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Commits on Aug 30, 2016
  1. @peterjc

    PEP8 whitespace

    peterjc committed Aug 30, 2016
  2. @peterjc

    Mention NEXUS work in NEWS file.

    Chris Warth is already in the contributors for this release.
    peterjc committed Aug 30, 2016
  3. @peterjc

    various Nexus parsing fixes

    - remove '/' from the list of prohibited characters in nexus identifiers.
    - allow ',' in nexus comments on internal nodes.  Perviously ',' was
      allowed in the comments on the whole tree (most encapsulating node)
      but through a quirk in the parser ',' could not appear in the
      comments of internal nodes.
    - add Nexus test cases to check if comment parsing is working as expected.
    Chris Warth committed with peterjc Nov 13, 2015
Commits on Aug 29, 2016
  1. @peterjc

    Show new dot-less description in the test output

    Closes GitHub #615.
    peterjc committed Feb 1, 2016
  2. @peterjc

    Update the GenBank.Record output to restore trailing dot

    Part of fixing #615
    peterjc committed Feb 1, 2016
  3. @peterjc
  4. @peterjc
  5. @bneron @peterjc

    fix issue #615

    #615
    ensure that the filed DEFINITION ends with a period as in Genbank
    format specifications.
    bneron committed with peterjc Sep 18, 2015
  6. @peterjc

    Thank Chris Warth for the PAML work

    peterjc committed Aug 29, 2016
  7. @peterjc

    Long taxa names and testing with PAML v4.8

    Squashed commit of pull request #671, includes docstring
    edits to better match PEP257.
    Chris Warth committed with peterjc Nov 16, 2015
Commits on Aug 28, 2016
  1. @peterjc

    Remove unused import (of deprecated module) in FSSP

    peterjc committed Aug 28, 2016
  2. @peterjc

    Avoid alphabet-only init warning

    peterjc committed Aug 28, 2016
  3. @peterjc

    Stop subclassing deprecated Alignment in MultipleSeqAlignment.

    Removes the original Alignment object which was defined in the
    deprecated Bio.Align.Generic module, so the base methods defined
    there need to be added to MultipleSeqAlignment.
    
    Note the docstring examples were updated to use the newer class
    name MultipleSeqAlignment.
    peterjc committed Aug 28, 2016
Commits on Aug 27, 2016
  1. @peterjc
  2. @peterjc
  3. @peterjc

    Remove backport of lgamma for Python 2.6

    peterjc committed Aug 27, 2016
  4. @peterjc
Commits on Aug 26, 2016
  1. @peterjc

    Thank Ben Fulton for Biopython 1.68 installers

    peterjc committed Aug 26, 2016
  2. @peterjc

    Drop Python 2.6 support

    peterjc committed Aug 26, 2016
  3. @peterjc
  4. @peterjc
  5. @peterjc @peterjc

    TravisCI: Install PhyML

    peterjc committed with peterjc Aug 26, 2016
Commits on Aug 25, 2016
  1. @peterjc

    Forgot to put v1.68 release date in NEWS file

    peterjc committed Aug 25, 2016
  2. @peterjc

    Call this Biopython 1.68

    peterjc committed Aug 25, 2016
  3. @peterjc

    Need to include Doc/examples/alpha.faa and beta.faa

    These are used in the Tutorial and its doctests.
    peterjc committed Aug 25, 2016
Commits on Aug 23, 2016
  1. @peterjc

    Fix LaTeX markup in alignment chapter.

    This was breaking hevea (rightly).
    peterjc committed Aug 23, 2016
  2. @MarkusPiotrowski @peterjc

    Update xbbtools

    MarkusPiotrowski committed with peterjc Aug 22, 2016
  3. @peterjc

    Thank Iddo for UniProt.GAO GAF 2.1 fix

    peterjc committed Aug 23, 2016
  4. @idoerg @peterjc

    Support for GAF 2.1 in the UniPort.GOA GAF parser.

    Fixed a bug in GOA GAF parser. The parser defaulted to GAF 1.0
    if it didn't recognizes the GAF version. Since there are now 3
    GAF versions (2.1, 2.0 and historically 1.0), the code makes an
    explicit choice when parsing the gene associate file header and
    raises an exception if the GAF version is not recognized.
    
    Squashed commit from GitHub pull request #818.
    idoerg committed with peterjc Apr 10, 2016
Commits on Aug 22, 2016
  1. @peterjc

    Thank Xiaoyu Zhuo for the EMBL fix

    See pull request #910 (manually rebased and applied as previous commits).
    peterjc committed Aug 22, 2016
  2. @xzhuo @peterjc

    Update test_EMBL_unittest.py

    xzhuo committed with peterjc Aug 8, 2016
  3. @xzhuo @peterjc

    Create embl_with_0nt_line.embl

    xzhuo committed with peterjc Aug 5, 2016
  4. @xzhuo @peterjc
  5. @peterjc

    Don't have Tutorial-dev.html and .pdf on GitHub based website

    It might be possible to do this via TravisCI (although unclear
    where to host the HTML and PDF output), but in any case, we
    would not want to record all the minor compiled tutorial
    changes in the GitHub repository for the website.
    peterjc committed Aug 22, 2016
Commits on Aug 15, 2016
  1. @peterjc

    Fix syntax in .codecov.yml

    Thank you to Steve Peak of CodeCov.io for his help
    peterjc committed Aug 15, 2016