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

PhysicochemicalFeaturizer.features() B
last analyzed 2016-09-01 14:43 UTC

↳ Parent: PhysicochemicalFeaturizer

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	10.5

Importance

Changes	2
Bugs	0	Features	0

Metric	Value
c	2
b	0
f	0
dl	0
loc	3
ccs	1
cts	2
cp	0.5
rs	8
cc	6
crap	10.5

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

"""
## skchem.descriptors.physicochemical

Physicochemical descriptors and associated functions are defined.

"""

from rdkit.Chem import Descriptors
# .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
import numpy as np
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from ..base import Transformer, Featurizer
from ..utils import camel_to_snail

DESCRIPTORS = {camel_to_snail(s): f for (s, f) in Descriptors.descList}


class PhysicochemicalFeaturizer(Transformer, Featurizer):

    """ Physicochemical descriptor generator using RDKit descriptor """

    def __init__(self, features='all', **kwargs):

        """ Create a physicochemical descriptor generator.

        Args:
            descriptors (list<(str, func)> or 'all'):
                Descriptors to calculate, or if 'all', use all descriptors."""

        super(PhysicochemicalFeaturizer, self).__init__(**kwargs)

        self.features = features

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

    @features.setter

    def features(self, features):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if features == 'all':
            features = DESCRIPTORS
        elif isinstance(features, str):
            features = {features: DESCRIPTORS[features]}
        elif isinstance(features, list):
            features = {feature: DESCRIPTORS[feature] for feature in features}
        elif isinstance(features, (dict, pd.Series)):
            features = features
        else:
            raise NotImplementedError('Cannot use features {}'.format(features))

        self._features = pd.Series(features)
class Foo:
    def __init__(self, x=None):
        self.x = x
        self._features.index.name = 'physicochemical_features'

    @property
    def name(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return 'physchem'

    @property
    def columns(self):
        return self.features.index

    def _transform_mol(self, mol):
        res = []
        for (n, f) in self.features.iteritems():

            try:
                res.append(f(mol))
            except ValueError:
                return res.append(np.NaN)

        return np.array(res)


1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2015-Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6	1		"""
7			## skchem.descriptors.physicochemical
8
9			Physicochemical descriptors and associated functions are defined.
10
11			"""
12
13	1		from rdkit.Chem import Descriptors
			0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report The import `rdkit.Chem` 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	1		import pandas as pd
			0 ignored issues – show Configuration introduced 2016-08-25 16:29 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...
15	1		import numpy as np
			0 ignored issues – show Configuration introduced 2016-08-25 16:29 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...
16
17	1		from ..base import Transformer, Featurizer
18	1		from ..utils import camel_to_snail
19
20	1		DESCRIPTORS = {camel_to_snail(s): f for (s, f) in Descriptors.descList}
21
22
23	1		class PhysicochemicalFeaturizer(Transformer, Featurizer):
24
25			""" Physicochemical descriptor generator using RDKit descriptor """
26
27	1		def __init__(self, features='all', **kwargs):
28
29			""" Create a physicochemical descriptor generator.
30
31			Args:
32			descriptors (list<(str, func)> or 'all'):
33			Descriptors to calculate, or if 'all', use all descriptors."""
34
35			super(PhysicochemicalFeaturizer, self).__init__(**kwargs)
36
37			self.features = features
38
39	1		@property
40			def features(self):
			0 ignored issues – show Coding Style introduced 2016-08-25 16:29 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...
41			return self._features
42
43	1	View Code Duplication	@features.setter
			0 ignored issues – show Duplication introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
44			def features(self, features):
			0 ignored issues – show Coding Style introduced 2016-08-25 16:29 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...
45			if features == 'all':
46			features = DESCRIPTORS
47			elif isinstance(features, str):
48			features = {features: DESCRIPTORS[features]}
49			elif isinstance(features, list):
50			features = {feature: DESCRIPTORS[feature] for feature in features}
51			elif isinstance(features, (dict, pd.Series)):
52			features = features
53			else:
54			raise NotImplementedError('Cannot use features {}'.format(features))
55
56			self._features = pd.Series(features)
			0 ignored issues – show Coding Style introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report The attribute `_features` 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...
57			self._features.index.name = 'physicochemical_features'
58
59	1		@property
60			def name(self):
			0 ignored issues – show Coding Style introduced 2016-08-25 16:29 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... Coding Style introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
61			return 'physchem'
62
63	1		@property
64			def columns(self):
65			return self.features.index
66
67	1		def _transform_mol(self, mol):
68			res = []
69			for (n, f) in self.features.iteritems():
			0 ignored issues – show Coding Style Naming introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report The name `n` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report The name `f` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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... Bug introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report The Instance of `str` does not seem to have a member named `iteritems`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history... Unused Code introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report The variable `n` seems to be unused. Loading history...
70			try:
71			res.append(f(mol))
72			except ValueError:
73			return res.append(np.NaN)
74
75			return np.array(res)
76

PhysicochemicalFeaturizer.features() B
last analyzed 2016-09-01 14:43 UTC

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

richlewis42 / scikit-chem

PhysicochemicalFeaturizer.features() B last analyzed 2016-09-01 14:43 UTC

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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PhysicochemicalFeaturizer.features() B
last analyzed 2016-09-01 14:43 UTC

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2. Missing init.py files

2. Missing init.py files