Commit b6788a47 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.72+dfsg

parent 0f7d18b8

.github/PULL_REQUEST_TEMPLATE.md

+3 −3
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@@ -7,6 +7,6 @@ I have read the ``CONTRIBUTING.rst`` file and understand that AppVeyor and 
TravisCI will be used to confirm the Biopython unit tests and ``flake8`` style

checks pass with these changes.



I am happy be thanked by name in the ``NEWS.rst`` and ``CONTRIB.rst`` files,

and have added myself to those files as part of this pull request. (*This

acknowledgement is optional. Note we list the names sorted alphabetically.*)
 
I have added my name to the alphabetical contributors listings in the files

``NEWS.rst`` and ``CONTRIB.rst`` as part of this pull request, am listed

already, or do not wish to be listed. (*This acknowledgement is optional.*)

.travis-tox.ini

+2 −1
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@@ -65,7 +65,7 @@ deps = 
    {py27,py34,py35,py35}: mysql-connector-python-rf

    {py27,py35,pypy}: rdflib

    {pypy,pypy3}: numpy==1.12.1

    {py27,py34,py35,py36}: numpy

    {py27,py34,py36}: numpy

    {py36}: scipy

    {py27}: networkx

    {py36}: matplotlib
@@ -94,6 +94,7 @@ deps = 
    flake8-rst-docstrings

    restructuredtext_lint

commands =

    flake8 --max-line-length 82 setup.py

    # These folders each have their own .flake8 file:

    flake8 BioSQL/

    flake8 Scripts/

.travis.yml

+6 −6
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@@ -104,10 +104,10 @@ before_install: 
  - |

    if [[ $TRAVIS_PYTHON_VERSION == 'pypy' ]]; then

        deactivate

        wget https://bitbucket.org/squeaky/portable-pypy/downloads/pypy-5.10.0-linux_x86_64-portable.tar.bz2

        tar -jxvf pypy-5.10.0-linux_x86_64-portable.tar.bz2

        wget https://bitbucket.org/squeaky/portable-pypy/downloads/pypy-6.0.0-linux_x86_64-portable.tar.bz2

        tar -jxvf pypy-6.0.0-linux_x86_64-portable.tar.bz2

        echo 'Setting up aliases...'

        cd pypy-5.10.0-linux_x86_64-portable/bin/

        cd pypy-6.0.0-linux_x86_64-portable/bin/

        export PATH=$PWD:$PATH

        ln -s pypy python

        echo 'Setting up pip...'
@@ -116,10 +116,10 @@ before_install: 
  - |

    if [[ $TRAVIS_PYTHON_VERSION == 'pypy3' ]]; then

        deactivate

        wget https://bitbucket.org/squeaky/portable-pypy/downloads/pypy3.5-5.10.1-linux_x86_64-portable.tar.bz2

        tar -jxvf pypy3.5-5.10.1-linux_x86_64-portable.tar.bz2

        wget https://bitbucket.org/squeaky/portable-pypy/downloads/pypy3.5-6.0.0-linux_x86_64-portable.tar.bz2

        tar -jxvf pypy3.5-6.0.0-linux_x86_64-portable.tar.bz2

        echo 'Setting up aliases...'

        cd pypy3.5-5.10.1-linux_x86_64-portable/bin/

        cd pypy3.5-6.0.0-linux_x86_64-portable/bin/

        export PATH=$PWD:$PATH

        ln -s pypy3 python

        echo 'Setting up pip...'

Bio/Align/AlignInfo.py

+8 −7
Original line number Diff line number Diff line 
# This code is part of the Biopython distribution and governed by its

# license.  Please see the LICENSE file that should have been included

# as part of this package.

# Copyright 2000 Brad Chapman.  All rights reserved.

#



# This file is part of the Biopython distribution and governed by your

# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".

# Please see the LICENSE file that should have been included as part of this

# package.

"""Extract information from alignment objects.



In order to try and avoid huge alignment objects with tons of functions,
@@ -179,7 +180,7 @@ class SummaryInfo(object): 
        return Seq(consensus, consensus_alpha)



    def _guess_consensus_alphabet(self, ambiguous):

        """Pick an (ungapped) alphabet for an alignment consesus sequence.

        """Pick an (ungapped) alphabet for an alignment consesus sequence (PRIVATE).



        This just looks at the sequences we have, checks their type, and

        returns as appropriate type which seems to make sense with the
@@ -319,7 +320,7 @@ class SummaryInfo(object): 
        return start_dict



    def _get_all_letters(self):

        """Return a string containing the expected letters in the alignment."""

        """Return a string containing the expected letters in the alignment (PRIVATE)."""

        all_letters = self.alignment._alphabet.letters

        if all_letters is None or \

                (isinstance(self.alignment._alphabet, Alphabet.Gapped) and
@@ -337,7 +338,7 @@ class SummaryInfo(object): 
        return all_letters



    def _get_base_replacements(self, skip_items=None):

        """Get a zeroed dictionary of all possible letter combinations.

        """Get a zeroed dictionary of all possible letter combinations (PRIVATE).



        This looks at the type of alphabet and gets the letters for it.

        It then creates a dictionary with all possible combinations of these

Bio/Align/Applications/_ClustalOmega.py

+4 −6
Original line number Diff line number Diff line
@@ -2,12 +2,10 @@ 
# Copyright 2011 by Andreas Wilm. All rights reserved.

# Based on ClustalW wrapper copyright 2009 by Cymon J. Cox.

#

# Wrapper for Clustal Omega by Andreas Wilm (2011). Used _Clustalw.py

# as template.

#

# This code is part of the Biopython distribution and governed by its

# license.  Please see the LICENSE file that should have been included

# as part of this package.

# This file is part of the Biopython distribution and governed by your

# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".

# Please see the LICENSE file that should have been included as part of this

# package.

"""Command line wrapper for the multiple alignment program Clustal Omega."""



from __future__ import print_function