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Commits on Jun 27, 2016
  1. @abradle @peterjc

    Expand on MTTF in tutorial

    Peter: Squashed commit of pull request #862, but with Tutorial
    doctests commented out pending revision.
    abradle committed with peterjc Jun 27, 2016
  2. @ctSkennerton @peterjc

    Support BioSQL DBSeqRecord slicing as SeqRecord

    Squashed commit of pull request #803, closes issue #797.
    
    Long term the DBSeqRecord could implement __getitem__,
    perhaps by extending __init__ to include start/end options
    (default to the full record) and acting as a windowed view
    of the full record (e.g. loading only selected features on
    demand).
    ctSkennerton committed with peterjc Jun 27, 2016
  3. @peterjc

    Document how test_Tutorial.py works

    Closes #863.
    peterjc committed Jun 27, 2016
Commits on Jun 24, 2016
  1. @peterjc
  2. @peterjc
  3. @peterjc

    Mention MMTF support in news; thank Anthony Bradley

    This closes pull request #854 via the preceeding squashed commit.
    peterjc committed Jun 24, 2016
  4. @abradle @peterjc
  5. @peterjc

    Use HTTPS to access QBLAST

    See http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2016-June/000104.html
    
    As of 1 September 2016, the NCBI seem to be planning to
    automatically redirect HTTP connections to HTTPS. From
    initial testing HTTPS support is already live, so we can
    make the switch now.
    peterjc committed Jun 22, 2016
  6. @peterjc

    Use HTTPS to access NCBI Entrez

    See http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2016-June/000104.html
    
    As of 1 September 2016, the NCBI seem to be planning to
    automatically redirect HTTP connections to HTTPS. From
    initial testing HTTPS support is already live, so we can
    make the switch now.
    peterjc committed Jun 22, 2016
  7. @carlosp420 @peterjc

    Bio.SeqUtils: use enumerate instead of range(len(x))

    Enumerate is more "Pythonic".
    
    The variable self.index is using codons as key for its dictionary, and
    its value is being taken from the list rcsu. The value in the index of
    the list rcsu was generated by this same codon in lines 103--105.
    
    Squashed commit of pull request #861.
    carlosp420 committed with peterjc Jun 24, 2016
Commits on Jun 22, 2016
  1. @peterjc

    More helpful message about bdist_wheel failing

    Now that NumPy provides precompiled wheels on PyPI,
    I would like us to do the same for Biopython. That
    means using 'python setup.py bdist_wheel' which in
    turn requires installing both setuptools and wheel.
    peterjc committed Jun 22, 2016
  2. @peterjc

    Thank Uwe Schmitt for the setuptools change.

    This was belatedly applied from pull request #446.
    peterjc committed Jun 22, 2016
  3. @uweschmitt @peterjc
  4. @carlosp420 @peterjc

    New tests for refactored Bio.Entrez

    Based on pull request #684 from Carlos Peña, which required manual
    merging. I have not included Carlos' changes to the post logic.
    Peter
    carlosp420 committed with peterjc Jun 21, 2016
  5. @carlosp420 @peterjc

    Refactor Bio/Entrez/__init__.py to facilitate testing.

    Based on pull request #684 from Carlos Peña, which required manual
    merging. I did not include Carlos' changes to the post logic, so
    there should be no behavioural changes from this commit. Peter.
    carlosp420 committed with peterjc Jun 21, 2016
  6. @peterjc
  7. @peterjc

    Add NCBI genetic code 26 Pachysolen tannophilus Nuclear Code

    This isn't in Version 4.0 of the machine readable file
    ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt so I have
    hand entered it based on the human readable information
    at http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG26
    
    Also includes basic tests for the recently added codon
    tables.
    peterjc committed Jun 22, 2016
  8. @peterjc

    Fix Archaeal

    peterjc committed Jun 22, 2016
  9. @peterjc

    Re-apply NCBI genetic codes v4.0

    Using revised code now in Scripts/update_ncbi_codon_table.py which
    makes some minor white-space changes, changes the dict order in
    table 25 (previously must have been generated by hand), and the
    following real change:
    
    Name of table 11 updated from 'Bacterial and Plant Plastid' to
    'Bacterial, Archaeal and Plant Plastid'.
    peterjc committed Jun 22, 2016
  10. @peterjc

    Simplify building the start/stop codon listing

    This ought to deal with PEP8 compliant line wrapping at 78 characters.
    peterjc committed Jun 22, 2016
  11. @peterjc
  12. @peterjc

    Move NCBI gc.prt code to Scripts/update_ncbi_codon_table.py

    No code changes, simply moved the (commented out) code in
    Bio/Data/CodonTable.py used to parse the NCBI genetic codes
    from ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt to
    update Bio/Data/CodonTable.py into a separate script as
    Scripts/update_ncbi_codon_table.py
    peterjc committed Jun 22, 2016
  13. @peterjc

    Mention SeqGui update in NEWS

    This closes pull request #856 (cherry-picked to master).
    peterjc committed Jun 22, 2016
  14. @peterjc
  15. @MarkusPiotrowski @peterjc
Commits on Jun 21, 2016
  1. @carlosp420 @peterjc

    Fix docstrings. PEP0257.

    (Merge conflicts resolved by Peter)
    carlosp420 committed with peterjc Dec 3, 2015
  2. @peterjc
  3. @carlosp420 @peterjc

    fixed typo

    carlosp420 committed with peterjc Dec 9, 2015
  4. @carlosp420 @peterjc

    PEP8

    carlosp420 committed with peterjc Nov 27, 2015
Commits on Jun 20, 2016
  1. @peterjc

    Python 3 fix for new egquery test

    Solves this error:
    
    ======================================================================
    ERROR: test_egquery (__main__.EntrezOnlineCase)
    ----------------------------------------------------------------------
    Traceback (most recent call last):
      File test_Entrez_online.py, line 179, in test_egquery
        self.assertTrue(row[Count] > 60)
    TypeError: unorderable types: StringElement() > int()
    
    ----------------------------------------------------------------------
    peterjc committed Jun 20, 2016
  2. @peterjc
  3. @peterjc

    TravisCI: Include online tests under Python 3.3

    Trying to balance making sure we're not breaking of the online
    functionality, including the online functionality in the test
    coverage stats, versus load imposed on the online resources and
    the fact temporary outages will cause false positive failues.
    peterjc committed Jun 17, 2016
  4. @peterjc @peterjc

    Revise comment

    peterjc committed with peterjc Jun 20, 2016
  5. @peterjc

    Minor style change removing redundant plus

    Surprisinly the pep8 tool doesn't flag these with
    a style warning (yet).
    peterjc committed Jun 20, 2016
Commits on Jun 19, 2016
  1. @MarkusPiotrowski
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