BaseFilter.transform() - Code Metrics - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

BaseFilter.transform() A
last analyzed 2016-09-01 14:43 UTC

↳ Parent: BaseFilter

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	5
CRAP Score	2

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
c	1
b	0
f	0
dl	0
loc	10
ccs	5
cts	5
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.filters

Chemical filters are defined.

"""

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

from ..base import BaseTransformer, Transformer
from .. import core
from ..utils import iterable_to_series, Defaults, optional_second_method


def not_all(x):

    """ Not all x """
    return not all(x)


def not_any(x):

    """ Not any x """
    return not any(x)


def identity(x):

    """ The identity """
    return x


AGGS = Defaults(defaults={
    'none': identity,
    'any': any,
    'all': all,
    'not all': not_all,
    'not any': not_any
})


class BaseFilter(BaseTransformer):

    """ The base Filter class. """

    def __init__(self, agg='any', **kwargs):
        self._agg = None
        super(BaseFilter, self).__init__(**kwargs)
        self.agg = agg

    def axes_names(self):
        return 'batch', self.columns.name

    @property
    def agg(self):
        """ callable: The aggregate function to use.  String aliases
        for `'any'`, `'not any'`, 'all', `'not all'` are available."""
        return self._agg

    @agg.setter
    def agg(self, val):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self._agg = AGGS.get(val)

    @property
    def columns(self):

        """ pd.Index: The column index to use. """

        return pd.Index([self.__class__.__name__])

    def _mask(self, mols=None, res=None, neg=False):

        """ Generate a mask from molecules, or from their result after transform.

        Args:
            mols (pd.Series<skchem.Mol>):
                The molecules to use to generate the mask.
            res (pd.Series):
                The result of a transform. Overrides mols.
            neg (bool):
                Whether the mask should be inversed.

        Returns:
            pd.Series<bool>
        """

        res = self.transform(mols, agg=False) if res is None else res
        res = (res != 0) & pd.notnull(res)
        if isinstance(res, pd.Series) and isinstance(mols, core.Mol):
            res = self.agg(res)

        if isinstance(res, pd.DataFrame):
            res = res.apply(self.agg, axis=1)
        return res == 0 if neg else res

    @optional_second_method
    def transform(self, mols, agg=True, **kwargs):

        # transform takes additional optional kwarg `agg`, that specifies to
        # transform to the aggregated value or return the full series.

        if agg:
            return self._mask(mols)
        else:
            return super(BaseFilter, self).transform(mols, **kwargs)

    def filter(self, mols, y=None, neg=False):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

        mask = self._mask(mols=mols, neg=neg)

        if isinstance(mols, core.Mol):
            return mols if mask else None

        elif not isinstance(mols, pd.Series):
            mols = iterable_to_series(mols)

        if y is None:
            return mols[mask]
        else:
            return mols[mask], y[mask]


class Filter(BaseFilter, Transformer):
    """ Filter base class.

     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

         Can take a series or dataframe:
         >>> mols = pd.Series({'anonymous': anonymous, 'ethane': ethane})
         >>> is_named.transform(mols)
         anonymous    False
         ethane        True
         Name: Filter, 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
     """
    def __init__(self, func=None, agg='any', n_jobs=1, verbose=True):

        """ Initialize a `Filter` object.

             Args:
             func (function: Mol => bool):
                 The function to use to filter the arguments.
             agg (str or function: iterable<bool> => bool):
                 The aggregation to use in the filter. Can be 'any', 'all',
                 'not any', 'not all' or a callable, for example `any` or `all`.
        """

        super(Filter, self).__init__(agg=agg, n_jobs=n_jobs, verbose=verbose)
        if func is not None:
            self._transform_mol = func

    def _transform_mol(self, mol):

        raise NotImplemented



class TransformFilter(BaseFilter):

    """ Transform Filter object.

     Implements `transform_filter`, which allows a transform, then a
     filter step returning the transformed values that are not `False`, `None`
     or `np.nan`.

     """

    def transform_filter(self, mols, y=None, neg=False):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

        res = self.transform(mols)
        mask = self._mask(res=res, neg=neg)

        if isinstance(mols, core.Mol):
            return res if mask else None

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


BaseFilter.transform() A
last analyzed 2016-09-01 14:43 UTC

Complexity

Size

Duplication

Code Coverage

Importance

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.filters
8
9		Chemical filters are defined.
10
11		"""
12
13	1	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	1	from ..base import BaseTransformer, Transformer
16	1	from .. import core
17	1	from ..utils import iterable_to_series, Defaults, optional_second_method
18
19
20	1	def not_all(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}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
21		""" Not all x """
22		return not all(x)
23
24
25	1	def not_any(x):
		0 ignored issues – show Coding Style Naming introduced 2016-08-18 20:05 UTC by Report Bug Copy Issue Report The name `x` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
26		""" Not any x """
27	1	return not any(x)
28
29
30	1	def identity(x):
		0 ignored issues – show Coding Style Naming introduced 2016-08-18 20:05 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...
31		""" The identity """
32		return x
33
34
35	1	AGGS = Defaults(defaults={
36		'none': identity,
37		'any': any,
38		'all': all,
39		'not all': not_all,
40		'not any': not_any
41		})
42
43
44	1	class BaseFilter(BaseTransformer):
45
46		""" The base Filter class. """
47
48	1	def __init__(self, agg='any', **kwargs):
49	1	self._agg = None
50	1	super(BaseFilter, self).__init__(**kwargs)
51	1	self.agg = agg
52
53	1	def axes_names(self):
54		return 'batch', self.columns.name
55
56	1	@property
57		def agg(self):
58		""" callable: The aggregate function to use. String aliases
59		for `'any'`, `'not any'`, 'all', `'not all'` are available."""
60	1	return self._agg
61
62	1	@agg.setter
63		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...
64	1	self._agg = AGGS.get(val)
65
66	1	@property
67		def columns(self):
68
69		""" pd.Index: The column index to use. """
70
71	1	return pd.Index([self.__class__.__name__])
72
73	1	def _mask(self, mols=None, res=None, neg=False):
74
75		""" Generate a mask from molecules, or from their result after transform.
76
77		Args:
78		mols (pd.Series<skchem.Mol>):
79		The molecules to use to generate the mask.
80		res (pd.Series):
81		The result of a transform. Overrides mols.
82		neg (bool):
83		Whether the mask should be inversed.
84
85		Returns:
86		pd.Series<bool>
87		"""
88
89	1	res = self.transform(mols, agg=False) if res is None else res
90	1	res = (res != 0) & pd.notnull(res)
91	1	if isinstance(res, pd.Series) and isinstance(mols, core.Mol):
92	1	res = self.agg(res)
		0 ignored issues – show Bug introduced 2016-08-16 15:32 UTC by Report Bug Copy Issue Report `self.agg` does not seem to be callable. Loading history...
93	1	if isinstance(res, pd.DataFrame):
94	1	res = res.apply(self.agg, axis=1)
95	1	return res == 0 if neg else res
96
97	1	@optional_second_method
98	1	def transform(self, mols, agg=True, **kwargs):
99
100		# transform takes additional optional kwarg `agg`, that specifies to
101		# transform to the aggregated value or return the full series.
102
103	1	if agg:
104	1	return self._mask(mols)
105		else:
106	1	return super(BaseFilter, self).transform(mols, **kwargs)
107
108	1	def filter(self, mols, y=None, neg=False):
		0 ignored issues – show Coding Style Naming introduced 2016-08-05 16:20 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... Coding Style introduced 2016-08-05 16:20 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...
109
110	1	mask = self._mask(mols=mols, neg=neg)
111
112	1	if isinstance(mols, core.Mol):
113		return mols if mask else None
114
115	1	elif not isinstance(mols, pd.Series):
116	1	mols = iterable_to_series(mols)
117
118	1	if y is None:
119	1	return mols[mask]
120		else:
121		return mols[mask], y[mask]
122
123
124	1	class Filter(BaseFilter, Transformer):
125		""" Filter base class.
126
127		Examples:
128
129		>>> import skchem
130
131		Initialize the filter with a function:
132		>>> is_named = skchem.filters.Filter(lambda m: m.name is not None)
133
134		Filter results can be found with `transform`:
135		>>> ethane = skchem.Mol.from_smiles('CC', name='ethane')
136		>>> is_named.transform(ethane)
137		True
138
139		>>> anonymous = skchem.Mol.from_smiles('c1ccccc1')
140		>>> is_named.transform(anonymous)
141		False
142
143		Can take a series or dataframe:
144		>>> mols = pd.Series({'anonymous': anonymous, 'ethane': ethane})
145		>>> is_named.transform(mols)
146		anonymous False
147		ethane True
148		Name: Filter, dtype: bool
149
150		Using `filter` will drop out molecules that fail the test:
151		>>> is_named.filter(mols)
152		ethane <Mol: CC>
153		dtype: object
154
155		Only failed are retained with the `neg` keyword argument:
156		>>> is_named.filter(mols, neg=True)
157		anonymous <Mol: c1ccccc1>
158		dtype: object
159		"""
160	1	def __init__(self, func=None, agg='any', n_jobs=1, verbose=True):
161
162		""" Initialize a `Filter` object.
163
164		Args:
165		func (function: Mol => bool):
166		The function to use to filter the arguments.
167		agg (str or function: iterable<bool> => bool):
168		The aggregation to use in the filter. Can be 'any', 'all',
169		'not any', 'not all' or a callable, for example `any` or `all`.
170		"""
171
172	1	super(Filter, self).__init__(agg=agg, n_jobs=n_jobs, verbose=verbose)
173	1	if func is not None:
174	1	self._transform_mol = func
175
176	1	def _transform_mol(self, mol):
		0 ignored issues – show Bug introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report This method seems to be hidden by an attribute defined in `skchem.filters.base` on line 174. Loading history...
177		raise NotImplemented
		0 ignored issues – show Best Practice introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report NotImplemented raised - should raise NotImplementedError Loading history...
178
179
180	1	class TransformFilter(BaseFilter):
181
182		""" Transform Filter object.
183
184		Implements `transform_filter`, which allows a transform, then a
185		filter step returning the transformed values that are not `False`, `None`
186		or `np.nan`.
187
188		"""
189
190	1	def transform_filter(self, mols, y=None, neg=False):
		0 ignored issues – show Coding Style Naming introduced 2016-08-05 16:20 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... Coding Style introduced 2016-08-05 16:20 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...
191
192		res = self.transform(mols)
193		mask = self._mask(res=res, neg=neg)
194
195		if isinstance(mols, core.Mol):
196		return res if mask else None
197
198		if y is None:
199		return res[mask]
200		else:
201		return res[mask], y[mask]
202

richlewis42 / scikit-chem

BaseFilter.transform() A last analyzed 2016-09-01 14:43 UTC

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2. Missing __init__.py files

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BaseFilter.transform() A
last analyzed 2016-09-01 14:43 UTC

2. Missing init.py files