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Apr 23, 2014

  1. Wibowo Arindrarto

    Update SearchIO blast XML warning test for py3.4 compatibility

    authored April 24, 2014
  2. Peter Cock

    Specify encoding for test to pass on Windows

    Also minor style changes (PEP8 white spaces).
    authored April 23, 2014

Apr 22, 2014

  1. Peter Cock

    Tweak doctest for int vs long issue on 64 bit Windows

    Rather than (7, 52), Manlio Calvi reports getting (7L, 52L)
    with 64 bit Python 2.7 under Windows 7, see mailing list:
    http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011276.html
    authored April 22, 2014
  2. Peter Cock

    Mark Tests/SubsMat/acc_rep_mat.pik as binary to solve Pickle problem

    If the pickle file has DOS/Windows newlines which can happen under
    Windows depending on how git was configured, the C based pickle code
    in Python 3.4 fails to to load it with this exception:
    
    _pickle.UnpicklingError: the STRING opcode argument must be quoted
    
    See test_SubsMat.py and this thread on the mailing list for background:
    http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011274.html
    authored April 22, 2014

Apr 21, 2014

  1. Peter Cock

    Split unit test method into three smaller tests

    authored April 21, 2014
  2. Peter Cock

    Thank Nigel for Newick unicode BOM fix

    authored April 21, 2014
  3. Check for unicode byte order marks (BOMs) in Newick trees under Python 2

    Cherry-picked from pull request #241 / #310
    authored April 21, 2014 peterjc committed April 21, 2014
  4. Peter Cock

    Style change, avoid unnecessary dictionary .keys() method call

    Based on a GitHub comment by @namn refering to Guido's email:
    https://mail.python.org/pipermail/python-dev/2014-April/134187.html
    authored April 21, 2014

Apr 20, 2014

  1. Eric Talevich

    CodonAlignment.get_dn_ds_matrix: fix TreeConstruction._DistanceMatrix…

    … import
    authored April 20, 2014
  2. Zheng Ruan

    using self.assertAlmostEquals() instead of self.assertEqual()

    authored January 31, 2014 etal committed April 20, 2014
  3. Zheng Ruan

    do not test mk method when numpy is not installed

    authored January 23, 2014 etal committed April 20, 2014
  4. Zheng Ruan

    resolve stop codon problems in mktest (using deepcopy for default_cod…

    …on_table)
    authored January 23, 2014 etal committed April 20, 2014
  5. Zheng Ruan

    change round() to 4 for python3 test to pass

    authored January 21, 2014 etal committed April 20, 2014
  6. Zheng Ruan

    rebase fix

    authored January 21, 2014 etal committed April 20, 2014
  7. Zheng Ruan

    python3 compatibility

    authored January 14, 2014 etal committed April 20, 2014
  8. Zheng Ruan

    unstaged changes

    authored December 18, 2013 etal committed April 20, 2014
  9. Zheng Ruan

    for pypy compatibility

    authored December 18, 2013 etal committed April 20, 2014
  10. Zheng Ruan

    python3 compatibility fix

    authored December 18, 2013 etal committed April 20, 2014
  11. Zheng Ruan

    remove dict comprehensive for python2.6 compatibility

    authored December 10, 2013 etal committed April 20, 2014
  12. Zheng Ruan

    not test yn00 if scipy.linalg.expm importing failed

    authored December 10, 2013 etal committed April 20, 2014
  13. Zheng Ruan

    skip ML testing if scipy importing failed

    authored December 09, 2013 etal committed April 20, 2014
  14. Zheng Ruan

    supress warnings in testing

    authored December 09, 2013 etal committed April 20, 2014
  15. Zheng Ruan

    add CodonAlign module into setup.py and Tests/run_tests.py

    authored December 09, 2013 etal committed April 20, 2014
  16. Zheng Ruan

    update test

    authored September 21, 2013 etal committed April 20, 2014
  17. Zheng Ruan

    add doc for CodonAlign

    authored September 18, 2013 etal committed April 20, 2014
  18. Zheng Ruan

    fix a small bug of NG86 (change log10 to log)

    authored August 11, 2013 etal committed April 20, 2014
  19. Zheng Ruan

    holiday update for CodonSeq

    authored July 22, 2013 etal committed April 20, 2014
  20. Zheng Ruan

    add full_translate method

    authored September 18, 2013 etal committed April 20, 2014
  21. Zheng Ruan

    add dN dS tree construction

    authored September 16, 2013 etal committed April 20, 2014
  22. Zheng Ruan

    terminate _dijkstra() when finding the end node

    authored September 15, 2013 etal committed April 20, 2014
  23. Zheng Ruan

    include biopython chi2 implementation for MKtest

    authored September 14, 2013 etal committed April 20, 2014
  24. Zheng Ruan

    re-organize cal_dn_ds method

    authored September 14, 2013 etal committed April 20, 2014
  25. Zheng Ruan

    modify toCodonAlignment to be a classmethod

    authored September 14, 2013 etal committed April 20, 2014
  26. Zheng Ruan

    allow different codon frequency vector in ML method

    authored September 14, 2013 etal committed April 20, 2014
  27. Zheng Ruan

    add Mcdonald-Kreitman Test

    authored September 08, 2013 etal committed April 20, 2014
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