ChemicalObjectView.to_list() - Code Metrics - Inspection of "added masking and indexing to ChemObjectView" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 39262f...560cc3 )

by Rich

created 2016-08-12 10:59 UTC

ChemicalObjectView.to_list() A

↳ Parent: ChemicalObjectView

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	1.125

Importance

Changes

Metric	Value
c	0
b	0
f	0
dl	0
loc	4
ccs	1
cts	2
cp	0.5
rs	10
cc	1
crap	1.125

#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
# License: 3-clause BSD

"""
## skchem.core.base

Define base classes for scikit chem objects
"""

from abc import ABCMeta, abstractmethod
import warnings
import numpy as np
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
import pandas as pd
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3


class ChemicalObject(object):

    """ A mixin for each chemical object in scikit-chem. """

    @classmethod
    def from_super(cls, obj):

        """A method that converts the class of an object of parent class to that of the child. """

        obj.__class__ = cls
        return obj


class ChemicalObjectView(object):

    """ Abstract iterable view of chemical objects.

    Concrete classes inheriting from it should implement `__getitem__` and `__len__`.
    """

    __metaclass__ = ABCMeta

    def __init__(self, owner):
        """ Return a view """
        self.owner = owner

    @abstractmethod
    def __getitem__(self, index):
        # subclass call this, then implement the actual get if None
        if isinstance(index, slice):
            return self.to_list()[index]
        if isinstance(index, list) \
                and all(isinstance(i, bool) for i in index) \
                and len(index) == len(self):
            return [self[i] for i, ix in enumerate(index) if ix]
        elif isinstance(index, (list, tuple)):
            return [self[ix] for ix in index]
        else:
            return None

    @abstractmethod
    def __len__(self):
        pass

    def __iter__(self):
        return ChemicalObjectIterator(self)

    def __str__(self):
        return str(list(str(obj) for obj in self))

    @property
    def props(self):
        """ Return a property view of the objects in the view. """

        return MolPropertyView(self)

    def to_list(self):
        """ Return a list of objects in the view. """

        return list(self)

    def __repr__(self):
        return '<{class_} values="{values}" at {address}>'.format(
            class_=self.__class__.__name__,
            values=str(self),
            address=hex(id(self)))


class ChemicalObjectIterator(object):

    """  Iterator for chemical object views.  """

    def __init__(self, view):
        """ Create an iterator from a chemical object view. """
        self.view = view
        self._current = 0
        self._high = len(self.view)

    def __next__(self):
        if self._current >= self._high:
            raise StopIteration
        else:
            self._current += 1
            return self.view[self._current - 1]

    # py2 compat
    next = __next__


class View(object):

    """ View wrapper interface.  Conforms to the dictionary interface.

    Objects inheriting from this should implement the `keys`, `getitem`,
    `setitem` and `delitem` methods."""

    __metaclass__ = ABCMeta

    @abstractmethod
    def keys(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return []

    def get(self, index, default=None):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if index in self.keys():
            return self[index]
        else:
            return default

    def pop(self, index, default=None):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if default:
            val = self.get(index, default)
        else:
            val = self[index]
        self.remove(index)
        return val

    def clear(self):
        """ Remove all properties from the object. """
        for idx in self.keys():
            self.remove(idx)

    def items(self):
        """ Return an iterable of key, value pairs. """

        return list((k, self[k]) for k in self.keys())

    def remove(self, key):
        """ Remove a property from the object. """
        self.__delitem__(key)

    @abstractmethod
    def __getitem__(self, key):
        pass

    @abstractmethod
    def __setitem__(self, key, value):
        pass

    @abstractmethod
    def __delitem__(self, key):
        pass

    def __iter__(self):
        return iter(self.keys())

    def __str__(self):
        return str(self.to_dict())

    def __len__(self):
        return len(self.keys())

    def __repr__(self):
        return '<{klass} values="{values}" at {address}>'.format(
            klass=self.__class__.__name__,
            values=str(self),
            address=hex(id(self)))

    def to_dict(self):
        """ Return a dict of the properties on the object. """
        return dict(self)

    def to_series(self):
        """ Return a pd.Series of the properties on the object. """
        return pd.Series(self.to_dict())


class PropertyView(View):
    """ Property object wrapper.

     This provides properties for rdkit objects. """

    def __init__(self, owner):
        """ Initialize a PropertyView.

        Args:
            owner(skchem.ChemicalObject):
                A chemical object with properties, such as `skchem.Atom`."""

        self._owner = owner

    def keys(self):
        """ The available property keys on the object. """

        return list(k for k in self._owner.GetPropNames() if k[:1] != '_')

    def __getitem__(self, key):

        # we manually work out if it was a float that was stored, as GetProp
        # returns floats and ints set by SetDoubleProp and SetIntProp as strings
        value = self._owner.GetProp(str(key))
        try:
            return int(value)
        except ValueError:
            try:
                return float(value)
            except ValueError:
                return value

    def __setitem__(self, key, value):

        if not isinstance(key, str):
            warnings.warn("RDKit property keys can only be of type `str`.  Using `{key}` as a `str`.".format(key=key))

            key = str(key)

        if key[0] == '_':
            warnings.warn("`{value}` is a private RDKit property key. "
                          "Using this may have unintended consequences.".format(value=value))

        if isinstance(value, str):
            self._owner.SetProp(key, value)
        elif isinstance(value, (int, np.int64, np.int32)):
            self._owner.SetIntProp(key, value)
        elif isinstance(value, (float, np.float64, np.float32)):
            self._owner.SetDoubleProp(key, value)
        else:
            warnings.warn("RDKit property keys can only be `str`, `int` or `float`."
                          "Using `{value}` as a `str`.".format(value=value))
            self._owner.SetProp(key, str(value))

    def __delitem__(self, index):
        self._owner.ClearProp(index)


class MolPropertyView(View):

    """ Mol property wrapper.

    This provides properties for the atom and bond views. """

    def __init__(self, obj_view):
        self._obj_view = obj_view

    def keys(self):
        """ The available property keys on the object. """

        res = set()
        for atom in self._obj_view:
            res = res.union(set(atom.props.keys()))
        return list(res)

    def get(self, key, default=None):
        return pd.Series((a.props.get(key, default) for a in self._obj_view), index=self._obj_view.index)


    def __getitem__(self, key):
        if key not in self.keys():
            raise KeyError('No atoms have the property set.')
        return self.get(key, None)

    def __setitem__(self, key, value):
        if isinstance(value, (pd.Series, dict)):
            for idx, val in pd.compat.iteritems(value):
                self._obj_view[int(idx)].props[key] = val
        else:
            assert len(self._obj_view) == len(value), "Must pass same number of values as atoms."
            for atom, val in zip(self._obj_view, value):
                atom.props[key] = val

    def __delitem__(self, key):
        for atom in self._obj_view:
            atom.props.remove(key)

    def to_frame(self):

        """ Return a DataFrame of the properties of the objects of the molecular view. """

        return pd.DataFrame(dict(self), index=self._obj_view.index)

    def to_dict(self):

        """ Return a dict of the properties of the objectos fo the molecular view. """

        return {k: v.tolist() for k, v in self.items()}

    def __str__(self):
        return str(self.to_dict())



Push — master ( 39262f...560cc3 )

ChemicalObjectView.to_list() A

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1		#! /usr/bin/env python
2		#
3		# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	"""
7		## skchem.core.base
8
9		Define base classes for scikit chem objects
10		"""
11
12	1	from abc import ABCMeta, abstractmethod
13	1	import warnings
14	1	import numpy as np
		0 ignored issues – show Configuration introduced 2016-05-24 17:01 UTC by Report Bug Copy Issue Report The import `numpy` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
15	1	import pandas as pd
		0 ignored issues – show Configuration introduced 2016-07-18 17:48 UTC by Report Bug Copy Issue Report The import `pandas` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
16
17
18	1	class ChemicalObject(object):
19
20		""" A mixin for each chemical object in scikit-chem. """
21
22	1	@classmethod
23		def from_super(cls, obj):
24
25		"""A method that converts the class of an object of parent class to that of the child. """
26
27	1	obj.__class__ = cls
28	1	return obj
29
30
31	1	class ChemicalObjectView(object):
32
33		""" Abstract iterable view of chemical objects.
34
35		Concrete classes inheriting from it should implement `__getitem__` and `__len__`.
36		"""
37
38	1	__metaclass__ = ABCMeta
39
40	1	def __init__(self, owner):
41		""" Return a view """
42	1	self.owner = owner
43
44	1	@abstractmethod
45		def __getitem__(self, index):
46		# subclass call this, then implement the actual get if None
47	1	if isinstance(index, slice):
48		return self.to_list()[index]
49	1	if isinstance(index, list) \
50		and all(isinstance(i, bool) for i in index) \
51		and len(index) == len(self):
52		return [self[i] for i, ix in enumerate(index) if ix]
53	1	elif isinstance(index, (list, tuple)):
54		return [self[ix] for ix in index]
55		else:
56	1	return None
57
58	1	@abstractmethod
59		def __len__(self):
60		pass
61
62	1	def __iter__(self):
63	1	return ChemicalObjectIterator(self)
64
65	1	def __str__(self):
66	1	return str(list(str(obj) for obj in self))
67
68	1	@property
69		def props(self):
70		""" Return a property view of the objects in the view. """
71
72	1	return MolPropertyView(self)
73
74	1	def to_list(self):
75		""" Return a list of objects in the view. """
76
77		return list(self)
78
79	1	def __repr__(self):
80	1	return '<{class_} values="{values}" at {address}>'.format(
81		class_=self.__class__.__name__,
82		values=str(self),
83		address=hex(id(self)))
84
85
86	1	class ChemicalObjectIterator(object):
87
88		""" Iterator for chemical object views. """
89
90	1	def __init__(self, view):
91		""" Create an iterator from a chemical object view. """
92	1	self.view = view
93	1	self._current = 0
94	1	self._high = len(self.view)
95
96	1	def __next__(self):
97	1	if self._current >= self._high:
98	1	raise StopIteration
99		else:
100	1	self._current += 1
101	1	return self.view[self._current - 1]
102
103		# py2 compat
104	1	next = __next__
105
106
107	1	class View(object):
108
109		""" View wrapper interface. Conforms to the dictionary interface.
110
111		Objects inheriting from this should implement the `keys`, `getitem`,
112		`setitem` and `delitem` methods."""
113
114	1	__metaclass__ = ABCMeta
115
116	1	@abstractmethod
117		def keys(self):
		0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
118		return []
119
120	1	def get(self, index, default=None):
		0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
121	1	if index in self.keys():
122	1	return self[index]
123		else:
124	1	return default
125
126	1	def pop(self, index, default=None):
		0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
127	1	if default:
128		val = self.get(index, default)
129		else:
130	1	val = self[index]
131	1	self.remove(index)
132	1	return val
133
134	1	def clear(self):
135		""" Remove all properties from the object. """
136	1	for idx in self.keys():
137	1	self.remove(idx)
138
139	1	def items(self):
140		""" Return an iterable of key, value pairs. """
141
142	1	return list((k, self[k]) for k in self.keys())
143
144	1	def remove(self, key):
145		""" Remove a property from the object. """
146	1	self.__delitem__(key)
147
148	1	@abstractmethod
149		def __getitem__(self, key):
150		pass
151
152	1	@abstractmethod
153		def __setitem__(self, key, value):
154		pass
155
156	1	@abstractmethod
157		def __delitem__(self, key):
158		pass
159
160	1	def __iter__(self):
161		return iter(self.keys())
162
163	1	def __str__(self):
164		return str(self.to_dict())
165
166	1	def __len__(self):
167	1	return len(self.keys())
168
169	1	def __repr__(self):
170	1	return '<{klass} values="{values}" at {address}>'.format(
171		klass=self.__class__.__name__,
172		values=str(self),
173		address=hex(id(self)))
174
175	1	def to_dict(self):
176		""" Return a dict of the properties on the object. """
177	1	return dict(self)
178
179	1	def to_series(self):
180		""" Return a pd.Series of the properties on the object. """
181	1	return pd.Series(self.to_dict())
182
183
184	1	class PropertyView(View):
185		""" Property object wrapper.
186
187		This provides properties for rdkit objects. """
188
189	1	def __init__(self, owner):
190		""" Initialize a PropertyView.
191
192		Args:
193		owner(skchem.ChemicalObject):
194		A chemical object with properties, such as `skchem.Atom`."""
195
196	1	self._owner = owner
197
198	1	def keys(self):
199		""" The available property keys on the object. """
200
201	1	return list(k for k in self._owner.GetPropNames() if k[:1] != '_')
202
203	1	def __getitem__(self, key):
204
205		# we manually work out if it was a float that was stored, as GetProp
206		# returns floats and ints set by SetDoubleProp and SetIntProp as strings
207	1	value = self._owner.GetProp(str(key))
208	1	try:
209	1	return int(value)
210	1	except ValueError:
211	1	try:
212	1	return float(value)
213	1	except ValueError:
214	1	return value
215
216	1	def __setitem__(self, key, value):
217
218	1	if not isinstance(key, str):
219	1	warnings.warn("RDKit property keys can only be of type `str`. Using `{key}` as a `str`.".format(key=key))
		0 ignored issues – show Coding Style introduced 2016-05-24 17:01 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (118/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
220	1	key = str(key)
221
222	1	if key[0] == '_':
223		warnings.warn("`{value}` is a private RDKit property key. "
224		"Using this may have unintended consequences.".format(value=value))
225
226	1	if isinstance(value, str):
227	1	self._owner.SetProp(key, value)
228	1	elif isinstance(value, (int, np.int64, np.int32)):
229	1	self._owner.SetIntProp(key, value)
230	1	elif isinstance(value, (float, np.float64, np.float32)):
231	1	self._owner.SetDoubleProp(key, value)
232		else:
233		warnings.warn("RDKit property keys can only be `str`, `int` or `float`."
234		"Using `{value}` as a `str`.".format(value=value))
235		self._owner.SetProp(key, str(value))
236
237	1	def __delitem__(self, index):
238	1	self._owner.ClearProp(index)
239
240
241	1	class MolPropertyView(View):
242
243		""" Mol property wrapper.
244
245		This provides properties for the atom and bond views. """
246
247	1	def __init__(self, obj_view):
248	1	self._obj_view = obj_view
249
250	1	def keys(self):
251		""" The available property keys on the object. """
252
253	1	res = set()
254	1	for atom in self._obj_view:
255	1	res = res.union(set(atom.props.keys()))
256	1	return list(res)
257
258	1	def get(self, key, default=None):
259	1	return pd.Series((a.props.get(key, default) for a in self._obj_view), index=self._obj_view.index)
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (105/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
260
261	1	def __getitem__(self, key):
262	1	if key not in self.keys():
263	1	raise KeyError('No atoms have the property set.')
264	1	return self.get(key, None)
265
266	1	def __setitem__(self, key, value):
267	1	if isinstance(value, (pd.Series, dict)):
268		for idx, val in pd.compat.iteritems(value):
269		self._obj_view[int(idx)].props[key] = val
270		else:
271	1	assert len(self._obj_view) == len(value), "Must pass same number of values as atoms."
272	1	for atom, val in zip(self._obj_view, value):
273	1	atom.props[key] = val
274
275	1	def __delitem__(self, key):
276	1	for atom in self._obj_view:
277	1	atom.props.remove(key)
278
279	1	def to_frame(self):
280
281		""" Return a DataFrame of the properties of the objects of the molecular view. """
282
283	1	return pd.DataFrame(dict(self), index=self._obj_view.index)
284
285	1	def to_dict(self):
286
287		""" Return a dict of the properties of the objectos fo the molecular view. """
288
289	1	return {k: v.tolist() for k, v in self.items()}
290
291	1	def __str__(self):
292	1	return str(self.to_dict())
293
294

richlewis42 / scikit-chem

Push — master ( 39262f...560cc3 )

ChemicalObjectView.to_list() A

Complexity

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Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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