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Commits on Aug 29, 2016
  1. 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
  2. Thank Chris Warth for the PAML work

    peterjc committed Aug 29, 2016
  3. 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. Remove unused import (of deprecated module) in FSSP

    peterjc committed Aug 28, 2016
  2. Avoid alphabet-only init warning

    peterjc committed Aug 28, 2016
  3. 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. Remove backport of lgamma for Python 2.6

    peterjc committed Aug 27, 2016
Commits on Aug 26, 2016
  1. Thank Ben Fulton for Biopython 1.68 installers

    peterjc committed Aug 26, 2016
  2. Drop Python 2.6 support

    peterjc committed Aug 26, 2016
  3. TravisCI: Install PhyML

    peterjc committed with peterjc Aug 26, 2016
Commits on Aug 25, 2016
  1. Forgot to put v1.68 release date in NEWS file

    peterjc committed Aug 25, 2016
  2. Call this Biopython 1.68

    peterjc committed Aug 25, 2016
  3. 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. Fix LaTeX markup in alignment chapter.

    This was breaking hevea (rightly).
    peterjc committed Aug 23, 2016
  2. Update xbbtools

    MarkusPiotrowski committed with peterjc Aug 22, 2016
  3. Thank Iddo for UniProt.GAO GAF 2.1 fix

    peterjc committed Aug 23, 2016
  4. 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. Thank Xiaoyu Zhuo for the EMBL fix

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

    xzhuo committed with peterjc Aug 8, 2016
  3. Create embl_with_0nt_line.embl

    xzhuo committed with peterjc Aug 5, 2016
  4. 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. Fix syntax in .codecov.yml

    Thank you to Steve Peak of CodeCov.io for his help
    peterjc committed Aug 15, 2016
  2. PEP8 import order; trailing whitespace; line length

    peterjc committed Aug 15, 2016
  3. Only need top level Bio.PopGen deprecation warnings.

    Also add DEPRECATED to the module docstrings.
    peterjc committed Aug 11, 2016
Commits on Aug 11, 2016
  1. Add .codecov.yml file to tweak coverage reports

    Side effect of including BioSQL coverage was including the Tests
    folder as well. Since I struggled to control this via the coverage
    tool command line (in our TravisCI/Tox setup), we'll instead use
    the CodeCov configuration to ignore the Tests folder.
    
    This file can be called codecov.yml or .codecov.yml which we're
    using as this is hidden on Linux/Mac like the TravisCI files.
    
    Coverage output online at https://codecov.io/gh/biopython/biopython
    peterjc committed Aug 11, 2016