richlewis42 / scikit-chem

skchem/data/datasets/base.py

#! /usr/bin/env python

This module should have a docstring.

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

import warnings
import tempfile
import os

import pandas as pd

The import pandas could not be resolved.

import h5py

The import h5py could not be resolved.

from fuel.datasets import H5PYDataset

The import fuel.datasets could not be resolved.

from fuel.utils import find_in_data_path

The import fuel.utils could not be resolved.

from fuel import config

The import fuel could not be resolved.

class Dataset(H5PYDataset):

    """ Abstract base class providing an interface to the skchem data format."""

    def __init__(self, **kwargs):

Use of super on an old style class

        kwargs.setdefault('load_in_memory', True)
        super(Dataset, self).__init__(
            file_or_path=find_in_data_path(self.filename), **kwargs)

The Instance of Dataset does not seem to have a member named filename.

    @classmethod
    def available_sources(cls):

This method should have a docstring.

        with h5py.File(find_in_data_path(cls.filename)) as f:

The Class Dataset does not seem to have a member named filename.

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

            return cls.get_all_sources(f)

The Class Dataset does not seem to have a member named get_all_sources.

    @classmethod
    def available_sets(cls):

This method should have a docstring.

        with h5py.File(find_in_data_path(cls.filename)) as f:

The Class Dataset does not seem to have a member named filename.

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

            return cls.get_all_splits(f)

The Class Dataset does not seem to have a member named get_all_splits.

    @classmethod
    def load_set(cls, set_name, sources=()):

        """ Load the sources for a single set.

        Args:
            set_name (str):
                The set name.
            sources (tuple[str]):
                The sources to return data for.

        Returns:
            tuple[np.array]
                The requested sources for the requested set.
        """
        if set_name == 'all':
            set_name = cls.set_names

The Class Dataset does not seem to have a member named set_names.

        else:
            set_name = (set_name,)
        if sources == 'all':
            sources = cls.sources_names

The Class Dataset does not seem to have a member named sources_names.

        return cls(which_sets=set_name, sources=sources, load_in_memory=True).data_sources

The Instance of Dataset does not seem to have a member named data_sources.

    @classmethod
    def load_data(cls, sets=(), sources=()):

        """ Load a set of sources.

        Args:
            sets (tuple[str]):
                The sets to return data for.
            sources:
                The sources to return data for.

        Example:
            (X_train, y_train), (X_test, y_test) = Dataset.load_data(sets=('train', 'test'), sources=('X', 'y'))

This line is too long as per the coding-style (112/100).

        """

        for set_name in sets:
            yield cls.load_set(set_name, sources)

    @classmethod
    def read_frame(cls, key, *args, **kwargs):

        """ Load a set of features from the dataset as a pandas object.

        Args:
            key (str):
                The HDF5 key for required data.  Typically, this will be one of

                - structure: for the raw molecules
                - smiles: for the smiles
                - features/{feat_name}: for the features
                - targets/{targ_name}: for the targets

        Returns:
            pd.Series or pd.DataFrame or pd.Panel
                The data as a dataframe.
        """

        with warnings.catch_warnings():
            warnings.simplefilter('ignore')
            data = pd.read_hdf(find_in_data_path(cls.filename), key, *args, **kwargs)

The Class Dataset does not seem to have a member named filename.

        if isinstance(data, pd.Panel):
            data = data.transpose(2, 1, 0)
        return data

    @classmethod
    def download(cls, output_directory=None, download_directory=None):

        """ Download the dataset and convert it.

        Args:
            output_directory (str):
                The directory to save the data to. Defaults to the first
                directory in the fuel data path.

            download_directory (str):
                The directory to save the raw files to. Defaults to a temporary
                directory.

        Returns:
            str:
                The path of the downloaded and processed dataset.
        """

        if not output_directory:
            output_directory = config.config['data_path']['yaml'].split(':')[0]

        output_directory = os.path.expanduser(output_directory)

        if not download_directory:
            download_directory = tempfile.mkdtemp()

        cls.downloader.download(directory=download_directory)

The Class Dataset does not seem to have a member named downloader.

        return cls.converter.convert(directory=download_directory,

The Class Dataset does not seem to have a member named converter.

                                     output_directory=output_directory)