improvements to docstrings (in `damask.Rotation`)

This commit is contained in:
Daniel Otto de Mentock 2023-03-02 18:46:00 +00:00 committed by Martin Diehl
parent 4e3dc69762
commit ad39577ea4
3 changed files with 306 additions and 143 deletions

View File

@ -9,31 +9,6 @@ from . import Crystal
from . import util
from . import tensor
_parameter_doc = \
"""
family : {'triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic'}, optional.
Name of the crystal family.
Family will be inferred if 'lattice' is given.
lattice : {'aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF'}, optional.
Name of the Bravais lattice in Pearson notation.
a : float, optional
Length of lattice parameter 'a'.
b : float, optional
Length of lattice parameter 'b'.
c : float, optional
Length of lattice parameter 'c'.
alpha : float, optional
Angle between b and c lattice basis.
beta : float, optional
Angle between c and a lattice basis.
gamma : float, optional
Angle between a and b lattice basis.
degrees : bool, optional
Angles are given in degrees. Defaults to False.
"""
MyType = TypeVar('MyType', bound='Orientation')
class Orientation(Rotation,Crystal):
@ -93,7 +68,7 @@ class Orientation(Rotation,Crystal):
"""
@util.extend_docstring(extra_parameters=_parameter_doc)
@util.extend_docstring(adopted_parameters=Crystal.__init__)
def __init__(self,
rotation: Union[FloatSequence, Rotation] = np.array([1.,0.,0.,0.]),
*,
@ -267,84 +242,84 @@ class Orientation(Rotation,Crystal):
@classmethod
@util.extend_docstring(Rotation.from_random,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_random, wrapped=__init__)
def from_random(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_quaternion,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_quaternion, wrapped=__init__)
def from_quaternion(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_Euler_angles,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_Euler_angles, wrapped=__init__)
def from_Euler_angles(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_axis_angle,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_axis_angle, wrapped=__init__)
def from_axis_angle(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_basis,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_basis, wrapped=__init__)
def from_basis(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_matrix,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_matrix, wrapped=__init__)
def from_matrix(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_Rodrigues_vector,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_Rodrigues_vector, wrapped=__init__)
def from_Rodrigues_vector(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_homochoric,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_homochoric, wrapped=__init__)
def from_homochoric(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_cubochoric,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_cubochoric, wrapped=__init__)
def from_cubochoric(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_spherical_component,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_spherical_component, wrapped=__init__)
def from_spherical_component(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(Rotation.from_fiber_component,
extra_parameters=_parameter_doc)
adopted_parameters=Crystal.__init__)
@util.pass_on('rotation', Rotation.from_fiber_component, wrapped=__init__)
def from_fiber_component(cls, **kwargs) -> 'Orientation':
return cls(**kwargs)
@classmethod
@util.extend_docstring(extra_parameters=_parameter_doc)
@util.extend_docstring(adopted_parameters=Crystal.__init__)
def from_directions(cls,
uvw: FloatSequence,
hkl: FloatSequence,

View File

@ -8,7 +8,7 @@ import shlex as _shlex
import re as _re
import signal as _signal
import fractions as _fractions
from collections import abc as _abc
from collections import abc as _abc, OrderedDict as _OrderedDict
from functools import reduce as _reduce, partial as _partial, wraps as _wraps
import inspect
from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
@ -541,10 +541,11 @@ def shapeblender(a: _Tuple[int, ...],
def _docstringer(docstring: _Union[str, _Callable],
extra_parameters: _Optional[str] = None,
# extra_examples: _Optional[str] = None,
# extra_notes: _Optional[str] = None,
return_type: _Union[None, str, _Callable] = None) -> str:
adopted_parameters: _Union[None, str, _Callable] = None,
adopted_return: _Union[None, str, _Callable] = None,
adopted_notes: _Union[None, str, _Callable] = None,
adopted_examples: _Union[None, str, _Callable] = None,
adopted_references: _Union[None, str, _Callable] = None) -> str:
"""
Extend a docstring.
@ -552,50 +553,85 @@ def _docstringer(docstring: _Union[str, _Callable],
----------
docstring : str or callable, optional
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.
adopted_* : str or callable, optional
Additional information to insert into/append to respective section.
Notes
-----
adopted_return fetches the typehint of a passed function instead of the docstring
"""
docstring_ = str( docstring if isinstance(docstring,str)
else docstring.__doc__ if hasattr(docstring,'__doc__')
else '')
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)
docstring_: str = str( docstring if isinstance(docstring,str)
else docstring.__doc__ if callable(docstring) and docstring.__doc__
else '').rstrip()+'\n'
sections = _OrderedDict(
Parameters=adopted_parameters,
Returns=adopted_return,
Examples=adopted_examples,
Notes=adopted_notes,
References=adopted_references)
if return_type is None:
return docstring_
else:
if isinstance(return_type,str):
return_type_ = return_type
for i, (key, adopted) in [(i,(k,v)) for (i,(k,v)) in enumerate(sections.items()) if v is not None]:
section_regex = fr'^([ ]*){key}\s*\n\1*{"-"*len(key)}\s*\n'
if key=='Returns':
if callable(adopted):
return_class = adopted.__annotations__.get('return','')
return_type_ = (_sys.modules[adopted.__module__].__name__.split('.')[0]
+'.'
+(return_class.__name__ if not isinstance(return_class,str) else return_class))
else:
return_type_ = adopted
docstring_ = _re.sub(fr'(^[ ]*{key}\s*\n\s*{"-"*len(key)}\s*\n[ ]*[A-Za-z0-9_ ]*: )(.*)\n',
fr'\1{return_type_}\n',
docstring_,flags=_re.MULTILINE)
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)
)
section_content_regex = fr'{section_regex}(?P<content>.*?)\n *(\n|\Z)'
adopted_: str = adopted.__doc__ if callable(adopted) else adopted #type: ignore
try:
if _re.search(fr'{section_regex}', adopted_, flags=_re.MULTILINE):
adopted_ = _re.search(section_content_regex, #type: ignore
adopted_,
flags=_re.MULTILINE|_re.DOTALL).group('content')
except AttributeError:
raise RuntimeError(f"Function docstring passed for docstring section '{key}' is invalid:\n{docstring}")
docstring_indent, adopted_indent = (min([len(line)-len(line.lstrip()) for line in section.split('\n') if line.strip()])
for section in [docstring_, adopted_])
shift = adopted_indent - docstring_indent
adopted_content = '\n'.join([(line[shift:] if shift > 0 else
f'{" "*-shift}{line}') for line in adopted_.split('\n') if line.strip()])
if _re.search(section_regex, docstring_, flags=_re.MULTILINE):
docstring_section_content = _re.search(section_content_regex, # type: ignore
docstring_,
flags=_re.MULTILINE|_re.DOTALL).group('content')
a_items, d_items = (_re.findall('^[ ]*([A-Za-z0-9_ ]*?)[ ]*:',content,flags=_re.MULTILINE)
for content in [adopted_content,docstring_section_content])
for item in a_items:
if item in d_items:
adopted_content = _re.sub(fr'^([ ]*){item}.*?(?:(\n)\1([A-Za-z0-9_])|([ ]*\Z))',
r'\1\3',
adopted_content,
flags=_re.MULTILINE|_re.DOTALL).rstrip(' \n')
docstring_ = _re.sub(fr'(^[ ]*{key}\s*\n\s*{"-"*len(key)}\s*\n.*?)\n *(\Z|\n)',
fr'\1\n{adopted_content}\n\2',
docstring_,
flags=_re.MULTILINE|_re.DOTALL)
else:
section_title = f'{" "*(shift+docstring_indent)}{key}\n{" "*(shift+docstring_indent)}{"-"*len(key)}\n'
section_matches = [_re.search(
fr'[ ]*{list(sections.keys())[index]}\s*\n\s*{"-"*len(list(sections.keys())[index])}\s*', docstring_)
for index in range(i,len(sections))]
subsequent_section = '\\Z' if not any(section_matches) else \
'\n'+next(item for item in section_matches if item is not None).group(0)
docstring_ = _re.sub(fr'({subsequent_section})',
fr'\n{section_title}{adopted_content}\n\1',
docstring_)
return docstring_
return _re.sub(r'(^([ ]*)Returns\s*\n\2-------\s*\n[ ]*[A-Za-z0-9_ ]*: )(.*)\n',
fr'\1{return_type_}\n',
docstring_,flags=_re.MULTILINE)
def extend_docstring(docstring: _Union[None, str, _Callable] = None,
extra_parameters: _Optional[str] = None) -> _Callable:
**kwargs) -> _Callable:
"""
Decorator: Extend the function's docstring.
@ -603,8 +639,8 @@ def extend_docstring(docstring: _Union[None, str, _Callable] = None,
----------
docstring : str or callable, optional
Docstring to extend. Defaults to that of decorated function.
extra_parameters : str, optional
Additional information to append to Parameters section.
adopted_* : str or callable, optional
Additional information to insert into/append to respective section.
Notes
-----
@ -612,10 +648,9 @@ def extend_docstring(docstring: _Union[None, str, _Callable] = None,
"""
def _decorator(func):
if 'adopted_return' not in kwargs: kwargs['adopted_return'] = func
func.__doc__ = _docstringer(func.__doc__ if docstring is None else docstring,
extra_parameters,
func if isinstance(docstring,_Callable) else None,
)
**kwargs)
return func
return _decorator
@ -657,7 +692,8 @@ def pass_on(keyword: str,
for f in [target] if wrapped is None else [target,wrapped]:
for param in inspect.signature(f).parameters.values():
if param.name != keyword \
and param.name not in [p.name for p in args_]+['self','cls', 'args', 'kwargs']: args_.append(param)
and param.name not in [p.name for p in args_]+['self','cls', 'args', 'kwargs']:
args_.append(param.replace(kind=inspect._ParameterKind.KEYWORD_ONLY))
wrapper.__signature__ = inspect.Signature(parameters=args_,return_annotation=inspect.signature(func).return_annotation)
return wrapper
return decorator

View File

@ -230,52 +230,30 @@ class TestUtil:
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',["""
@pytest.mark.parametrize('adopted_parameters',[
pytest.param("""
p2 : str, optional
p2 description 1
p2 description 2
""",
"""
id = 'standard'),
pytest.param("""
p2 : str, optional
p2 description 1
p2 description 2
""",
"""
id = 'indented'),
pytest.param("""
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):
""",
id = 'no_indent')])
def test_extend_docstring_parameters_string(self,adopted_parameters):
test_docstring = """
Function description
Function description.
Parameters
----------
@ -285,10 +263,10 @@ p2 : str, optional
p1 : int, optional
p1 description
Remaining description
Remaining description\n"""
assert util._docstringer(test_docstring,adopted_parameters) ==\
"""
expected = """
Function description
Function description.
Parameters
----------
@ -301,47 +279,221 @@ 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)
Remaining description\n"""
def test_replace_docstring_return_type(self):
def test_extend_docstring_parameters_function(self):
test_docstring = """
Function description.
Parameters
----------
p0 : numpy.ndarray, shape (...,4)
p0 description 1
"""
def testfunction_1():
"""
Function description.
Parameters
----------
p1 : int, optional
p1 description
Notes
-----
Function Notes 1
Function Notes 2
References
----------
Reference 1
<reference link>
Reference 2
<reference link>
"""
pass
assert (test_docstring:=util._docstringer(test_docstring,adopted_references = testfunction_1)) == \
"""
Function description.
Parameters
----------
p0 : numpy.ndarray, shape (...,4)
p0 description 1
References
----------
Reference 1
<reference link>
Reference 2
<reference link>\n"""
assert (test_docstring:=util._docstringer(test_docstring,adopted_notes = testfunction_1)) == \
"""
Function description.
Parameters
----------
p0 : numpy.ndarray, shape (...,4)
p0 description 1
Notes
-----
Function Notes 1
Function Notes 2
References
----------
Reference 1
<reference link>
Reference 2
<reference link>\n"""
def testfunction_2():
"""
Function description.
References
----------
Reference 3
<reference link>
"""
assert (test_docstring:=util._docstringer(test_docstring,adopted_references = testfunction_2)) == \
"""
Function description.
Parameters
----------
p0 : numpy.ndarray, shape (...,4)
p0 description 1
Notes
-----
Function Notes 1
Function Notes 2
References
----------
Reference 1
<reference link>
Reference 2
<reference link>
Reference 3
<reference link>\n"""
def return_bound_method():
class TestClassDecorated:
def decorated_func_bound(self) -> 'TestClassDecorated':
pass
return TestClassDecorated.decorated_func_bound
def return_simple_function():
class TestClassDecorated:
pass
def decorated_func() -> TestClassDecorated:
pass
return decorated_func
@pytest.mark.parametrize('adopted_return',[
pytest.param(return_simple_function(),
id = 'decorated_func'),
pytest.param(return_bound_method(),
id = 'decorated_func_bound'),
pytest.param('test_util.TestClassDecorated',
id = 'decorated_func_bound')])
def test_replace_docstring_return(self,adopted_return):
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
Function description.
Returns
-------
Return value : test_util.TestClassOriginal
Remaining description
"""
"""
expected = """
Function description/Parameters
assert util._docstringer(original_func,adopted_return=adopted_return) == """
Function description.
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)
Remaining description\n"""
@pytest.mark.parametrize('adopted_func_doc',[
pytest.param("""
Function description.
Parameters
----------
b : float 4
b description
c : float 5
c description differing
d : float 6
d description
Remaining description\n
""",
id = 'append'),
pytest.param("""
Function description.
Parameters
----------
d : float 6
d description
a : float 7
a description\n""",
id = 'insert')])
def test_extend_docstring_overlapping_section_content(self,adopted_func_doc):
original_func_doc = """
Function description.
Parameters
----------
a : float 1
a description
b : float 2
b description
c : float 3
c description
Remaining description\n"""
expected = """
Function description.
Parameters
----------
a : float 1
a description
b : float 2
b description
c : float 3
c description
d : float 6
d description
Remaining description\n"""
assert util._docstringer(original_func_doc,adopted_parameters=adopted_func_doc) == expected
def test_passon_result(self):
def testfunction_inner(a=None,b=None):
@ -377,4 +529,4 @@ p2 : str, optional
return kwargs['inner_result']+kwargs['c']+kwargs['d']
assert pydoc.render_doc(testfunction_outer, renderer=pydoc.plaintext).split("\n")[-2] ==\
'testfunction_outer(a=None, b=None, *, c=None, d=None) -> int'
'testfunction_outer(*, a=None, b=None, c=None, d=None) -> int'