Filter.neg() - Code Metrics - Inspection of "changed testing to py.test" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

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Push — master ( 97f98d...9ca1ad )

by Rich

created 2016-06-30 13:42 UTC

Filter.neg() A

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Lines	0
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Importance

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c	2
b	0
f	0
dl	0
loc	3
rs	10
cc	1

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

"""
# skchem.filters

Chemical filters are defined.

"""

import pandas as pd
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from ..utils import method_takes_mol_series, method_takes_pandas

def _identity(x):

    return x

def _identity_meth(_, x):

    return x

class Filter(object):

    """ Filter base class

    Args:
        func (function: Mol => bool):
            The function to use to filter the arguments.
        agg (function: iterable<bool> => bool):
            The aggregation to use in the filter, for example `any` or `all`.

    Examples:

        >>> import skchem

        Initialize the filter with a function:
        >>> is_named = skchem.filters.Filter(lambda m: m.name is not None)

        Filter results can be found with `transform`:
        >>> ethane = skchem.Mol.from_smiles('CC', name='ethane')
        >>> is_named.transform(ethane)
        True

        >>> anonymous = skchem.Mol.from_smiles('c1ccccc1')
        >>> is_named.transform(anonymous)
        False

        The filter can also be used as a function:
        >>> ethane = skchem.Mol.from_smiles('CC', name='ethane')
        >>> is_named.transform(ethane)
        True

        Apply can take a series or dataframe:
        >>> mols = pd.Series({'anonymous': anonymous, 'ethane': ethane})
        >>> is_named.transform(mols)
        anonymous    False
        ethane        True
        dtype: bool

        Using `filter` will drop out molecules that fail the test:
        >>> is_named.filter(mols)
        ethane    <Mol: CC>
        dtype: object

        Only failed are retained with the `neg` keyword argument:
        >>> is_named.filter(mols, neg=True)
        anonymous    <Mol: c1ccccc1>
        dtype: object
    """

    _DEFAULT_AGG = _identity_meth
    _DEFAULT_IS_NEG = False

    def __init__(self, func,  agg=None, neg=False, **kwargs):


        self.func = func
        self.agg = self._get_agg(agg) if agg is not None else self._DEFAULT_AGG
        self.neg = neg
        self.kwargs = kwargs

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

    @agg.setter
    def agg(self, val):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self._agg = self._get_agg(val)
class Foo:
    def __init__(self, x=None):
        self.x = x

    def _get_agg(self, val):
        if val is True:
            return self._DEFAULT_AGG
        elif val is False:
            return _identity
        elif val is None:
            return self.agg
        else:
            return val

    @property
    def neg(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self._get_neg(self._neg)

    @neg.setter
    def neg(self, val):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

        # xor
        self._neg = self._get_neg(val)
class Foo:
    def __init__(self, x=None):
        self.x = x


    def _get_neg(self, val):
        if self._DEFAULT_IS_NEG:
            return not val
        else:
            return val

    @method_takes_mol_series
    def transform(self, mols, agg=None, neg=None):

        """ Apply the function and return the boolean values. """

        agg = self._get_agg(agg)

        if neg is None:
            neg = self._neg
        else:
            neg = self._get_neg(neg)

        res = self._transform(mols)

        if isinstance(res, pd.DataFrame):
            res = res.apply(agg, axis=1)

        if neg:
            res = ~res

        return res

    def _transform(self, ser):
        return ser.apply(self.func, **self.kwargs)

    @method_takes_pandas
    def filter(self, X, y=None, agg=None, neg=None):


        """ Apply the function and return filtered values.

        Args:
            X (pd.Series or pd.DataFrame):
                The compound dataframe. """

        if neg is None:
            neg = self.neg

        agg = self._get_agg(agg)

        res = self.transform(X, neg=neg, agg=agg)

        if y is None:
            return X[res]
        else:
            return X[res], y[res]

    def __call__(self, *args, **kwargs):

        return self.transform(*args, **kwargs)


1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			# skchem.filters
8
9			Chemical filters are defined.
10
11			"""
12
13			import pandas as pd
			0 ignored issues – show Configuration introduced 2016-06-28 09:56 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...
14
15			from ..utils import method_takes_mol_series, method_takes_pandas
16
17			def _identity(x):
			0 ignored issues – show Coding Style Naming introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report The name `x` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
18			return x
19
20			def _identity_meth(_, x):
			0 ignored issues – show Coding Style Naming introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report The name `x` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
21			return x
22
23			class Filter(object):
24
25			""" Filter base class
26
27			Args:
28			func (function: Mol => bool):
29			The function to use to filter the arguments.
30			agg (function: iterable<bool> => bool):
31			The aggregation to use in the filter, for example `any` or `all`.
32
33			Examples:
34
35			>>> import skchem
36
37			Initialize the filter with a function:
38			>>> is_named = skchem.filters.Filter(lambda m: m.name is not None)
39
40			Filter results can be found with `transform`:
41			>>> ethane = skchem.Mol.from_smiles('CC', name='ethane')
42			>>> is_named.transform(ethane)
43			True
44
45			>>> anonymous = skchem.Mol.from_smiles('c1ccccc1')
46			>>> is_named.transform(anonymous)
47			False
48
49			The filter can also be used as a function:
50			>>> ethane = skchem.Mol.from_smiles('CC', name='ethane')
51			>>> is_named.transform(ethane)
52			True
53
54			Apply can take a series or dataframe:
55			>>> mols = pd.Series({'anonymous': anonymous, 'ethane': ethane})
56			>>> is_named.transform(mols)
57			anonymous False
58			ethane True
59			dtype: bool
60
61			Using `filter` will drop out molecules that fail the test:
62			>>> is_named.filter(mols)
63			ethane <Mol: CC>
64			dtype: object
65
66			Only failed are retained with the `neg` keyword argument:
67			>>> is_named.filter(mols, neg=True)
68			anonymous <Mol: c1ccccc1>
69			dtype: object
70			"""
71
72			_DEFAULT_AGG = _identity_meth
73			_DEFAULT_IS_NEG = False
74
75			def __init__(self, func, agg=None, neg=False, **kwargs):
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Exactly one space required after comma def __init__(self, func, agg=None, neg=False, **kwargs): ^ Loading history...
76
77			self.func = func
78			self.agg = self._get_agg(agg) if agg is not None else self._DEFAULT_AGG
79			self.neg = neg
80			self.kwargs = kwargs
81
82			@property
83			def agg(self):
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 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...
84			return self._agg
85
86			@agg.setter
87			def agg(self, val):
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 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...
88			self._agg = self._get_agg(val)
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report The attribute `_agg` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
89
90			def _get_agg(self, val):
91			if val is True:
92			return self._DEFAULT_AGG
93			elif val is False:
94			return _identity
95			elif val is None:
96			return self.agg
97			else:
98			return val
99
100			@property
101			def neg(self):
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 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...
102			return self._get_neg(self._neg)
103
104			@neg.setter
105			def neg(self, val):
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 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
107			# xor
108			self._neg = self._get_neg(val)
			0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report The attribute `_neg` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
109
110
111			def _get_neg(self, val):
112			if self._DEFAULT_IS_NEG:
113			return not val
114			else:
115			return val
116
117			@method_takes_mol_series
118			def transform(self, mols, agg=None, neg=None):
119
120			""" Apply the function and return the boolean values. """
121
122			agg = self._get_agg(agg)
123
124			if neg is None:
125			neg = self._neg
126			else:
127			neg = self._get_neg(neg)
128
129			res = self._transform(mols)
130
131			if isinstance(res, pd.DataFrame):
132			res = res.apply(agg, axis=1)
133
134			if neg:
135			res = ~res
136
137			return res
138
139			def _transform(self, ser):
140			return ser.apply(self.func, **self.kwargs)
141
142			@method_takes_pandas
143			def filter(self, X, y=None, agg=None, neg=None):
			0 ignored issues – show Coding Style Naming introduced 2016-06-28 09:56 UTC by Report Bug Copy Issue Report The name `X` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2016-06-28 09:56 UTC by Report Bug Copy Issue Report The name `y` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
144
145			""" Apply the function and return filtered values.
146
147			Args:
148			X (pd.Series or pd.DataFrame):
149			The compound dataframe. """
150
151			if neg is None:
152			neg = self.neg
153
154			agg = self._get_agg(agg)
155
156			res = self.transform(X, neg=neg, agg=agg)
157
158			if y is None:
159			return X[res]
160			else:
161			return X[res], y[res]
162
163			def __call__(self, args, *kwargs):
164
165			return self.transform(args, *kwargs)
166

richlewis42 / scikit-chem

Push — master ( 97f98d...9ca1ad )

Filter.neg() A

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

Filter issues like

2. Missing init.py files