Bio/ PEP8 reformat & cleanup

Reformat all files to conform to PEP8 using autopep.

These commits introduce *no* logic changes, only the formatting standards
from PEP8: http://www.python.org/dev/peps/pep-0008/

All PEP8 standards enabled, except:
E101: indentation contains mixed spaces and tabs
E501: line too long
W191: indentation contains tabs
W291: trailing whitespace

You can generate these cleanups yourself using:

$ pip install autopep
$ find . -type f -name "*.py" -exec sh -c "nice -n19 autopep8 --ignore=E101,E501,W191,W291 -i {} &" \;

NOTE: This will spawn one job per .py file, which should be fine on a semi-fast machine.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
BioSQL/ PEP8 reformat & cleanup

Reformat all files to conform to PEP8 using autopep.

These commits introduce *no* logic changes, only the formatting standards
from PEP8: http://www.python.org/dev/peps/pep-0008/

All PEP8 standards enabled, except:
E101: indentation contains mixed spaces and tabs
E501: line too long
W191: indentation contains tabs
W291: trailing whitespace

You can generate these cleanups yourself using:

$ pip install autopep
$ find . -type f -name "*.py" -exec sh -c "nice -n19 autopep8 --ignore=E101,E501,W191,W291 -i {} &" \;

NOTE: This will spawn one job per .py file, which should be fine on a semi-fast machine.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Doc/ PEP8 reformat & cleanup

Reformat all files to conform to PEP8 using autopep.

These commits introduce *no* logic changes, only the formatting standards
from PEP8: http://www.python.org/dev/peps/pep-0008/

All PEP8 standards enabled, except:
E101: indentation contains mixed spaces and tabs
E501: line too long
W191: indentation contains tabs
W291: trailing whitespace

You can generate these cleanups yourself using:

$ pip install autopep
$ find . -type f -name "*.py" -exec sh -c "nice -n19 autopep8 --ignore=E101,E501,W191,W291 -i {} &" \;

NOTE: This will spawn one job per .py file, which should be fine on a semi-fast machine.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Scripts/ PEP8 reformat & cleanup

Reformat all files to conform to PEP8 using autopep.

These commits introduce *no* logic changes, only the formatting standards
from PEP8: http://www.python.org/dev/peps/pep-0008/

All PEP8 standards enabled, except:
E101: indentation contains mixed spaces and tabs
E501: line too long
W191: indentation contains tabs
W291: trailing whitespace

You can generate these cleanups yourself using:

$ pip install autopep
$ find . -type f -name "*.py" -exec sh -c "nice -n19 autopep8 --ignore=E101,E501,W191,W291 -i {} &" \;

NOTE: This will spawn one job per .py file, which should be fine on a semi-fast machine.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Scripts/ PEP8 reformat & cleanup

Reformat all files to conform to PEP8 using autopep.

These commits introduce *no* logic changes, only the formatting standards
from PEP8: http://www.python.org/dev/peps/pep-0008/

All PEP8 standards enabled, except:
E101: indentation contains mixed spaces and tabs
E501: line too long
W191: indentation contains tabs
W291: trailing whitespace

You can generate these cleanups yourself using:

$ pip install autopep
$ find . -type f -name "*.py" -exec sh -c "nice -n19 autopep8 --ignore=E101,E501,W191,W291 -i {} &" \;

NOTE: This will spawn one job per .py file, which should be fine on a semi-fast machine.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
/ PEP8 reformat & cleanup

Reformat all files to conform to PEP8 using autopep.

These commits introduce *no* logic changes, only the formatting standards
from PEP8: http://www.python.org/dev/peps/pep-0008/

All PEP8 standards enabled, except:
E101: indentation contains mixed spaces and tabs
E501: line too long
W191: indentation contains tabs
W291: trailing whitespace

You can generate these cleanups yourself using:

$ pip install autopep
$ find . -type f -name "*.py" -exec sh -c "nice -n19 autopep8 --ignore=E101,E501,W191,W291 -i {} &" \;

NOTE: This will spawn one job per .py file, which should be fine on a semi-fast machine.