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Commits on Feb 2, 2016
  1. @mdehoon

    Merge pull request #679 from sefakilic/master

    mdehoon committed
    Correct descsription of Patser threshold
Commits on Feb 1, 2016
  1. @wojdyr @peterjc

    PDBParser: uppercase element names

    wojdyr committed with peterjc
    Avoid problems with lower/mixed case element names, as discussed on ML:
    http://mailman.open-bio.org/pipermail/biopython/2015-May/015619.html
  2. @peterjc

    PEP8 whitespace

    peterjc committed
  3. @vincentdavis @peterjc

    Update Entrez journal search examples to use nlmcatalog

    vincentdavis committed with peterjc
    Squashed commit of GitHub pull request #736
Commits on Jan 29, 2016
  1. @mdehoon

    Merge pull request #764 from zachcp/patch-1

    mdehoon committed
    change from_uid to id to match docstrings
Commits on Jan 27, 2016
  1. @zachcp

    change from_uid to id to match docstrings

    zachcp committed
    from_uid -> id as per the doctrings
  2. Fixed a small error in the Bio.Medline.parse() docstring

    Andrew Barros committed
Commits on Jan 26, 2016
  1. Support RaxML testing on Windows

    Ben Fulton committed
Commits on Jan 24, 2016
  1. @mdehoon

    Describe the Cluster file format explicitly, instead of referring to …

    mdehoon committed
    …a now non-existant website.
Commits on Jan 19, 2016
  1. @peterjc

    Need universal_newlines=True for Python 3

    peterjc committed
    Spotted by Tiago, see GitHub issue #748.
    
    The other use of subprocess.Popen(...) in this file was
    already using universal newlines to get text mode stdout.
  2. @peterjc

    PEP8 spacing in Tutorial example

    peterjc committed
    TODO: Use context managers once possible on all supported
    versions of Python.
Commits on Jan 18, 2016
  1. @peterjc
  2. @peterjc
  3. @peterjc

    Only use EvilHandleHack under Python 3.3

    peterjc committed
    See issue #721
  4. @peterjc

    Fix Tutorial links to my_blast.xml and my_blat.psl

    peterjc committed
    See GitHub issue #749
  5. @peterjc

    Cope with change to samtools sort API in test.

    peterjc committed
    This hides the test failure but does not updated the
    wrapper itself to offer the new samtools sort API.
    See GitHub issue #625.
  6. @peterjc

    samtools 1.3 will give a warning here

    peterjc committed
    See #475 for this and related test problems with samtools changes
Commits on Jan 11, 2016
  1. @peterjc
Commits on Jan 10, 2016
  1. @peterjc

    Fix path issue in test_Tutorial.py

    peterjc committed
    Closes #704, based on proposed solution in #744 by @sticken88
Commits on Jan 8, 2016
  1. @peterjc
  2. @peterjc
  3. @peterjc

    Even more SFF error testing

    peterjc committed
  4. @peterjc

    More SFF error testing

    peterjc committed
Commits on Jan 7, 2016
  1. @peterjc

    Added NCBI genetic code table 25

    peterjc committed
    See pull request #746, this closes issue 448.
Commits on Jan 6, 2016
  1. @ctSkennerton
  2. @ctSkennerton
Commits on Jan 5, 2016
  1. @peterjc

    Thank Conner for BioSQL+SQLite3 foreign keys

    peterjc committed
    Closes GitHub pull request #743
  2. @ctSkennerton @peterjc

    Updated BioSQL sqlite3 schema to include foreign keys

    ctSkennerton committed with peterjc
    Fix for GitHub issue #741 by changing the sqlite3 database schema
    to use foreign keys. A new test has been added in that explicitly
    tests to make sure associated data with a bioentry is removed.
    
    To accommodate the use of foreign keys the connection to an sqlite
    database must set the PRAGMA, which is now done automatically when
    opening the database.
    
    The upstream BioSQL schema for sqlite3 has also been updated, see
    biosql/biosql#3
  3. @peterjc

    Test some SFF error conditions

    peterjc committed
    This is how I spotted the 13 vs 31 typo fixed in the previous commit.
  4. @peterjc
Commits on Jan 4, 2016
  1. @peterjc
  2. @peterjc
  3. @peterjc
  4. @peterjc

    Remove redundant module level global

    peterjc committed
    QuantifiedCode.com grumbled:
    
    "Using the `global` statement is unnecessary at module level"
  5. @peterjc

    Make sure don't load seq just for length in BioSQL

    peterjc committed
    Also avoids a naked except clause which is what made me look
    at this part of the code.
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