From 92cbb5745353e16dea1d0882fbea139c8dc365ba Mon Sep 17 00:00:00 2001
From: Sebastian Weigand <s.weigand.phy@gmail.com>
Date: Fri, 22 Oct 2021 19:43:03 +0200
Subject: [PATCH] =?UTF-8?q?=F0=9F=94=A7=E2=99=BB=EF=B8=8F=20Remove=20param?=
 =?UTF-8?q?eter.py=20from=20linter=20exceptions=20(#862)?=
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* 🔧👌 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: https://github.com/terrencepreilly/darglint/issues/180
---
 .pre-commit-config.yaml                 |  70 ++++++-------
 glotaran/parameter/parameter.py         | 130 ++++++++++++------------
 glotaran/parameter/parameter_group.py   |  28 ++---
 glotaran/parameter/parameter_history.py |   2 +-
 setup.cfg                               |   3 -
 tox.ini                                 |   6 ++
 6 files changed, 118 insertions(+), 121 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 12c35fa8a..7e82fbc4c 100644
--- a/.pre-commit-config.yaml
+++ b/.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]
@@ -32,7 +32,7 @@ repos:
         types_or: [python, pyi]
 
   - repo: https://github.com/psf/black
-    rev: 21.6b0
+    rev: 21.9b0
     hooks:
       - id: black
         types: [file]
@@ -40,7 +40,7 @@ repos:
         language_version: python3
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.9.1
+    rev: 5.9.3
     hooks:
       - id: isort
         types: [file]
@@ -48,19 +48,19 @@ repos:
         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]
@@ -75,26 +75,38 @@ 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)"
@@ -102,30 +114,12 @@ repos:
         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
diff --git a/glotaran/parameter/parameter.py b/glotaran/parameter/parameter.py
index fac046a19..b42d30027 100644
--- a/glotaran/parameter/parameter.py
+++ b/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,
@@ -439,18 +437,18 @@ 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_:"
@@ -458,116 +456,116 @@ def __str__(self) -> str:  # noqa D400
             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
 
 
diff --git a/glotaran/parameter/parameter_group.py b/glotaran/parameter/parameter_group.py
index a603ec3c1..db2fb2084 100644
--- a/glotaran/parameter/parameter_group.py
+++ b/glotaran/parameter/parameter_group.py
@@ -22,7 +22,7 @@
 class ParameterNotFoundException(Exception):
     """Raised when a Parameter is not found in the Group."""
 
-    def __init__(self, path, label):
+    def __init__(self, path, label):  # noqa: D107
         super().__init__(f"Cannot find parameter {'.'.join(path+[label])!r}")
 
 
@@ -30,21 +30,23 @@ class ParameterGroup(dict):
     """Represents are group of parameters.
 
     Can contain other groups, creating a tree-like hierarchy.
-
-    Parameters
-    ----------
-    label : str
-        The label of the group.
-    root_group : ParameterGroup
-        The root group
-
-    Raises
-    ------
-    ValueError
-        Raised if the an invalid label is given.
     """
 
     def __init__(self, label: str = None, root_group: ParameterGroup = None):
+        """Initialize a :class:`ParameterGroup` instance with ``label``.
+
+        Parameters
+        ----------
+        label : str
+            The label of the group.
+        root_group : ParameterGroup
+            The root group
+
+        Raises
+        ------
+        ValueError
+            Raised if the an invalid label is given.
+        """
         if label is not None and not Parameter.valid_label(label):
             raise ValueError(f"'{label}' is not a valid group label.")
         self._label = label
diff --git a/glotaran/parameter/parameter_history.py b/glotaran/parameter/parameter_history.py
index 9ab64dd25..15b8f163f 100644
--- a/glotaran/parameter/parameter_history.py
+++ b/glotaran/parameter/parameter_history.py
@@ -10,7 +10,7 @@
 class ParameterHistory:
     """A class representing a history of parameters."""
 
-    def __init__(self):
+    def __init__(self):  # noqa: D107
 
         self._parameter_labels: list[str] = []
         self._parameters: list[np.ndarray] = []
diff --git a/setup.cfg b/setup.cfg
index b584563e6..794aa23ef 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -81,9 +81,6 @@ ignore_messages = xarraydoc
 docstring_style = numpy
 ignore_regex = test_.+|.*wrapper.*|inject_warn_into_call|.*dummy.*|__(.+?)__
 
-[pydocstyle]
-convention = numpy
-
 [mypy]
 ignore_missing_imports = True
 scripts_are_modules = True
diff --git a/tox.ini b/tox.ini
index 9972404d9..fb5dd6105 100644
--- a/tox.ini
+++ b/tox.ini
@@ -32,6 +32,12 @@ per-file-ignores =
     # Allow printing in test file
     test_*.py: T001
 
+[pydocstyle]
+convention = numpy
+# this is needed due to the following issue:
+# https://github.com/PyCQA/pydocstyle/issues/368
+ignore_decorators = wrap_func_as_method
+
 [testenv:docs]
 direct = true
 whitelist_externals = make