Issues in desc_vis.py (master) - Issues in master - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Issues (942)

skchem/interact/desc_vis.py (31 issues)

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#! /usr/bin/env python
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
#
# Copyright (C) 2016 Rich Lewis <[email protected]>
# License: 3-clause BSD

import matplotlib.pyplot as plt
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from .. import features
from .. import core
from .. import vis
from ipywidgets import Dropdown, Text, VBox, HBox, Valid, HTML
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from IPython import get_ipython
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from IPython.display import clear_output, display
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3


class Visualizer(object):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    def __init__(self, fper='morgan', smiles='c1ccccc1O', dpi=200):

        self.initialize_ipython()

        if isinstance(fper, str):
            self.fper = features.get(fper)
        else:
            self.fper = fper

        self.smiles_input = Text(smiles, description='smiles')
        self.smiles_input.on_submit(self.update_smiles)
        self.smiles_input.observe(self.typing)

        self.valid = Valid(True)

        self.dropdown = Dropdown(options=[], description='bit')
        self.dropdown.observe(self.plot)

        self.dpi_input = Text(str(dpi), description='dpi')
        self.dpi_input.on_submit(self.plot)

        self.ui = VBox([

            HTML('<h2>Visualizer</h2>'),
            HBox([self.smiles_input, self.valid]),
            self.dropdown,
            self.dpi_input])

        self.update_smiles(None)
        self.display()

    @staticmethod
    def initialize_ipython():
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        ipython = get_ipython()
        try:
            ipython.magic('matplotlib inline')
        except:

            pass

    def typing(self, _):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self.valid.visible = False

    @property
    def dpi(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        try:
            return int(self.dpi_input.value)
        except:

            return 50

    @dpi.setter
    def dpi(self, value):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self.dpi_input.value = str(value)

    def display(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        display(self.ui)

    def update_smiles(self, _):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        try:
            self._mol = core.Mol.from_smiles(self.smiles_input.value)

            self.valid.value = True
        except ValueError:
            self.valid.value = False
            return
        finally:
            self.valid.visible = True
        return self.calculate()

    def calculate(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        fp = self.fper.transform(self.mol)

        self.fp = fp[fp == 1].index
class Foo:
    def __init__(self, x=None):
        self.x = x
        self.fpg = self.fper.grad(self.mol).ix[self.fp]
class Foo:
    def __init__(self, x=None):
        self.x = x
        return self.update_dropdown()

    def update_dropdown(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self.dropdown.options.append(self.fp[0])
        self.dropdown.value = self.fp[0]
        self.dropdown.options = self.fp.tolist()
        return self.plot(self.dropdown.value)

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

    @mol.setter
    def mol(self, mol):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        self._mol = mol
class Foo:
    def __init__(self, x=None):
        self.x = x
        self.smiles_input.value = mol.to_smiles()
        self.calculate()

    @property
    def current_smiles(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self.smiles_input.value

    @property
    def current_bit(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self.dropdown.value

    def plot(self, _):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        clear_output()
        plt.clf()
        plt.rcParams['savefig.dpi'] = self.dpi
        vis.plot_weights(self.mol, self.fpg.ix[self.current_bit],
                         quality=4, ax=plt.gca())


1		#! /usr/bin/env python
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this This module 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...
2		#
3		# Copyright (C) 2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	import matplotlib.pyplot as plt
		0 ignored issues – show Configuration introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `matplotlib.pyplot` 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...
7
8	1	from .. import features
9	1	from .. import core
10	1	from .. import vis
11	1	from ipywidgets import Dropdown, Text, VBox, HBox, Valid, HTML
		0 ignored issues – show Configuration introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `ipywidgets` 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	1	from IPython import get_ipython
		0 ignored issues – show Configuration introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `IPython` 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...
13	1	from IPython.display import clear_output, display
		0 ignored issues – show Configuration introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `IPython.display` 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
16	1	class Visualizer(object):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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... best-practice introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this Too many instance attributes (9/7) Loading history...
17	1	def __init__(self, fper='morgan', smiles='c1ccccc1O', dpi=200):
18
19		self.initialize_ipython()
20
21		if isinstance(fper, str):
22		self.fper = features.get(fper)
23		else:
24		self.fper = fper
25
26		self.smiles_input = Text(smiles, description='smiles')
27		self.smiles_input.on_submit(self.update_smiles)
28		self.smiles_input.observe(self.typing)
29
30		self.valid = Valid(True)
31
32		self.dropdown = Dropdown(options=[], description='bit')
33		self.dropdown.observe(self.plot)
34
35		self.dpi_input = Text(str(dpi), description='dpi')
36		self.dpi_input.on_submit(self.plot)
37
38		self.ui = VBox([
		0 ignored issues – show Coding Style Naming introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The name `ui` does not conform to the attribute 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...
39		HTML('<h2>Visualizer</h2>'),
40		HBox([self.smiles_input, self.valid]),
41		self.dropdown,
42		self.dpi_input])
43
44		self.update_smiles(None)
45		self.display()
46
47	1	@staticmethod
48		def initialize_ipython():
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
49		ipython = get_ipython()
50		try:
51		ipython.magic('matplotlib inline')
52		except:
		0 ignored issues – show Coding Style Best Practice introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this General except handlers without types should be used sparingly. Typically, you would use general except handlers when you intend to specifically handle all types of errors, f.e. when logging. Otherwise, such general error handlers can mask errors in your application that you want to know of. Loading history...
53		pass
54
55	1	def typing(self, _):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
56		self.valid.visible = False
57
58	1	@property
59		def dpi(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
60		try:
61		return int(self.dpi_input.value)
62		except:
		0 ignored issues – show Coding Style Best Practice introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this General except handlers without types should be used sparingly. Typically, you would use general except handlers when you intend to specifically handle all types of errors, f.e. when logging. Otherwise, such general error handlers can mask errors in your application that you want to know of. Loading history...
63		return 50
64
65	1	@dpi.setter
66		def dpi(self, value):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
67		self.dpi_input.value = str(value)
68
69	1	def display(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
70		display(self.ui)
71
72	1	def update_smiles(self, _):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
73		try:
74		self._mol = core.Mol.from_smiles(self.smiles_input.value)
		0 ignored issues – show Bug introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The Class `Mol` does not seem to have a member named `from_smiles`. 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...
75		self.valid.value = True
76		except ValueError:
77		self.valid.value = False
78		return
79		finally:
80		self.valid.visible = True
81		return self.calculate()
82
83	1	def calculate(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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		fp = self.fper.transform(self.mol)
		0 ignored issues – show Coding Style Naming introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The name `fp` 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 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The Instance of `str` does not seem to have a member named `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...
85		self.fp = fp[fp == 1].index
		0 ignored issues – show Coding Style Naming introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The name `fp` does not conform to the attribute 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 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `fp` 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...
86		self.fpg = self.fper.grad(self.mol).ix[self.fp]
		0 ignored issues – show Bug introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The Instance of `str` does not seem to have a member named `grad`. 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... Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `fpg` 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...
87		return self.update_dropdown()
88
89	1	def update_dropdown(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
90		self.dropdown.options.append(self.fp[0])
91		self.dropdown.value = self.fp[0]
92		self.dropdown.options = self.fp.tolist()
93		return self.plot(self.dropdown.value)
94
95	1	@property
96		def mol(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
97		return self._mol
98
99	1	@mol.setter
100		def mol(self, mol):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
101		self._mol = mol
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this The attribute `_mol` 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...
102		self.smiles_input.value = mol.to_smiles()
103		self.calculate()
104
105	1	@property
106		def current_smiles(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
107		return self.smiles_input.value
108
109	1	@property
110		def current_bit(self):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
111		return self.dropdown.value
112
113	1	def plot(self, _):
		0 ignored issues – show Coding Style introduced 2016-06-30 13:44 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
114		clear_output()
115		plt.clf()
116		plt.rcParams['savefig.dpi'] = self.dpi
117		vis.plot_weights(self.mol, self.fpg.ix[self.current_bit],
118		quality=4, ax=plt.gca())
119

Issues (942)

skchem/interact/desc_vis.py (31 issues)

Labels

Severity

Introduced By

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

Issues (942)

skchem/interact/desc_vis.py (31 issues)

Labels

Severity

Introduced By

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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2. Missing init.py files

2. Missing init.py files

2. Missing init.py files

2. Missing init.py files