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Push — master ( 1b49d8...c3d981 )

by Rich

created 2016-08-08 14:38 UTC

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Lines	0
Ratio	0 %

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Tests	4
CRAP Score	2

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Metric	Value
c	0
b	0
f	0
dl	0
loc	5
ccs	4
cts	4
cp	1
rs	9.4285
cc	2
crap	2

#! /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):

    """ Atom interface wrapper """

    def __init__(self, owner):
        self.owner = owner

    def __iter__(self):
        return ChemObjectIterator(self)

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

    @property
    def props(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return MolPropertyView(self)

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


class ChemObjectIterator(object):

    """ Atom iterator """

    def __init__(self, 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 """
    __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):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        for idx in self.keys():
            self.remove(idx)

    def items(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return list((k, self[k]) for k in self.keys())

    def remove(self, key):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self.__delitem__(key)

    def __getitem__(self, key):
        raise NotImplemented


    def __setitem__(self, key, value):
        raise NotImplemented


    def __delitem__(self, key):
        raise NotImplemented


    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):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return dict(self)

    def to_series(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return pd.Series(self.to_dict())


class PropertyView(View):

    """ Property object wrapper """

    def __init__(self, owner):
        self._owner = owner

    def keys(self):
        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 """

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

    def keys(self):
        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):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return pd.DataFrame(dict(self), index=self._obj_view.index)

    def to_dict(self):
        return {k: v.tolist() for k, v in pd.compat.iteritems(self)}

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



Push — master ( 1b49d8...c3d981 )

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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		""" Atom interface wrapper """
34
35	1	def __init__(self, owner):
36	1	self.owner = owner
37	1
38		def __iter__(self):
39	1	return ChemObjectIterator(self)
40	1
41	1	def __str__(self):
42		return str(list(str(obj) for obj in self))
43	1
44	1	@property
45		def props(self):
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 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...
46	1	return MolPropertyView(self)
47	1
48		def __repr__(self):
49	1	return '<{class_} values="{values}" at {address}>'.format(
50		class_=self.__class__.__name__,
51		values=str(self),
52	1	address=hex(id(self)))
53
54
55		class ChemObjectIterator(object):
56	1
57		""" Atom iterator """
58
59		def __init__(self, view):
60	1	self.view = view
61		self._current = 0
62		self._high = len(self.view)
63
64	1	def __next__(self):
65		if self._current >= self._high:
66		raise StopIteration
67		else:
68	1	self._current += 1
69		return self.view[self._current - 1]
70
71		# py2 compat
72		next = __next__
73
74
75	1	class View(object):
76
77		""" View wrapper interface """
78		__metaclass__ = ABCMeta
79	1
80	1	@abstractmethod
81	1	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...
82	1	return []
83
84	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...
85	1	if index in self.keys():
86	1	return self[index]
87		else:
88	1	return default
89	1
90		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...
91		if default:
92	1	val = self.get(index, default)
93		else:
94		val = self[index]
95	1	self.remove(index)
96		return val
97
98	1	def clear(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...
99		for idx in self.keys():
100	1	self.remove(idx)
101
102		def items(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...
103		return list((k, self[k]) for k in self.keys())
104	1
105	1	def remove(self, key):
		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...
106	1	self.__delitem__(key)
107
108	1	def __getitem__(self, key):
109		raise NotImplemented
		0 ignored issues – show Best Practice introduced 2016-05-24 17:01 UTC by Report Bug Copy Issue Report NotImplemented raised - should raise NotImplementedError Loading history...
110	1
111	1	def __setitem__(self, key, value):
112		raise NotImplemented
		0 ignored issues – show Best Practice introduced 2016-05-24 17:01 UTC by Report Bug Copy Issue Report NotImplemented raised - should raise NotImplementedError Loading history...
113
114	1	def __delitem__(self, key):
115	1	raise NotImplemented
		0 ignored issues – show Best Practice introduced 2016-05-24 17:01 UTC by Report Bug Copy Issue Report NotImplemented raised - should raise NotImplementedError Loading history...
116	1
117		def __iter__(self):
118	1	return iter(self.keys())
119	1
120	1	def __str__(self):
121		return str(self.to_dict())
122	1
123	1	def __len__(self):
124		return len(self.keys())
125	1
126	1	def __repr__(self):
127		return '<{klass} values="{values}" at {address}>'.format(
128	1	klass=self.__class__.__name__,
129		values=str(self),
130		address=hex(id(self)))
131	1
132		def to_dict(self):
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 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...
133		return dict(self)
134	1
135		def to_series(self):
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 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...
136		return pd.Series(self.to_dict())
137	1
138
139		class PropertyView(View):
140	1
141		""" Property object wrapper """
142
143	1	def __init__(self, owner):
144	1	self._owner = owner
145
146	1	def keys(self):
147		return list(k for k in self._owner.GetPropNames() if k[:1] != '_')
148
149		def __getitem__(self, key):
150
151		# we manually work out if it was a float that was stored, as GetProp
152		# returns floats and ints set by SetDoubleProp and SetIntProp as strings
153	1	value = self._owner.GetProp(str(key))
154		try:
155		return int(value)
156		except ValueError:
157	1	try:
158	1	return float(value)
159		except ValueError:
160	1	return value
161	1
162		def __setitem__(self, key, value):
163	1
164		if not isinstance(key, str):
165		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...
166		key = str(key)
167	1
168	1	if key[0] == '_':
169	1	warnings.warn("`{value}` is a private RDKit property key. "
170	1	"Using this may have unintended consequences.".format(value=value))
171	1
172	1	if isinstance(value, str):
173	1	self._owner.SetProp(key, value)
174	1	elif isinstance(value, (int, np.int64, np.int32)):
175		self._owner.SetIntProp(key, value)
176	1	elif isinstance(value, (float, np.float64, np.float32)):
177		self._owner.SetDoubleProp(key, value)
178	1	else:
179	1	warnings.warn("RDKit property keys can only be `str`, `int` or `float`."
180	1	"Using `{value}` as a `str`.".format(value=value))
181		self._owner.SetProp(key, str(value))
182	1
183		def __delitem__(self, index):
184		self._owner.ClearProp(index)
185
186	1
187	1
188	1	class MolPropertyView(View):
189	1
190	1	""" Mol property wrapper """
191	1
192		def __init__(self, obj_view):
193		self._obj_view = obj_view
194
195		def keys(self):
196		res = set()
197	1	for atom in self._obj_view:
198	1	res = res.union(set(atom.props.keys()))
199		return list(res)
200
201	1	def get(self, key, default=None):
202		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...
203
204		def __getitem__(self, key):
205	1	if key not in self.keys():
206	1	raise KeyError('No atoms have the property set.')
207		return self.get(key, None)
208	1
209	1	def __setitem__(self, key, value):
210	1	if isinstance(value, (pd.Series, dict)):
211	1	for idx, val in pd.compat.iteritems(value):
212	1	self._obj_view[int(idx)].props[key] = val
213		else:
214	1	assert len(self._obj_view) == len(value), "Must pass same number of values as atoms."
215	1	for atom, val in zip(self._obj_view, value):
216		atom.props[key] = val
217	1
218	1	def __delitem__(self, key):
219	1	for atom in self._obj_view:
220	1	atom.props.remove(key)
221
222	1	def to_frame(self):
		0 ignored issues – show Coding Style introduced 2016-08-08 14:55 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...
223	1	return pd.DataFrame(dict(self), index=self._obj_view.index)
224	1
225	1	def to_dict(self):
226		return {k: v.tolist() for k, v in pd.compat.iteritems(self)}
227	1
228	1	def __str__(self):
229	1	return str(self.to_dict())
230
231

richlewis42 / scikit-chem

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