StructureMethods.__init__() - Code Metrics - Inspection of "added progressbar to requirements and added stderr..." - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 971a6f...39262f )

by Rich

created 2016-08-11 21:51 UTC

StructureMethods.init() A

↳ Parent: StructureMethods

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	1.125

Importance

Changes	2
Bugs	0	Features	1

Metric	Value
c	2
b	0
f	1
dl	0
loc	2
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.pandas.structure_methods

 Tools for adding a default attribute to pandas objects."""

from sklearn.manifold import TSNE, MDS
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from sklearn.decomposition import PCA
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from matplotlib import pyplot as plt
# .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

from pandas.core.base import NoNewAttributesMixin, AccessorProperty
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from pandas.core.series import Series
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from pandas.core.index import Index
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from .. import core
from .. import descriptors

DIM_RED = {
    'tsne': TSNE,
    'pca': PCA,
    'mds': MDS
}


class StructureMethods(NoNewAttributesMixin):

    """ Accessor for calling chemical methods on series of molecules. """

    def __init__(self, data):
        self._data = data

    def add_hs(self, **kwargs):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self._data.apply(lambda m: m.add_hs(**kwargs))


    def remove_hs(self, **kwargs):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self._data.apply(lambda m: m.remove_hs(**kwargs))


    def visualize(self, fper='morgan', dim_red='tsne', dim_red_kw={}, **kwargs):
# Bad:
# If array_param is modified inside the function, the next invocation will
# receive the modified object.
def some_function(array_param=[]):
    # ...

# Better: Create an array on each invocation
def some_function(array_param=None):
    array_param = array_param or []
    # ...

        if isinstance(dim_red, str):
            dim_red = DIM_RED.get(dim_red.lower())(**dim_red_kw)


        fper = descriptors.get(fper)
        fper.verbose = False
        feats = fper.transform(self._data)
        feats = feats.fillna(feats.mean())
        twod = pd.DataFrame(dim_red.fit_transform(feats))

        ax = twod.plot.scatter(x=0, y=1, **kwargs)

        ax.set_xticklabels([])
        ax.set_xlabel('')
        ax.set_yticklabels([])
        ax.set_ylabel('')

    @property
    def atoms(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self._data.apply(lambda m: m.atoms)


def only_contains_mols(ser):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    return ser.apply(lambda s: isinstance(s, core.Mol)).all()


class StructureAccessorMixin(object):

    """ Mixin to bind chemical methods to objects. """

    def _make_structure_accessor(self):
        if isinstance(self, Index):
            raise AttributeError('Can only use .mol accessor with molecules,'
                                 'which use np.object_ in scikit-chem.')
        if not only_contains_mols(self):
            raise AttributeError('Can only use .mol accessor with '
                                 'Series that only contain mols.')

        return StructureMethods(self)
    mol = AccessorProperty(StructureMethods, _make_structure_accessor)

Series.__bases__ += StructureAccessorMixin,


1		#! /usr/bin/env python
2		#
3		# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	""" # skchem.pandas.structure_methods
7
8		Tools for adding a default attribute to pandas objects."""
9
10	1	from sklearn.manifold import TSNE, MDS
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The import `sklearn.manifold` 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...
11	1	from sklearn.decomposition import PCA
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The import `sklearn.decomposition` 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...
12
13	1	from matplotlib import pyplot as plt
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The import `matplotlib` 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... Unused Code introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Unused pyplot imported from matplotlib as plt Loading history...
14	1	import pandas as pd
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 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
16	1	from pandas.core.base import NoNewAttributesMixin, AccessorProperty
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The import `pandas.core.base` 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...
17	1	from pandas.core.series import Series
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The import `pandas.core.series` 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...
18	1	from pandas.core.index import Index
		0 ignored issues – show Configuration introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The import `pandas.core.index` 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...
19
20	1	from .. import core
21	1	from .. import descriptors
22
23	1	DIM_RED = {
24		'tsne': TSNE,
25		'pca': PCA,
26		'mds': MDS
27		}
28
29
30	1	class StructureMethods(NoNewAttributesMixin):
31
32		""" Accessor for calling chemical methods on series of molecules. """
33
34	1	def __init__(self, data):
35		self._data = data
36
37	1	def add_hs(self, **kwargs):
		0 ignored issues – show 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...
38		return self._data.apply(lambda m: m.add_hs(**kwargs))
		0 ignored issues – show Coding Style introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Usage of `` or `` arguments should usually be done with care. Generally, there is nothing wrong with usage of `` or `**` arguments. For readability of the code base, we suggest to not over-use these language constructs though. For more information, we can recommend this blog post from Ned Batchelder including its comments which also touches this aspect. Loading history...
39
40	1	def remove_hs(self, **kwargs):
		0 ignored issues – show 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...
41		return self._data.apply(lambda m: m.remove_hs(**kwargs))
		0 ignored issues – show Coding Style introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Usage of `` or `` arguments should usually be done with care. Generally, there is nothing wrong with usage of `` or `**` arguments. For readability of the code base, we suggest to not over-use these language constructs though. For more information, we can recommend this blog post from Ned Batchelder including its comments which also touches this aspect. Loading history...
42
43	1	def visualize(self, fper='morgan', dim_red='tsne', dim_red_kw={}, **kwargs):
		0 ignored issues – show Bug Best Practice introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The default value `{}` might cause unintended side-effects. Objects as default values are only created once in Python and not on each invocation of the function. If the default object is modified, this modification is carried over to the next invocation of the method. # Bad: # If array_param is modified inside the function, the next invocation will # receive the modified object. def some_function(array_param=[]): # ... # Better: Create an array on each invocation def some_function(array_param=None): array_param = array_param or [] # ... 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...
44
45		if isinstance(dim_red, str):
46		dim_red = DIM_RED.get(dim_red.lower())(**dim_red_kw)
		0 ignored issues – show Coding Style introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Usage of `` or `` arguments should usually be done with care. Generally, there is nothing wrong with usage of `` or `**` arguments. For readability of the code base, we suggest to not over-use these language constructs though. For more information, we can recommend this blog post from Ned Batchelder including its comments which also touches this aspect. Loading history...
47
48		fper = descriptors.get(fper)
49		fper.verbose = False
50		feats = fper.transform(self._data)
51		feats = feats.fillna(feats.mean())
52		twod = pd.DataFrame(dim_red.fit_transform(feats))
		0 ignored issues – show Bug introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The Instance of `str` does not seem to have a member named `fit_transform`. 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...
53		ax = twod.plot.scatter(x=0, y=1, **kwargs)
		0 ignored issues – show Coding Style Naming introduced 2016-08-11 21:55 UTC by Report Bug Copy Issue Report The name `ax` 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...
54		ax.set_xticklabels([])
55		ax.set_xlabel('')
56		ax.set_yticklabels([])
57		ax.set_ylabel('')
58
59	1	@property
60		def atoms(self):
		0 ignored issues – show 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...
61		return self._data.apply(lambda m: m.atoms)
62
63
64	1	def only_contains_mols(ser):
		0 ignored issues – show Coding Style introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report This function 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...
65		return ser.apply(lambda s: isinstance(s, core.Mol)).all()
66
67
68	1	class StructureAccessorMixin(object):
69
70		""" Mixin to bind chemical methods to objects. """
71
72	1	def _make_structure_accessor(self):
73		if isinstance(self, Index):
74		raise AttributeError('Can only use .mol accessor with molecules,'
75		'which use np.object_ in scikit-chem.')
76		if not only_contains_mols(self):
77		raise AttributeError('Can only use .mol accessor with '
78		'Series that only contain mols.')
79
80		return StructureMethods(self)
81	1	mol = AccessorProperty(StructureMethods, _make_structure_accessor)
82
83		Series.__bases__ += StructureAccessorMixin,
84

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StructureMethods.init() A

Complexity

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1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

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

Push — master ( 971a6f...39262f )

StructureMethods.__init__() A

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

1. Missing Dependencies

2. Missing __init__.py files

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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StructureMethods.init() A

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