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Commits on Feb 22, 2017
  1. Mention pydocstyle in CONTRIBUTING

    peterjc committed Feb 22, 2017
  2. Remove unwanted white space after docstrings (etc)

    $ pydocstyle Bio/ BioSQL/ Tests/ Scripts/ Doc/ --select D202
    ...
    D202: No blank lines allowed after function docstring
    peterjc committed Feb 22, 2017
  3. TravisCI/Tox: Rename the pep8 target to style

    peterjc committed Feb 22, 2017
  4. Avoid mutable list for __all__

    peterjc committed Feb 22, 2017
  5. Thank FGastaldello

    See previous commit from pull request 1063,
    working towards issue #820 on improving test
    coverage.
    peterjc committed Feb 22, 2017
  6. remove "if __name__ == '__main__':" block

    Gasta88 committed with peterjc Feb 15, 2017
Commits on Feb 14, 2017
  1. Fix sort order

    peterjc committed Feb 14, 2017
  2. TravisCI: Replace PyPy & PyPy3 with latest portable binaries

    Using https://github.com/squeaky-pl/portable-pypy#portable-pypy-distribution-for-linux in order to just download, unzip, and run the latest versions of PyPy and PyPy3 under TravisCI.
    
    Hopefully by setting aliases under ~/bin this will be a drop-in replacement for the TravisCI provided (older) versions.
    peterjc committed Feb 14, 2017
  3. Fix unit test, failed under PyPy 5.6.0

    PyPy rightly complained this was calling assertTrue with an extra argument.
    peterjc committed Feb 14, 2017
Commits on Feb 13, 2017
  1. Flesh out stubs for unimplemented MAF i/e/q lines

    We could issue a BiopythonParserWarning about ignoring the lines?
    peterjc committed Feb 13, 2017
  2. Avoid ValueError for file not found

    Aim here was to be user friendly, but a file-system relevant
    exception is probably better for error handling.
    peterjc committed Feb 13, 2017
  3. Top-level imports in MafIO

    Following pattern in Bio/File.py for missing SQLite3.
    Issues flagged by Wibowo Arindrarto during review.
    peterjc committed Feb 13, 2017
  4. Update copyright for MafIO.py

    peterjc committed Feb 8, 2017
  5. PEP8

    peterjc committed Feb 7, 2017
  6. Allowing multiple sequences with the same IDs in MAFs.

    I want this functionality and I don't see anything against it in
    the spec at <https://cgwb.nci.nih.gov/FAQ/FAQformat.html#format5>.
    adamnovak committed with peterjc Apr 18, 2015
  7. Fixing minor defects.

    Fixed MafIndex not inheriting from object.
    
    Fixed use of "+1" and "-1" to represent strands; changed to 1 and -1 (ints) like in Bio.SeqFeature.
    
    Removed trailing whitespace in MafIO.py.
    adamnovak committed with peterjc Oct 6, 2014
  8. Changing MafIO search to use built-in SQL DISTINCT instead of a dict,…

    … and giving it a deterministic SQL-defined result ordering.
    adamnovak committed with peterjc Jul 25, 2014