Merge branch 'extend_docstring_layout' into 'development'

util.extend_docstring: fix broken layout

Closes #212 and #169

See merge request damask/DAMASK!658

python/damask/_orientation.py

@@ -94,7 +94,7 @@ class Orientation(Rotation,Crystal):
 
     """
 
-    @util.extend_docstring(_parameter_doc)
+    @util.extend_docstring(extra_parameters=_parameter_doc)
     def __init__(self,
                  rotation: Union[FloatSequence, Rotation] = np.array([1.,0.,0.,0.]),
                  *,
@@ -300,84 +300,95 @@ class Orientation(Rotation,Crystal):
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_random, _parameter_doc)
+    @util.extend_docstring(Rotation.from_random,
+                           extra_parameters=_parameter_doc)
     def from_random(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_random)
         return cls(rotation=Rotation.from_random(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_quaternion,_parameter_doc)
+    @util.extend_docstring(Rotation.from_quaternion,
+                           extra_parameters=_parameter_doc)
     def from_quaternion(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_quaternion)
         return cls(rotation=Rotation.from_quaternion(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_Euler_angles,_parameter_doc)
+    @util.extend_docstring(Rotation.from_Euler_angles,
+                           extra_parameters=_parameter_doc)
     def from_Euler_angles(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_Euler_angles)
         return cls(rotation=Rotation.from_Euler_angles(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_axis_angle,_parameter_doc)
+    @util.extend_docstring(Rotation.from_axis_angle,
+                           extra_parameters=_parameter_doc)
     def from_axis_angle(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_axis_angle)
         return cls(rotation=Rotation.from_axis_angle(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_basis,_parameter_doc)
+    @util.extend_docstring(Rotation.from_basis,
+                           extra_parameters=_parameter_doc)
     def from_basis(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_basis)
         return cls(rotation=Rotation.from_basis(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_matrix,_parameter_doc)
+    @util.extend_docstring(Rotation.from_matrix,
+                           extra_parameters=_parameter_doc)
     def from_matrix(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_matrix)
         return cls(rotation=Rotation.from_matrix(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_Rodrigues_vector,_parameter_doc)
+    @util.extend_docstring(Rotation.from_Rodrigues_vector,
+                           extra_parameters=_parameter_doc)
     def from_Rodrigues_vector(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_Rodrigues_vector)
         return cls(rotation=Rotation.from_Rodrigues_vector(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_homochoric,_parameter_doc)
+    @util.extend_docstring(Rotation.from_homochoric,
+                           extra_parameters=_parameter_doc)
     def from_homochoric(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_homochoric)
         return cls(rotation=Rotation.from_homochoric(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_cubochoric,_parameter_doc)
+    @util.extend_docstring(Rotation.from_cubochoric,
+                           extra_parameters=_parameter_doc)
     def from_cubochoric(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_cubochoric)
         return cls(rotation=Rotation.from_cubochoric(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_spherical_component,_parameter_doc)
+    @util.extend_docstring(Rotation.from_spherical_component,
+                           extra_parameters=_parameter_doc)
     def from_spherical_component(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_spherical_component)
         return cls(rotation=Rotation.from_spherical_component(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extended_docstring(Rotation.from_fiber_component,_parameter_doc)
+    @util.extend_docstring(Rotation.from_fiber_component,
+                           extra_parameters=_parameter_doc)
     def from_fiber_component(cls, **kwargs) -> 'Orientation':
         kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_fiber_component)
         return cls(rotation=Rotation.from_fiber_component(**kwargs_rot),**kwargs_ori)
 
 
     @classmethod
-    @util.extend_docstring(_parameter_doc)
+    @util.extend_docstring(extra_parameters=_parameter_doc)
     def from_directions(cls,
                         uvw: FloatSequence,
                         hkl: FloatSequence,
@@ -392,6 +403,10 @@ class Orientation(Rotation,Crystal):
         hkl : numpy.ndarray, shape (...,3)
             Lattice plane normal aligned with lab frame z-direction.
 
+        Returns
+        -------
+        new : damask.Orientation
+
         """
         o = cls(**kwargs)
         x = o.to_frame(uvw=uvw)
@@ -538,8 +553,7 @@ class Orientation(Rotation,Crystal):
 
         Notes
         -----
-        Currently requires same crystal family for both orientations.
+        Requires same crystal family for both orientations.
-        For extension to cases with differing symmetry see A. Heinz and P. Neumann 1991 and 10.1107/S0021889808016373.
 
         Examples
         --------
@@ -569,6 +583,8 @@ class Orientation(Rotation,Crystal):
         >>> plt.show()
 
         """
+        # For extension to cases with differing symmetry see
+        # https://doi.org/10.1107/S0021889808016373 and https://doi.org/10.1107/S0108767391006864
         if self.family != other.family:
             raise NotImplementedError('disorientation between different crystal families')
 

python/damask/_rotation.py

@@ -768,6 +768,10 @@ class Rotation:
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         qu = np.array(q,dtype=float)
         if qu.shape[:-2:-1] != (4,): raise ValueError('invalid shape')
@@ -800,6 +804,10 @@ class Rotation:
         degrees : bool, optional
             Euler angles are given in degrees. Defaults to False.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         Notes
         -----
         Bunge Euler angles correspond to a rotation axis sequence of z–x'–z''.
@@ -834,6 +842,10 @@ class Rotation:
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         ax = np.array(axis_angle,dtype=float)
         if ax.shape[:-2:-1] != (4,): raise ValueError('invalid shape')
@@ -898,6 +910,10 @@ class Rotation:
         R : numpy.ndarray, shape (...,3,3)
             Rotation matrix with det(R) = 1 and R.T ∙ R = I.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         return Rotation.from_basis(R)
 
@@ -914,6 +930,10 @@ class Rotation:
         b : numpy.ndarray, shape (...,2,3)
             Corresponding three-dimensional vectors of second basis.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         a_ = np.array(a,dtype=float)
         b_ = np.array(b,dtype=float)
@@ -946,6 +966,10 @@ class Rotation:
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         ro = np.array(rho,dtype=float)
         if ro.shape[:-2:-1] != (4,): raise ValueError('invalid shape')
@@ -974,6 +998,10 @@ class Rotation:
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         ho = np.array(h,dtype=float)
         if ho.shape[:-2:-1] != (3,): raise ValueError('invalid shape')
@@ -999,6 +1027,10 @@ class Rotation:
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         cu = np.array(x,dtype=float)
         if cu.shape[:-2:-1] != (3,): raise ValueError('invalid shape')
@@ -1025,6 +1057,10 @@ class Rotation:
             A seed to initialize the BitGenerator.
             Defaults to None, i.e. unpredictable entropy will be pulled from the OS.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         """
         rng = np.random.default_rng(rng_seed)
         r = rng.random(3 if shape is None else tuple(shape)+(3,) if hasattr(shape, '__iter__') else (shape,3)) # type: ignore
@@ -1066,6 +1102,10 @@ class Rotation:
             A seed to initialize the BitGenerator.
             Defaults to None, i.e. unpredictable entropy will be pulled from the OS.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         Notes
         -----
         Due to the distortion of Euler space in the vicinity of ϕ = 0, probability densities, p, defined on
@@ -1150,7 +1190,7 @@ class Rotation:
                              sigma: float = 0.,
                              shape: Union[int, IntSequence] = None,
                              degrees: bool = False,
-                             rng_seed: NumpyRngSeed = None):
+                             rng_seed: NumpyRngSeed = None) -> 'Rotation':
         """
         Initialize with samples from a Gaussian distribution around a given direction.
 
@@ -1173,6 +1213,10 @@ class Rotation:
             A seed to initialize the BitGenerator.
             Defaults to None, i.e. unpredictable entropy will be pulled from the OS.
 
+        Returns
+        -------
+        new : damask.Rotation
+
         Notes
         -----
         The crystal direction for (θ=0,φ=0) is [0 0 1],

python/damask/seeds.py

@@ -1,4 +1,3 @@
-
 """Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
 
 from typing import Tuple as _Tuple

python/damask/util.py

@@ -210,6 +210,14 @@ def open_text(fname: _FileHandle,
            open(_Path(fname).expanduser(),mode,newline=('\n' if mode == 'w' else None))
 
 
+def execution_stamp(class_name: str,
+                    function_name: str = None) -> str:
+    """Timestamp the execution of a (function within a) class."""
+    now = _datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
+    _function_name = '' if function_name is None else f'.{function_name}'
+    return f'damask.{class_name}{_function_name} v{_version} ({now})'
+
+
 def natural_sort(key: str) -> _List[_Union[int, str]]:
     """
     Natural sort.
@@ -403,13 +411,6 @@ def project_equal_area(vector: _np.ndarray,
     return _np.roll(_np.block([v[...,:2]/_np.sqrt(1.0+_np.abs(v[...,2:3])),_np.zeros_like(v[...,2:3])]),
                     -shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
 
-def execution_stamp(class_name: str,
-                    function_name: str = None) -> str:
-    """Timestamp the execution of a (function within a) class."""
-    now = _datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
-    _function_name = '' if function_name is None else f'.{function_name}'
-    return f'damask.{class_name}{_function_name} v{_version} ({now})'
-
 
 def hybrid_IA(dist: _np.ndarray,
               N: int,
@@ -528,37 +529,82 @@ def shapeblender(a: _Tuple[int, ...],
     return a + b[i:]
 
 
-def extend_docstring(extra_docstring: str) -> _Callable:
+def _docstringer(docstring: _Union[str, _Callable],
+                 extra_parameters: str = None,
+                 # extra_examples: str = None,
+                 # extra_notes: str = None,
+                 return_type: _Union[str, _Callable] = None) -> str:
     """
-    Decorator: Append to function's docstring.
+    Extend a docstring.
 
     Parameters
     ----------
-    extra_docstring : str
+    docstring : str or callable, optional
-       Docstring to append.
+       Docstring (of callable) to extend.
+    extra_parameters : str, optional
+       Additional information to append to Parameters section.
+    return_type : str or callable, optional
+       Type of return variable.
 
     """
-    def _decorator(func):
+    docstring_ = str(     docstring if isinstance(docstring,str)
-        func.__doc__ += extra_docstring
+                     else docstring.__doc__ if hasattr(docstring,'__doc__')
-        return func
+                     else '')
-    return _decorator
+    d = dict(Parameters=extra_parameters,
+             # Examples=extra_examples,
+             # Notes=extra_notes,
+             )
+    for key,extra in [(k,v) for (k,v) in d.items() if v is not None]:
+        if not (heading := _re.search(fr'^([ ]*){key}\s*\n\1{"-"*len(key)}',
+                                      docstring_,flags=_re.MULTILINE)):
+            raise RuntimeError(f"Docstring {docstring_} lacks a correctly formatted {key} section to insert values into")
+        content = [line for line in extra.split('\n') if line.strip()]
+        indent = len(heading.group(1))
+        shift = min([len(line)-len(line.lstrip(' '))-indent for line in content])
+        extra = '\n'.join([(line[shift:] if shift > 0 else
+                          f'{" "*-shift}{line}') for line in content])
+        docstring_ = _re.sub(fr'(^([ ]*){key}\s*\n\2{"-"*len(key)}[\n ]*[A-Za-z0-9 ]*: ([^\n]+\n)*)',
+                             fr'\1{extra}\n',
+                             docstring_,flags=_re.MULTILINE)
 
+    if return_type is None:
+        return docstring_
+    else:
+        if isinstance(return_type,str):
+            return_type_ = return_type
+        else:
+            return_class = return_type.__annotations__.get('return','')
+            return_type_ = (_sys.modules[return_type.__module__].__name__.split('.')[0]
+                            +'.'
+                            +(return_class.__name__ if not isinstance(return_class,str) else return_class)
+                           )
 
-def extended_docstring(f: _Callable,
+        return _re.sub(r'(^([ ]*)Returns\s*\n\2-------\s*\n[ ]*[A-Za-z0-9 ]*: )(.*)\n',
-                       extra_docstring: str) -> _Callable:
+                           fr'\1{return_type_}\n',
+                           docstring_,flags=_re.MULTILINE)
+
+def extend_docstring(docstring: _Union[str, _Callable] = None,
+                     extra_parameters: str = None) -> _Callable:
     """
-    Decorator: Combine another function's docstring with a given docstring.
+    Decorator: Extend the function's docstring.
 
     Parameters
     ----------
-    f : function
+    docstring : str or callable, optional
-       Function of which the docstring is taken.
+       Docstring to extend. Defaults to that of decorated function.
-    extra_docstring : str
+    extra_parameters : str, optional
-       Docstring to append.
+       Additional information to append to Parameters section.
+
+    Notes
+    -----
+    Return type will become own type if docstring is callable.
 
     """
     def _decorator(func):
-        func.__doc__ = f.__doc__ + extra_docstring
+        func.__doc__ = _docstringer(func.__doc__ if docstring is None else docstring,
+                                    extra_parameters,
+                                    func if isinstance(docstring,_Callable) else None,
+                                   )
         return func
     return _decorator
 
@@ -649,7 +695,6 @@ def Bravais_to_Miller(*,
                                               [0,0,0,1]]))
     return _np.einsum('il,...l',basis,axis)
 
-
 def Miller_to_Bravais(*,
                       uvw: _np.ndarray = None,
                       hkl: _np.ndarray = None) -> _np.ndarray:
@@ -706,7 +751,6 @@ def dict_prune(d: _Dict) -> _Dict:
 
     return new
 
-
 def dict_flatten(d: _Dict) -> _Dict:
     """
     Recursively remove keys of single-entry dictionaries.

python/tests/test_util.py

@@ -8,7 +8,6 @@ import h5py
 
 from damask import util
 
-
 class TestUtil:
 
     @pytest.mark.xfail(sys.platform == 'win32', reason='echo is not a Windows command')
@@ -208,3 +207,128 @@ class TestUtil:
     @pytest.mark.parametrize('kw_Miller,kw_Bravais',[('uvw','uvtw'),('hkl','hkil')])
     def test_Bravais_Miller_Bravais(self,vector,kw_Miller,kw_Bravais):
         assert np.all(vector == util.Miller_to_Bravais(**{kw_Miller:util.Bravais_to_Miller(**{kw_Bravais:vector})}))
+
+
+    @pytest.mark.parametrize('extra_parameters',["""
+            p2 : str, optional
+                p2 description 1
+                p2 description 2
+            """,
+            """
+
+                        p2 : str, optional
+                            p2 description 1
+                            p2 description 2
+
+            """,
+            """
+p2 : str, optional
+    p2 description 1
+    p2 description 2
+            """])
+    @pytest.mark.parametrize('invalid_docstring',["""
+                        Function description
+
+                        Parameters ----------
+                        p0 : numpy.ndarray, shape (...,4)
+                            p0 description 1
+                            p0 description 2
+                        p1 : int, optional
+                            p1 description
+
+                        Remaining description
+                    """,
+                    """
+                        Function description
+
+                        Parameters
+                         ----------
+                        p0 : numpy.ndarray, shape (...,4)
+                            p0 description 1
+                            p0 description 2
+                        p1 : int, optional
+                            p1 description
+
+                        Remaining description
+                    """,])
+    def test_extend_docstring_parameters(self,extra_parameters,invalid_docstring):
+        test_docstring = """
+            Function description
+
+            Parameters
+            ----------
+            p0 : numpy.ndarray, shape (...,4)
+                p0 description 1
+                p0 description 2
+            p1 : int, optional
+                p1 description
+
+            Remaining description
+        """
+        invalid_docstring = """
+            Function description
+
+            Parameters ----------
+            p0 : numpy.ndarray, shape (...,4)
+                p0 description 1
+                p0 description 2
+            p1 : int, optional
+                p1 description
+
+            Remaining description
+        """
+        expected = """
+            Function description
+
+            Parameters
+            ----------
+            p0 : numpy.ndarray, shape (...,4)
+                p0 description 1
+                p0 description 2
+            p1 : int, optional
+                p1 description
+            p2 : str, optional
+                p2 description 1
+                p2 description 2
+
+            Remaining description
+        """.split("\n")
+        assert expected == util._docstringer(test_docstring,extra_parameters).split('\n')
+        with pytest.raises(RuntimeError):
+            util._docstringer(invalid_docstring,extra_parameters)
+
+    def test_replace_docstring_return_type(self):
+        class TestClassOriginal:
+            pass
+
+        def original_func() -> TestClassOriginal:
+            pass
+
+        class TestClassDecorated:
+            def decorated_func_bound(self) -> 'TestClassDecorated':
+                pass
+
+        def decorated_func() -> TestClassDecorated:
+            pass
+
+        original_func.__doc__ = """
+            Function description/Parameters
+
+            Returns
+            -------
+            Return value : test_util.TestClassOriginal
+
+            Remaining description
+        """
+
+        expected = """
+            Function description/Parameters
+
+            Returns
+            -------
+            Return value : test_util.TestClassDecorated
+
+            Remaining description
+        """
+        assert expected == util._docstringer(original_func,return_type=decorated_func)
+        assert expected == util._docstringer(original_func,return_type=TestClassDecorated.decorated_func_bound)