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Commits on May 24, 2016
  1. @MarkusPiotrowski
  2. @peterjc

    Fix RST warning from epydoc

    Warning: Line 13: Definition list ends without a blank line; unexpected unindent.
    Warning: Lines 16, 30: Unexpected indentation.
    Warning: Lines 17, 31: Block quote ends without a blank line; unexpected unindent.
    peterjc committed May 24, 2016
  3. @peterjc

    Fix RST warnings from epydoc

    Warning: Lines 684, 688, 691: Definition list ends without a blank line; unexpected unindent.
    peterjc committed May 24, 2016
  4. @peterjc

    Add doctests to CheckSum.py

    peterjc committed May 24, 2016
  5. @peterjc

    Remove redundant self-test

    Already covered by test_SeqUtils.py - see GitHub issue #820
    peterjc committed May 24, 2016
  6. @peterjc
  7. @peterjc
  8. @peterjc
  9. @peterjc

    Use our standard doctest stub

    peterjc committed May 24, 2016
  10. @peterjc
  11. @peterjc

    Make import explicit in doctest

    This was also important for running the doctests directly
    via the __main__ trick as otherwise an isinstance check
    was failing.
    peterjc committed May 24, 2016
  12. @peterjc
  13. @peterjc
  14. @peterjc

    PEP8 E402, imports first

    peterjc committed May 24, 2016
  15. @peterjc
  16. @peterjc
  17. @peterjc
  18. @peterjc
  19. @peterjc
  20. @peterjc

    Remove redundant Bio.SeqIO.SeqXmlIO test

    Parsing this file was covered in test_SeqXmlIO.py anyway.
    See GitHub issue #820.
    peterjc committed May 24, 2016
  21. @peterjc

    Remove redundant self-test in Bio.SeqIO.SwissIO

    This was covered by test_SwissProt.py anyway, see GitHub issue #820.
    peterjc committed May 24, 2016
  22. @peterjc

    Avoid mutable lists as default arguments.

    The Bio.Cluster code already allowed passing single entry
    indexes as integers, so doing that instead.
    peterjc committed May 24, 2016
  23. @peterjc
  24. @peterjc
  25. @peterjc
  26. @MarkusPiotrowski @peterjc
  27. @peterjc
Commits on May 23, 2016
  1. @peterjc

    Fix default mutable args in Bio.Restriction with empty tuples.

    Tweak code to allow for tuples or lists by using sorted(x)
    in place of calling x.sort() which only works on a list,
    not a tuple.
    peterjc committed May 24, 2016
  2. @peterjc
  3. @peterjc

    PEP8 whitespace

    peterjc committed May 23, 2016
  4. @peterjc

    Simplify use of all(...)

    Closes #710.
    peterjc committed May 23, 2016
  5. @vincentdavis @peterjc

    use with open()

    vincentdavis committed with peterjc Dec 3, 2015
  6. @vincentdavis @peterjc

    open with and fixed re-use of variable name

    fixed Variable 'filename' already declared in 'for' loop or
    'with' statement above (at line 635), and use with open()
    vincentdavis committed with peterjc Dec 3, 2015
  7. @vincentdavis @peterjc

    use with open

    vincentdavis committed with peterjc Dec 3, 2015
  8. @vincentdavis @peterjc

    use with open

    vincentdavis committed with peterjc Dec 3, 2015
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