PhysicochemicalFingerprinter - Code Metrics - Inspection of "updated pylintrc" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

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by Rich

created 2016-04-14 16:47 UTC

PhysicochemicalFingerprinter A

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	14
Duplicated Lines	0 %

Metric	Value
dl	0
loc	14
rs	10
wmc	4

2 Methods

Rating	Name	Duplication	Size	Complexity
A	_transform()	0	3	2
A	__init__()	0	6	2

#! /usr/bin/env python
#
# Copyright (C) 2007-2009 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

from .fingerprints import Fingerprinter
from ..utils import camel_to_snail

def molecular_weight(m):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    return Descriptors.MolWt(m)

DESCRIPTORS = [(camel_to_snail(s), f) for (s, f) in Descriptors.descList]

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

    NAME = 'physchem'
    

    def __init__(self, descriptors='all'):
class SomeParent:
    def __init__(self):
        self.x = 1

class SomeChild(SomeParent):
    def __init__(self):
        # Initialize the super class
        SomeParent.__init__(self)
        if descriptors == 'all':
            self.descriptors = DESCRIPTORS
        else:
            self.descriptors = descriptors
        self.descriptor_names, _ = zip(*self.descriptors)

    def _transform(self, mol):

        return pd.Series({n: f(mol) for (n, f) in self.descriptors}, name=mol.name)


Push — master ( 2bc047...202252 )

PhysicochemicalFingerprinter A

Complexity

Size/Duplication

2 Methods

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) 2007-2009 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			skchem.descriptors.physicochemical
8
9			Physicochemical descriptors and associated functions are defined.
10
11			"""
12
13			from rdkit.Chem import Descriptors
			0 ignored issues – show Configuration introduced 2016-04-14 16:48 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			import pandas as pd
			0 ignored issues – show Configuration introduced 2016-04-14 16:48 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...
15
16			from .fingerprints import Fingerprinter
17			from ..utils import camel_to_snail
18
19			def molecular_weight(m):
			0 ignored issues – show Coding Style introduced 2016-01-19 16:21 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... Coding Style Naming introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The name `m` 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...
20			return Descriptors.MolWt(m)
21
22			DESCRIPTORS = [(camel_to_snail(s), f) for (s, f) in Descriptors.descList]
23
24			class PhysicochemicalFingerprinter(Fingerprinter):
			0 ignored issues – show Coding Style introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report This class 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...
25
26			NAME = 'physchem'
27
			0 ignored issues – show Coding Style introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
28			def __init__(self, descriptors='all'):
			0 ignored issues – show Bug introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The `__init__` method of the super-class `Fingerprinter` is not called. It is generally advisable to initialize the super-class by calling its `__init__` method: class SomeParent: def __init__(self): self.x = 1 class SomeChild(SomeParent): def __init__(self): # Initialize the super class SomeParent.__init__(self) Loading history...
29			if descriptors == 'all':
30			self.descriptors = DESCRIPTORS
31			else:
32			self.descriptors = descriptors
33			self.descriptor_names, _ = zip(*self.descriptors)
34
35			def _transform(self, mol):
36
37			return pd.Series({n: f(mol) for (n, f) in self.descriptors}, name=mol.name)
38

richlewis42 / scikit-chem

Push — master ( 2bc047...202252 )

PhysicochemicalFingerprinter A

Complexity

Size/Duplication

2 Methods

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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2. Missing init.py files

2. Missing init.py files