       - id: black
         types: [file]
         types_or: [python, pyi]
         language_version: python3
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.9.1
+    rev: 5.9.3
     hooks:
       - id: isort
         types: [file]
         types_or: [python, pyi]
         minimum_pre_commit_version: 2.9.0
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.17.0
+    rev: v1.18.0
     hooks:
       - id: setup-cfg-fmt
 
   # Notebook tools
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.4.0
+    rev: 0.5.0
     hooks:
       - id: nbstripout
         args: [--strip-empty-cells]
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 0.13.1
+    rev: 1.1.1
     hooks:
       - id: nbqa-black
         additional_dependencies: [black==21.6b0]
@@ -75,57 +75,51 @@ repos:
         args: [--nbqa-mutate]
 
   # Linters
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.2.3
+    hooks:
+      - id: yesqa
+        types: [file]
+        types_or: [python, pyi]
+        additional_dependencies: [flake8-docstrings, flake8-print]
 
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.1.1
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
     hooks:
-      - id: pydocstyle
-        files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project)"
-        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]
+      - id: flake8
+        name: "flake8 lint code"
+        types: [file]
+        types_or: [python, pyi]
+        additional_dependencies:
+          [flake8-pyi, flake8-comprehensions, flake8-print]
 
-  - repo: https://github.com/terrencepreilly/darglint
-    rev: v1.8.0
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
     hooks:
-      - id: darglint
+      - id: flake8
+        alias: flake8-docs
+        args:
+          - "--select=D,DAR"
+        name: "flake8 lint docstrings"
         files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project)"
         exclude: "docs|tests?/"
+        additional_dependencies: [flake8-docstrings, darglint==1.8.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910
+    rev: v0.910-1
     hooks:
       - id: mypy
         files: "^glotaran/(plugin_system|utils|deprecation|testing|parameter|project)"
         exclude: "docs"
         additional_dependencies: [types-all]
 
   - repo: https://github.com/econchick/interrogate
-    rev: 1.4.0
+    rev: 1.5.0
     hooks:
       - id: interrogate
         args: [-vv, --config=pyproject.toml, glotaran]
         pass_filenames: false
 
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.2.3
-    hooks:
-      - id: yesqa
-        types: [file]
-        types_or: [python, pyi]
-        additional_dependencies: [flake8-docstrings, flake8-print]
-        exclude: "parameter.py"
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
-    hooks:
-      - id: flake8
-        types: [file]
-        types_or: [python, pyi]
-        additional_dependencies:
-          [flake8-pyi, flake8-comprehensions, flake8-print]
-
   - repo: https://github.com/myint/rstcheck
     rev: "3f92957478422df87bd730abde66f089cc1ee19b"
     hooks:
@@ -137,7 +131,7 @@ repos:
     hooks:
       - id: rst-backticks
       - id: python-check-blanket-noqa
-        exclude: "parameter.py|docs|tests?"
+        exclude: "docs|tests?"
       - id: python-check-blanket-type-ignore
         exclude: "docs|tests?"
       - id: python-use-type-annotations

glotaran/parameter/parameter.py

@@ -334,7 +334,6 @@ def transformed_expression(self) -> str | None:
         -------
         str | None
             The transformed expression.
-
         """
         if self.expression is not None and self._transformed_expression is None:
             self._transformed_expression = PARAMETER_EXPRESION_REGEX.sub(
@@ -343,15 +342,14 @@ def transformed_expression(self) -> str | None:
         return self._transformed_expression
 
     @property
-    def standard_error(self) -> float:  # noqa D401
+    def standard_error(self) -> float:
         """Standard error of the optimized parameter.
 
         Returns
         -------
         float
             The standard error of the parameter.
-        """
-
+        """  # noqa: D401
         return self._stderr
 
     @standard_error.setter
@@ -411,7 +409,7 @@ def set_value_from_optimization(self, value: float):
         """
         self.value = np.exp(value) if self.non_negative else value
 
-    def __getstate__(self):  # noqa D400
+    def __getstate__(self):
         """Get state for pickle."""
         return (
             self.label,
@@ -425,7 +423,7 @@ def __getstate__(self):  # noqa D400
             self.vary,
         )
 
-    def __setstate__(self, state):  # noqa D400
+    def __setstate__(self, state):
         """Set state from pickle."""
         (
             self.label,
@@ -439,135 +437,135 @@ def __setstate__(self, state):  # noqa D400
             self.vary,
         ) = state
 
-    def __repr__(self):  # noqa D400
+    def __repr__(self):
         """Representation used by repl and tracebacks."""
         return (
             f"{type(self).__name__}(label={self.label!r}, value={self.value!r},"
             f" expression={self.expression!r}, vary={self.vary!r})"
         )
 
-    def __array__(self):  # noqa D400
-        """array"""
+    def __array__(self):
+        """array"""  # noqa: D400, D403
         return np.array(float(self._value), dtype=float)
 
-    def __str__(self) -> str:  # noqa D400
+    def __str__(self) -> str:
         """Representation used by print and str."""
         return (
             f"__{self.label}__: _Value_: {self.value}, _StdErr_: {self.standard_error}, _Min_:"
             f" {self.minimum}, _Max_: {self.maximum}, _Vary_: {self.vary},"
             f" _Non-Negative_: {self.non_negative}, _Expr_: {self.expression}"
         )
 
-    def __abs__(self):  # noqa D400
-        """abs"""
+    def __abs__(self):
+        """abs"""  # noqa: D400, D403
         return abs(self._value)
 
-    def __neg__(self):  # noqa D400
-        """neg"""
+    def __neg__(self):
+        """neg"""  # noqa: D400, D403
         return -self._value
 
-    def __pos__(self):  # noqa D400
-        """positive"""
+    def __pos__(self):
+        """positive"""  # noqa: D400, D403
         return +self._value
 
-    def __int__(self):  # noqa D400
-        """int"""
+    def __int__(self):
+        """int"""  # noqa: D400, D403
         return int(self._value)
 
-    def __float__(self):  # noqa D400
-        """float"""
+    def __float__(self):
+        """float"""  # noqa: D400, D403
         return float(self._value)
 
-    def __trunc__(self):  # noqa D400
-        """trunc"""
+    def __trunc__(self):
+        """trunc"""  # noqa: D400, D403
         return self._value.__trunc__()
 
-    def __add__(self, other):  # noqa D400
-        """+"""
+    def __add__(self, other):
+        """+"""  # noqa: D400
         return self._value + other
 
-    def __sub__(self, other):  # noqa D400
-        """-"""
+    def __sub__(self, other):
+        """-"""  # noqa: D400
         return self._value - other
 
-    def __truediv__(self, other):  # noqa D400
-        """/"""
+    def __truediv__(self, other):
+        """/"""  # noqa: D400
         return self._value / other
 
-    def __floordiv__(self, other):  # noqa D400
-        """//"""
+    def __floordiv__(self, other):
+        """//"""  # noqa: D400
         return self._value // other
 
-    def __divmod__(self, other):  # noqa D400
-        """divmod"""
+    def __divmod__(self, other):
+        """divmod"""  # noqa: D400, D403
         return divmod(self._value, other)
 
-    def __mod__(self, other):  # noqa D400
-        """%"""
+    def __mod__(self, other):
+        """%"""  # noqa: D400
         return self._value % other
 
-    def __mul__(self, other):  # noqa D400
-        """*"""
+    def __mul__(self, other):
+        """*"""  # noqa: D400
         return self._value * other
 
-    def __pow__(self, other):  # noqa D400
-        """**"""
+    def __pow__(self, other):
+        """**"""  # noqa: D400
         return self._value ** other
 
-    def __gt__(self, other):  # noqa D400
-        """>"""
+    def __gt__(self, other):
+        """>"""  # noqa: D400
         return self._value > other
 
-    def __ge__(self, other):  # noqa D400
-        """>="""
+    def __ge__(self, other):
+        """>="""  # noqa: D400
         return self._value >= other
 
-    def __le__(self, other):  # noqa D400
-        """<="""
+    def __le__(self, other):
+        """<="""  # noqa: D400
         return self._value <= other
 
-    def __lt__(self, other):  # noqa D400
-        """<"""
+    def __lt__(self, other):
+        """<"""  # noqa: D400
         return self._value < other
 
-    def __eq__(self, other):  # noqa D400
-        """=="""
+    def __eq__(self, other):
+        """=="""  # noqa: D400
         return self._value == other
 
-    def __ne__(self, other):  # noqa D400
-        """!="""
+    def __ne__(self, other):
+        """!="""  # noqa: D400
         return self._value != other
 
-    def __radd__(self, other):  # noqa D400
-        """+ (right)"""
+    def __radd__(self, other):
+        """+ (right)"""  # noqa: D400
         return other + self._value
 
-    def __rtruediv__(self, other):  # noqa D400
-        """/ (right)"""
+    def __rtruediv__(self, other):
+        """/ (right)"""  # noqa: D400
         return other / self._value
 
-    def __rdivmod__(self, other):  # noqa D400
-        """divmod (right)"""
+    def __rdivmod__(self, other):
+        """divmod (right)"""  # noqa: D400, D403
         return divmod(other, self._value)
 
-    def __rfloordiv__(self, other):  # noqa D400
-        """// (right)"""
+    def __rfloordiv__(self, other):
+        """// (right)"""  # noqa: D400
         return other // self._value
 
-    def __rmod__(self, other):  # noqa D400
-        """% (right)"""
+    def __rmod__(self, other):
+        """% (right)"""  # noqa: D400
         return other % self._value
 
-    def __rmul__(self, other):  # noqa D400
-        """* (right)"""
+    def __rmul__(self, other):
+        """* (right)"""  # noqa: D400
         return other * self._value
 
-    def __rpow__(self, other):  # noqa D400
-        """** (right)"""
+    def __rpow__(self, other):
+        """** (right)"""  # noqa: D400
         return other ** self._value
 
-    def __rsub__(self, other):  # noqa D400
-        """- (right)"""
+    def __rsub__(self, other):
+        """- (right)"""  # noqa: D400
         return other - self._value