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

PhysPropConverter.process_txt() A
last analyzed 2016-09-01 14:43 UTC

↳ Parent: PhysPropConverter

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	4.6796

Importance

Changes	1
Bugs	0	Features	1

Metric	Value
c	1
b	0
f	1
dl	0
loc	8
ccs	1
cts	8
cp	0.125
rs	9.4285
cc	2
crap	4.6796

#! /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 zipfile
import logging
LOGGER = logging.getLogger(__name__)

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 ... import io
from .base import Converter, contiguous_order

from ...cross_validation import SimThresholdSplit

TXT_COLUMNS = [l.lower() for l in """CAS
Formula
Mol_Weight
Chemical_Name
WS
WS_temp
WS_type
WS_reference
LogP
LogP_temp
LogP_type
LogP_reference
VP
VP_temp
VP_type
VP_reference
DC_pKa
DC_temp
DC_type
DC_reference
henry_law Constant
HL_temp
HL_type
HL_reference
OH
OH_temp
OH_type
OH_reference
BP_pressure
MP
BP
FP""".split('\n')]

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

    def __init__(self, directory, output_directory, output_filename='physprop.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)

        sdf, txt = self.extract(directory)
        mols, data = self.process_sdf(sdf), self.process_txt(txt)

        LOGGER.debug('Compounds with data extracted: %s', len(data))

        data = mols.to_frame().join(data)
        data = self.drop_inconsistencies(data)

        y = self.process_targets(data)

        LOGGER.debug('Compounds with experimental: %s', len(y))

        data = data.ix[y.index]
        data.columns.name = 'targets'
        ms, y = data.structure, data.drop('structure', axis=1)


        cv = SimThresholdSplit(min_threshold=0.6, block_width=4000, n_jobs=-1).fit(ms)

        train, valid, test = cv.split((70, 15, 15))

        (ms, y, train, valid, test) = contiguous_order((ms, y, train, valid, test), (train, valid, test))

        splits = (('train', train), ('valid', valid), ('test', test))

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

    def extract(self, directory):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        LOGGER.info('Extracting from %s', directory)
        with zipfile.ZipFile(os.path.join(directory, 'phys_sdf.zip')) as f:

            sdf = f.extract('PhysProp.sdf')
        with zipfile.ZipFile(os.path.join(directory, 'phys_txt.zip')) as f:

            txt = f.extract('PhysProp.txt')
        return sdf, txt

    def process_sdf(self, path):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        LOGGER.info('Processing sdf at %s', path)
        mols = io.read_sdf(path, read_props=False).structure
        mols.index = mols.apply(lambda m: m.GetProp('CAS'))
        mols.index.name = 'cas'
        LOGGER.debug('Structures extracted: %s', len(mols))
        return mols

    def process_txt(self, path):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        LOGGER.info('Processing txt at %s', path)
        data = pd.read_table(path, header=None, engine='python').iloc[:, :32]
        data.columns = TXT_COLUMNS
        data_types = data.columns[[s.endswith('_type') for s in data.columns]]
        data[data_types] = data[data_types].fillna('NAN')
        data = data.set_index('cas')
        return data

    def drop_inconsistencies(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        LOGGER.info('Dropping inconsistent data...')
        formula = data.structure.apply(lambda m: m.to_formula())
        LOGGER.info('Inconsistent compounds: %s', (formula != data.formula).sum())
        data = data[formula == data.formula]
        return data

    def process_targets(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        LOGGER.info('Dropping estimated data...')
        data = pd.concat([self.process_logS(data),
                          self.process_logP(data),
                          self.process_mp(data),
                          self.process_bp(data)], axis=1)
        LOGGER.info('Dropped compounds: %s', data.isnull().all(axis=1).sum())
        data = data[data.notnull().any(axis=1)]
        LOGGER.debug('Compounds with experimental activities: %s', len(data))
        return data

    def process_logS(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        cleaned = pd.DataFrame(index=data.index)

        S = 0.001 * data.ws / data.mol_weight

        logS = np.log10(S)

        return logS[data.ws_type == 'EXP']

    def process_logP(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        logP = data.logp[data.logp_type == 'EXP']

        return logP[logP > -10]

    def process_mp(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return data.mp.apply(self.fix_temp)

    def process_bp(self, data):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return data.bp.apply(self.fix_temp)

    @staticmethod
    def fix_temp(s, mean_range=5):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        try:
            return float(s)
        except ValueError:
            if '<' in s or '>' in s:
                return np.nan
            s = s.strip(' dec')
            s = s.strip(' sub')
            if '-' in s and mean_range:
                rng = [float(n) for n in s.split('-')]
                if len(rng) > 2:
                    return np.nan
                if np.abs(rng[1] - rng[0]) < mean_range:
                    return (rng[0] + rng[1])/2
            try:
                return float(s)
            except ValueError:
                return np.nan



if __name__ == '__main__':
    logging.basicConfig(level=logging.INFO)
    LOGGER.info('Converting PhysProp Dataset...')
    PhysPropConverter.convert()


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	1	import os
7	1	import zipfile
8	1	import logging
9	1	LOGGER = logging.getLogger(__name__)
10
11	1	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...
12	1	import numpy as np
		0 ignored issues – show Configuration introduced 2016-06-12 20:23 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...
13
14	1	from ... import io
15	1	from .base import Converter, contiguous_order
16
17	1	from ...cross_validation import SimThresholdSplit
18
19	1	TXT_COLUMNS = [l.lower() for l in """CAS
20		Formula
21		Mol_Weight
22		Chemical_Name
23		WS
24		WS_temp
25		WS_type
26		WS_reference
27		LogP
28		LogP_temp
29		LogP_type
30		LogP_reference
31		VP
32		VP_temp
33		VP_type
34		VP_reference
35		DC_pKa
36		DC_temp
37		DC_type
38		DC_reference
39		henry_law Constant
40		HL_temp
41		HL_type
42		HL_reference
43		OH
44		OH_temp
45		OH_type
46		OH_reference
47		BP_pressure
48		MP
49		BP
50		FP""".split('\n')]
51
52	1	class PhysPropConverter(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...
53
54	1	def __init__(self, directory, output_directory, output_filename='physprop.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... Comprehensibility introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report This function exceeds the maximum number of variables (16/15). Loading history...
55
56		output_path = os.path.join(output_directory, output_filename)
57
58		sdf, txt = self.extract(directory)
59		mols, data = self.process_sdf(sdf), self.process_txt(txt)
60
61		LOGGER.debug('Compounds with data extracted: %s', len(data))
62
63		data = mols.to_frame().join(data)
64		data = self.drop_inconsistencies(data)
65
66		y = self.process_targets(data)
		0 ignored issues – show 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}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
67		LOGGER.debug('Compounds with experimental: %s', len(y))
68
69		data = data.ix[y.index]
70		data.columns.name = 'targets'
71		ms, y = data.structure, data.drop('structure', axis=1)
		0 ignored issues – show Coding Style Naming introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The name `ms` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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 2016-08-05 16:20 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}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
72
73		cv = SimThresholdSplit(min_threshold=0.6, block_width=4000, n_jobs=-1).fit(ms)
		0 ignored issues – show Coding Style Naming introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The name `cv` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
74		train, valid, test = cv.split((70, 15, 15))
75
76		(ms, y, train, valid, test) = contiguous_order((ms, y, train, valid, test), (train, valid, test))
		0 ignored issues – show Coding Style introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (105/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... Coding Style Naming introduced 2016-08-05 16:20 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}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The name `y` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
77		splits = (('train', train), ('valid', valid), ('test', test))
78
79		self.run(ms, y, output_path=output_path, splits=splits)
80
81	1	def extract(self, directory):
		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...
82		LOGGER.info('Extracting from %s', directory)
83		with zipfile.ZipFile(os.path.join(directory, 'phys_sdf.zip')) as f:
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 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}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
84		sdf = f.extract('PhysProp.sdf')
85		with zipfile.ZipFile(os.path.join(directory, 'phys_txt.zip')) as f:
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `f` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
86		txt = f.extract('PhysProp.txt')
87		return sdf, txt
88
89	1	def process_sdf(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...
90		LOGGER.info('Processing sdf at %s', path)
91		mols = io.read_sdf(path, read_props=False).structure
92		mols.index = mols.apply(lambda m: m.GetProp('CAS'))
93		mols.index.name = 'cas'
94		LOGGER.debug('Structures extracted: %s', len(mols))
95		return mols
96
97	1	def process_txt(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...
98		LOGGER.info('Processing txt at %s', path)
99		data = pd.read_table(path, header=None, engine='python').iloc[:, :32]
100		data.columns = TXT_COLUMNS
101		data_types = data.columns[[s.endswith('_type') for s in data.columns]]
102		data[data_types] = data[data_types].fillna('NAN')
103		data = data.set_index('cas')
104		return data
105
106	1	def drop_inconsistencies(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...
107		LOGGER.info('Dropping inconsistent data...')
108		formula = data.structure.apply(lambda m: m.to_formula())
109		LOGGER.info('Inconsistent compounds: %s', (formula != data.formula).sum())
110		data = data[formula == data.formula]
111		return data
112
113	1	def process_targets(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...
114		LOGGER.info('Dropping estimated data...')
115		data = pd.concat([self.process_logS(data),
116		self.process_logP(data),
117		self.process_mp(data),
118		self.process_bp(data)], axis=1)
119		LOGGER.info('Dropped compounds: %s', data.isnull().all(axis=1).sum())
120		data = data[data.notnull().any(axis=1)]
121		LOGGER.debug('Compounds with experimental activities: %s', len(data))
122		return data
123
124	1	def process_logS(self, data):
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `process_logS` does not conform to the method naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history... Coding Style introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
125		cleaned = pd.DataFrame(index=data.index)
		0 ignored issues – show Unused Code introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The variable `cleaned` seems to be unused. Loading history...
126		S = 0.001 * data.ws / data.mol_weight
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `S` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
127		logS = np.log10(S)
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `logS` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
128		return logS[data.ws_type == 'EXP']
129
130	1	def process_logP(self, data):
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `process_logP` does not conform to the method naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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 2016-06-12 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...
131		logP = data.logp[data.logp_type == 'EXP']
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `logP` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
132		return logP[logP > -10]
133
134	1	def process_mp(self, data):
		0 ignored issues – show Coding Style introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
135		return data.mp.apply(self.fix_temp)
136
137	1	def process_bp(self, data):
		0 ignored issues – show Coding Style introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
138		return data.bp.apply(self.fix_temp)
139
140	1	@staticmethod
141	1	def fix_temp(s, mean_range=5):
		0 ignored issues – show Coding Style Naming introduced 2016-06-12 20:23 UTC by Report Bug Copy Issue Report The name `s` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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... 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...
142		try:
143		return float(s)
144		except ValueError:
145		if '<' in s or '>' in s:
146		return np.nan
147		s = s.strip(' dec')
148		s = s.strip(' sub')
149		if '-' in s and mean_range:
150		rng = [float(n) for n in s.split('-')]
151		if len(rng) > 2:
152		return np.nan
153		if np.abs(rng[1] - rng[0]) < mean_range:
154		return (rng[0] + rng[1])/2
155		try:
156		return float(s)
157		except ValueError:
158		return np.nan
159
160
161
162	1	if __name__ == '__main__':
163		logging.basicConfig(level=logging.INFO)
164		LOGGER.info('Converting PhysProp Dataset...')
165		PhysPropConverter.convert()
166

PhysPropConverter.process_txt() A
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

richlewis42 / scikit-chem

PhysPropConverter.process_txt() A 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

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PhysPropConverter.process_txt() A
last analyzed 2016-09-01 14:43 UTC

2. Missing init.py files

2. Missing init.py files