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Commits on May 1, 2016
  1. @peterjc

    Thank Owen for iterator fix.

    See pull request #817.
    
    Also fixed alphabetical sorting in NEWS entry.
    peterjc committed May 1, 2016
  2. @odoublewen @peterjc

    Update __init__.py

    Removed useless and deprecated `raise StopIteration` inside generator (see PEP 0479)
    odoublewen committed with peterjc Apr 29, 2016
  3. @etal

    NexusIO: omit [&U] before each tree (closes #796)

    In Newick syntax [&U] is a comment, but for PAUP* it indicates an unrooted tree.
    Not all trees written by Phylo are unrooted, so @cymon suggested dropping it.
    etal committed Apr 30, 2016
Commits on Apr 27, 2016
  1. @peterjc

    Update http://biopython.org/DIST/docs/tutorial/examples/ URLs

    As a knock on effect of moving the website to GitHub Pages,
    we must now use GitHub raw for example files, see
    biopython/biopython.github.io#57
    peterjc committed Apr 27, 2016
  2. @peterjc

    Fix off-by-one error in GenBank/EMBL locations using UnknownPosition

    Spotted by chance while browsing code, includes basic unit test.
    peterjc committed Apr 27, 2016
Commits on Apr 16, 2016
  1. @peterjc

    Mention Conner's BioSQL taxonomy work in NEWS.

    Closes #809.
    peterjc committed Apr 16, 2016
  2. @ctSkennerton @peterjc

    Set the left/right taxonomy tree values in BioSQL

    Squashed commit from Pull Request #809.
    
    Set the left and right values of the taxon table
    
    Set the left value to the max in case there are multiple top levels
    
    provide an executemany method to _CursorWrapper and Adaptor
    
    (Peter: I also fixed minor white space complaints from PEP8 checking)
    ctSkennerton committed with peterjc Apr 15, 2016
Commits on Apr 7, 2016
  1. @peterjc
Commits on Apr 6, 2016
  1. @peterjc
  2. @cbrueffer @peterjc

    Improve NEWS file wording.

    cbrueffer committed with peterjc Apr 4, 2016
  3. @peterjc

    Fixed typo in method docstring

    peterjc committed Apr 6, 2016
  4. @peterjc
  5. @brandoninvergo @peterjc
  6. @peterjc

    Currently testing with PyPy 5.0 (not PyPy 2.4 etc)

    See recent changes to buildbot and README file.
    peterjc committed Apr 6, 2016
  7. @peterjc

    Update NEWS about MMCIF

    Closes #778 and #779 via pull request #800 from @JoaoRodrigues
    peterjc committed Apr 6, 2016
Commits on Apr 5, 2016
  1. @JoaoRodrigues

    Silenced most warnings in the tests: added QUIET=1, fixed old-style w…

    …arning catching in favour of catch_warnings()
    JoaoRodrigues committed Apr 5, 2016
  2. @JoaoRodrigues
  3. @JoaoRodrigues

    Added unit test to compare SMCRA representations of the same structur…

    …e in CIF and PDB formats
    JoaoRodrigues committed Apr 5, 2016
  4. @JoaoRodrigues

    Changed chain assignment to auth_sym_id key in the mmCIF specificatio…

    …n to match PDB chain ids.
    JoaoRodrigues committed Apr 5, 2016
  5. @JoaoRodrigues

    Standardize structures in the test suite: remove 1MOT.pdb and add 1LC…

    …D.pdb (to match existing .cif)
    JoaoRodrigues committed Apr 5, 2016
Commits on Apr 4, 2016
  1. @peterjc

    Just updated my machines and buildbot to use PyPy 5.0

    Didn't notice any new problems under  PyPy 2.4/2.5/2.6, but
    there was a XML related JIT failure in a test under PyPy 4.0
    which I don't want to worry about.
    
    PyPy 5.0 looks fine under Linux and Mac (64 bit), and under
    Windows XP (32 bit).
    peterjc committed Apr 4, 2016
  2. @peterjc
Commits on Mar 28, 2016
  1. @peterjc

    Update GenBank virus SeqIO.index_db example in Tutorial

    This dataset has roughly doubled in size since I wrote the example,
    meaning it has become uncomfortably large for use as an example -
    see GitHub issue #714.
    
    Changed the example to use just the first four chunks as suggested
    by Tiago (@tiagoantao), currently the test record is in the first
    chunk.
    
    Also using glob to build the file list rather than hard coding
    the number of files expected.
    peterjc committed Dec 14, 2015
  2. @mdehoon

    Merge pull request #791 from peterjc/entrez_stringio

    Python 3: Cope with StringIO in Entrez parser
    mdehoon committed Mar 28, 2016
Commits on Mar 26, 2016
  1. @peterjc
  2. @peterjc
Commits on Mar 25, 2016
  1. @ctSkennerton
  2. @ctSkennerton
  3. @ctSkennerton

    Added test to convert int to str in efetch

    Some NCBI identifiers are integers, such as taxonomy ids or GI
    numbers. It is natural then that a user may code them as integers
    in python. This additional test automatically converts an ID given
    to efetch as an integer to a string, which is required by the
    entrez API
    ctSkennerton committed Dec 29, 2015
  4. @ctSkennerton @peterjc

    Enforce BioSQL namespace (biodatabase) in __getitem__ and __delitem__

    Squashed commit from GitHub pull request #767.
    ctSkennerton committed with peterjc Feb 8, 2016
  5. @peterjc
  6. @peterjc

    Tweak test for PyPy3 v2.4.0

    peterjc committed Mar 25, 2016
  7. @peterjc
Commits on Mar 23, 2016
  1. @peterjc

    Entrez parser tests for text vs binary handles

    Note the TODO entries - would like to handle StringIO
    as in example raised in passing on GitHub issue #788.
    peterjc committed Mar 23, 2016
Commits on Mar 22, 2016
  1. @peterjc

    Fix typo in SeqRecord slicing example

    Spotted by @erkisala, closes GitHub issue #790.
    peterjc committed Mar 22, 2016
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