ChEMBLConverter.__init__()

Complexity

Conditions

1

Size

Total Lines

33

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	1.7703

Importance

Changes	2
Bugs	0	Features	1

#! /usr/bin/env python
    def __init__(self, directory, output_directory, output_filename='chembl.h5'):

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

        output_path = os.path.join(output_directory, output_filename)

        infile = os.path.join(directory, 'chembl_raw.h5')
        ms, y = self.parse_infile(infile)

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}$).

        pipeline = default_pipeline()

        ms, y = pipeline.transform_filter(ms, y)

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}$).

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

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

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

This line is too long as per the coding-style (105/100).

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}$).

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

        features = (

The variable features seems to be unused.

        Feature(fper=descriptors.MorganFeaturizer(),

Wrong hanging indentation.
Feature(fper=descriptors.MorganFeaturizer(),
^ |

                key='X_morg',
                axis_names=['batch', 'features']),
        Feature(fper=descriptors.PhysicochemicalFeaturizer(),

Wrong hanging indentation.
Feature(fper=descriptors.PhysicochemicalFeaturizer(),
^ |

                key='X_pc',
                axis_names=['batch', 'features']),
        Feature(fper=descriptors.AtomFeaturizer(max_atoms=100),

Wrong hanging indentation.
Feature(fper=descriptors.AtomFeaturizer(max_atoms=100),
^ |

                key='A',
                axis_names=['batch', 'atom_idx', 'features']),
        Feature(fper=descriptors.GraphDistanceTransformer(max_atoms=100),

Wrong hanging indentation.
Feature(fper=descriptors.GraphDistanceTransformer(max_atoms=100),
^ |

                key='G',
                axis_names=['batch', 'atom_idx', 'atom_idx']),
        Feature(fper=descriptors.SpacialDistanceTransformer(max_atoms=100),

Wrong hanging indentation.
Feature(fper=descriptors.SpacialDistanceTransformer(max_atoms=100),
^ |

                key='G_d'))

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

        return ms, y

Final newline missing