BradleyOpenMPConverter

Complexity

Total Complexity

4

Size/Duplication

Total Lines	25
Duplicated Lines	0 %

Importance

Changes	1
Bugs	0	Features	1

4 Methods

Rating	Name	Duplication	Size	Complexity
A	__init__()	0	9	1
A	filter_bad()	0	5	1
A	parse_data()	0	3	1
A	fix_mp()	0	3	1

#! /usr/bin/env python

This module should have a docstring.

#
# Copyright (C) 2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

import os
import logging
logger = logging.getLogger(__name__)

The name logger does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

import pandas as pd

The import pandas could not be resolved.

from ... import core

The import core seems to be unused.

from .base import Converter

class BradleyOpenMPConverter(Converter):

This class should have a docstring.

    def __init__(self, directory, output_directory, output_filename='bradley_open_mp.h5'):

The __init__ method of the super-class Converter is not called.

        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)

The name ms does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

The name y does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

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

    def parse_data(self, path):

This method should have a docstring.

This method could be written as a function/class method.

        logger.info('Parsing data at %s...', path)
        return pd.read_excel(path, index_col=0)

    def filter_bad(self, data):

This method should have a docstring.

This method could be written as a function/class method.

        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):

This method should have a docstring.

This method could be written as a function/class method.

        logger.info('Converting temperature to Kelvin...')
        return data.mpC + 278.15

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