MOEDescriptorCalculator._transform_series() - Code Metrics - Inspection of "added named progressbars" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 9b11f9...01edc4 )

by Rich

created 2016-07-13 13:47 UTC

MOEDescriptorCalculator._transform_series() A

↳ Parent: MOEDescriptorCalculator

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	17
rs	9.4285
cc	3

#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
# License: 3-clause BSD

"""
## skchem.descriptors.moe

Module specifying moe descriptors.
"""

class MOEDescriptorCalculator(object):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""


    def __init__(self):
        pass

    def transform(self, obj):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if isinstance(obj, core.Mol):

            return self._transform_series(pd.Series(obj)).iloc[0]

        elif isinstance(obj, pd.Series):

            return self._transform_series(obj)
        elif isinstance(obj, pd.DataFrame):

            return self._transform_series(obj.structure)
        elif isinstance(obj, (tuple, list)):
            return self._transform_series(obj)
        else:
            raise NotImplementedError

    def _transform_series(self, series):

        with tempfile.NamedTemporaryFile(suffix='.sdf') as in_file, tempfile.NamedTemporaryFile() as out_file:

            # write mols to file
            write_sdf(series, in_file.name)

            args = ['mddesc', in_file.name, '-o', out_file.name] + self.index


            LOGGER.info('Running: ' + ' '.join(args))


            # call command line
            subprocess.call(args)

            try:
                finished = pd.read_table(out_file.name).set_index('id')

            except Exception:

                finished = None
        finished.index = series.index
        return finished




1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			## skchem.descriptors.moe
8
9			Module specifying moe descriptors.
10			"""
11
12			class MOEDescriptorCalculator(object):
			0 ignored issues – show Coding Style introduced 2016-07-13 13:49 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...
13
14
15			def __init__(self):
16			pass
17
18			def transform(self, obj):
			0 ignored issues – show Coding Style introduced 2016-07-13 13:49 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...
19			if isinstance(obj, core.Mol):
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'core' Loading history...
20			return self._transform_series(pd.Series(obj)).iloc[0]
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'pd' Loading history...
21			elif isinstance(obj, pd.Series):
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'pd' Loading history...
22			return self._transform_series(obj)
23			elif isinstance(obj, pd.DataFrame):
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'pd' Loading history...
24			return self._transform_series(obj.structure)
25			elif isinstance(obj, (tuple, list)):
26			return self._transform_series(obj)
27			else:
28			raise NotImplementedError
29
30			def _transform_series(self, series):
31
32			with tempfile.NamedTemporaryFile(suffix='.sdf') as in_file, tempfile.NamedTemporaryFile() as out_file:
			0 ignored issues – show Coding Style introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (110/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'tempfile' Loading history...
33			# write mols to file
34			write_sdf(series, in_file.name)
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'write_sdf' Loading history...
35			args = ['mddesc', in_file.name, '-o', out_file.name] + self.index
			0 ignored issues – show Bug introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report The Instance of `MOEDescriptorCalculator` does not seem to have a member named `index`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
36
37			LOGGER.info('Running: ' + ' '.join(args))
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'LOGGER' Loading history...
38
39			# call command line
40			subprocess.call(args)
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'subprocess' Loading history...
41			try:
42			finished = pd.read_table(out_file.name).set_index('id')
			0 ignored issues – show Comprehensibility Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Undefined variable 'pd' Loading history...
43			except Exception:
			0 ignored issues – show Best Practice introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report Catching very general exceptions such as `Exception` is usually not recommended. Generally, you would want to handle very specific errors in the exception handler. This ensure that you do not hide other types of errors which should be fixed. So, unless you specifically plan to handle any error, consider adding a more specific exception. Loading history...
44			finished = None
45			finished.index = series.index
46			return finished
47
48
49

richlewis42 / scikit-chem

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MOEDescriptorCalculator._transform_series() A

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