BradleyOpenMPConverter.parse_data() - Code Metrics - Inspection of "added first pass at datasets" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 4d243d...e4a84f )

by Rich

created 2016-06-12 20:22 UTC

BradleyOpenMPConverter.parse_data() A

↳ Parent: BradleyOpenMPConverter

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	0	Features	1

Metric	Value
c	1
b	0
f	1
dl	0
loc	3
rs	10
cc	1

#! /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 os
import logging
logger = logging.getLogger(__name__)


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

from ... import core

from .base import Converter

class BradleyOpenMPConverter(Converter):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def __init__(self, directory, output_directory, output_filename='bradley_open_mp.h5'):
class SomeParent:
    def __init__(self):
        self.x = 1

class SomeChild(SomeParent):
    def __init__(self):
        # Initialize the super class
        SomeParent.__init__(self)

        output_path = os.path.join(output_directory, output_filename)
        data = self.parse_data(os.path.join(directory, 'bradley_melting_point_dataset.xlsx'))
        data = self.filter_bad(data)
        data['structure'] = self.standardize(data.smiles)
        data = self.filter(data)
        ms, y = data.structure, self.fix_mp(data)

        self.run(ms, y, output_path=output_path)

    def parse_data(self, path):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        logger.info('Parsing data at %s...', path)
        return pd.read_excel(path, index_col=0)

    def filter_bad(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        logger.info('Removing manually annotated errors...')
        bad_data = data.donotuse.notnull()
        logger.debug('Removed %s', bad_data.sum())
        return data[~bad_data]

    def fix_mp(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        logger.info('Converting temperature to Kelvin...')
        return data.mpC + 278.15

if __name__ == '__main__':
    logging.basicConfig(level=logging.INFO)
    BradleyOpenMPConverter.convert()


Push — master ( 4d243d...e4a84f )

BradleyOpenMPConverter.parse_data() A

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing init.py files

1			#! /usr/bin/env python
			0 ignored issues – show Coding Style introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report 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			import os
7			import logging
8			logger = logging.getLogger(__name__)
			0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `logger` does not conform to the constant naming conventions (`(([A-Z_][A-Z0-9_])\|(__.__))$`). 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...
9
10			import pandas as pd
			0 ignored issues – show Configuration introduced 2016-06-12 20:23 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...
11
12			from ... import core
			0 ignored issues – show Unused Code introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The import `core` seems to be unused. Loading history...
13			from .base import Converter
14
15			class BradleyOpenMPConverter(Converter):
			0 ignored issues – show Coding Style introduced 2016-06-12 20:23 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...
16
17			def __init__(self, directory, output_directory, output_filename='bradley_open_mp.h5'):
			0 ignored issues – show Bug introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The `__init__` method of the super-class `Converter` 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...
18
19			output_path = os.path.join(output_directory, output_filename)
20			data = self.parse_data(os.path.join(directory, 'bradley_melting_point_dataset.xlsx'))
21			data = self.filter_bad(data)
22			data['structure'] = self.standardize(data.smiles)
23			data = self.filter(data)
24			ms, y = data.structure, self.fix_mp(data)
			0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `ms` 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 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `y` 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...
25			self.run(ms, y, output_path=output_path)
26
27			def parse_data(self, path):
			0 ignored issues – show Coding Style introduced 2016-06-12 20:23 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 2016-06-12 20:23 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...
28			logger.info('Parsing data at %s...', path)
29			return pd.read_excel(path, index_col=0)
30
31			def filter_bad(self, data):
			0 ignored issues – show Coding Style introduced 2016-06-12 20:23 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 2016-06-12 20:23 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...
32			logger.info('Removing manually annotated errors...')
33			bad_data = data.donotuse.notnull()
34			logger.debug('Removed %s', bad_data.sum())
35			return data[~bad_data]
36
37			def fix_mp(self, data):
			0 ignored issues – show Coding Style introduced 2016-06-12 20:23 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 2016-06-12 20:23 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...
38			logger.info('Converting temperature to Kelvin...')
39			return data.mpC + 278.15
40
41			if __name__ == '__main__':
42			logging.basicConfig(level=logging.INFO)
43			BradleyOpenMPConverter.convert()
44

richlewis42 / scikit-chem

Push — master ( 4d243d...e4a84f )

BradleyOpenMPConverter.parse_data() A

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

Filter issues like

2. Missing init.py files