New upstream version 1.73+dfsg

This pull request addresses issue #...

I hereby agree to dual licence this and any previous contributions under both

<!--- Please read each of the following items and confirm by replacing

 !--the [ ] with a [X] --->

- [ ] I hereby agree to dual licence this and any previous contributions under both

the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_.

I have read the ``CONTRIBUTING.rst`` file and understand that AppVeyor and

- [ ] 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 have added my name to the alphabetical contributors listings in the files

- [ ] 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.*)

#TODO - The unit tests shouldn't leave temp files after running:

Tests/BioSQL/temp_sqlite.db

Tests/BioSQL/temp_sqlite.db-journal

Tests/Cluster/cyano_result*

#TODO - The Tutorial doctests should leave example files after

#running Tests/test_Tutorial.py

Doc/examples/other_trees.nwk

Doc/examples/tree1.nwk

#Ignore LaTeX temp files, and compiled output

Doc/*.aux

    style

    sdist

    bdist_wheel

    api

    {py27,py34,py35,py36,pypy,pypy3}-cover

    {py27,py34,py35,py36,pypy,pypy3}-nocov

    TRAVIS_*

    TOXENV

    CODECOV_*

    HOME_4_TCOFFEE

whitelist_externals =

    bash

    echo

    #Leaving py34 without any soft dependencies (just numpy)

    cover: coverage

    cover: codecov

    {py27}: unittest2

    {py27}: mysql-python

    {py27,py36}: mmtf-python

    {py27,py35}: reportlab

    {py27,py34,py35,py36}: psycopg2-binary

    {py27,py34,py35,py35}: mysql-connector-python-rf

    {py27,py35,pypy}: rdflib

    {pypy,pypy3}: numpy==1.12.1

    {py27,py34,py36}: numpy

    {py36}: scipy

    {py27}: networkx

    {py36}: matplotlib

    py27: unittest2

    py27: mysql-python

    py27,py36: mmtf-python

    py27,py35: reportlab

    py27,py34,py35,py36: psycopg2-binary

    py27,py34,py35,py35: mysql-connector-python-rf

    py27,py35,pypy: rdflib

    pypy,pypy3: numpy==1.12.1

    py27,py34,py36: numpy

    py36: scipy

    py27: networkx

    py36: matplotlib

commands =

    #The bash call is a work around for special characters

    #The /dev/null is to hide the verbose output but leave warnings

skip_install = True

whitelist_externals =

    flake8

    doc8

    rst-lint

    bash

deps =

    flake8-docstrings

    flake8-blind-except

    flake8-rst-docstrings

    py34,py35,py36: flake8-bugbear

    restructuredtext_lint

    doc8

commands =

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

    # These folders each have their own .flake8 file:

    bash -c \'grep "^- " CONTRIB.rst | LC_ALL=C sort -u -c -f\'

    # Check copyright date

    bash -c \'grep "1999-`date +'%Y'`" LICENSE.rst\'

    # Would like to tell doc8 to just check *.rst but does *.txt too:

    bash -c "doc8 --ignore-path 'Doc/examples/ec_*.txt' *.rst Doc/"

    # Check no __docformat__ lines

    bash -c "if grep --include '*.py' -rn '^__docformat__ ' Bio BioSQL Tests Scripts Doc ; then echo 'Remove __docformat__ line(s), we assume restructuredtext.'; false; fi"

    # Check DOI link style, see https://www.crossref.org/display-guidelines/

    numpy

commands =

    python setup.py bdist_wheel

[testenv:api]

# Note Sphinx likes to have the code installed so can import it

skip_install = False

whitelist_externals =

    bash

    sphinx-apidoc

    make

deps =

    mmtf-python

    mysql-connector-python-rf

    numpy

    rdflib

    reportlab

    scipy

    sphinx>=1.8.0

    numpydoc

commands =

    bash -c \'python setup.py install > /dev/null\'

    bash -c \'mkdir -p Doc/api/_templates Doc/api/_static Doc/api/_build\'

    make -C Doc/api/ html

        apt:

          packages:

      before_install: echo "Going to run basic checks"

    - stage: test

      python: 2.7

      env: TOXENV=api

      addons:

        apt:

          packages:

      before_install: echo "Going to build API docs"

    - stage: test

      python: 2.7

      env: TOXENV=py27-cover

    - probcons

    - samtools

    - wise

    - t-coffee

    - ncbi-blast+

# We setup $HOME/bin and add it to the $PATH for extra binaries we're using.

#

  - curl -L -O https://anaconda.org/bioconda/genepop/4.5.1/download/linux-64/genepop-4.5.1-0.tar.bz2

  # This will create ./bin/Genepop and a harmless ./info/ folder.

  - tar -jxvf genepop-4.5.1-0.tar.bz2

  # Setup environment for t-coffee

  - mkdir -p $HOME/tcoffee_temp

  - export HOME_4_TCOFFEE=$HOME/tcoffee_temp

  # There are TravisCI provided versions of PyPy and PyPy3, but currently too old.

  # We therefore deactivate that, and download and unzip portable PyPy binaries.

  - |

  - tox -c .travis-tox.ini -e $TOXENV --notest

script:

  - travis_wait tox -c .travis-tox.ini -e $TOXENV

  - travis_wait 30 tox -c .travis-tox.ini -e $TOXENV

notifications:

  email: false

    # =======================

    # flake: E###, F###, W###

    # =======================

    # pycodestyle v2.3.1 default ignore is E121,E123,E126,E226,E24,E704,W503

    # flake8 v3.3.0 default ignore is      E121,E123,E126,E226,E24,E704,W503,W504

    #

    # pycodestyle v2.4.0 default ignore is E121,E123,E126,E226,E24,E704,W503,W504

    # flake8 v3.6.0 default ignore is      E121,E123,E126,E226,E24,E704,W503,W504

    # These are ignored by default:

    E122,E123,E126,W503,

    E122,E123,E126,W503,W504,

    # These are not ignored by default:

    # E127	continuation line over-indented for visual indent

    # E128	continuation line under-indented for visual indent

    # F401	module imported but unused

    # F841	local variable name is assigned to but never used

    # TODO: Fix some of these?

    E127,E128,E501,E731,F401,F841,

    E501,E731,F401,F841,

    # =====================================

    # pydocstyle: D1## - Missing Docstrings

    # =====================================

    # D211	No blank lines allowed before class docstring

    # We ignore D203 deliberately in favour of passing D211,

    D203,

    # ====================

    # flake8-bugbear: B###

    # ====================

    # B007	Loop control variable not used within the loop body.

    #           If this is intended, start the name with an underscore.

    B007,

    # ================================================

    # flake8-commas: C#### (in case installed locally)

    # ================================================