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Oct 18, 2013

  1. Peter Cock

    Use unittest methods instead of assert statement

    authored October 18, 2013

Sep 06, 2013

  1. Peter Cock

    Replace commands.getoutput (or subprocess.getoutput) via Bio._py3k

    This is a small step towards targetting both Python 2 and 3 without
    needing to run 2to3.
    authored September 06, 2013

Aug 26, 2013

  1. Eric Talevich

    test_Prank_tool: find ".best.nex" output file from the latest Prank

    In yet another twist, the latest version of Prank names its output files
    "*.best.nex", "*.best.fas", etc. instead of the established "*.2.nex" which the
    unittest expected. The unittest now checks for both extensions.
    authored August 26, 2013
  2. Eric Talevich

    test_Prank_tool: handle Prank's new stdout logging style

    Old Prank output:
    
    PRANK: converting 'Quality/example.fasta' to 'temp with space.fas'
    
    New Prank output:
    
    -----------------
     PRANK v.130820:
    -----------------
    
    Input for the analysis
     - converting 'Quality/example.fasta' to 'temp with space.fas'
    authored August 26, 2013

Aug 15, 2013

  1. Eric Talevich

    test_Prank_tool: removed uses of -noxml and -notree options

    These options no longer exist in Prank. Instead, "no" is now the default, and
    -showxml and -showtree are available options.
    authored August 15, 2013

May 28, 2013

  1. Peter Cock

    Further test updates due to escaping change

    authored May 28, 2013

Mar 29, 2013

  1. Christian Brueffer

    Prank: PEP8 whitespace cleanup.

    authored December 19, 2012 peterjc committed March 29, 2013

Dec 17, 2012

  1. Christian Brueffer

    Remove unused imports.

    Imports in tests that hint at untested functionality were left in place.
    authored December 17, 2012 peterjc committed December 17, 2012

Dec 06, 2012

  1. Christian Brueffer

    Fix spacing around inline comments (E261, E262).

    authored December 06, 2012
  2. Christian Brueffer

    Add blank lines where needed (PEP8 E302).

    authored December 06, 2012

Dec 05, 2012

  1. Christian Brueffer

    Zap redundant backslashes between brackets (PEP8 E502).

    authored December 05, 2012 peterjc committed December 05, 2012
  2. Christian Brueffer

    Avoid multiple statements on one line (PEP8 E701).

    authored December 05, 2012 peterjc committed December 05, 2012

Dec 04, 2012

  1. Christian Brueffer

    Trim EOL whitespace (PEP8 W291, W293), batch 3.

    authored December 04, 2012

Dec 26, 2010

  1. Peter Cock

    Use the application wrapper rather than subprocess

    authored December 26, 2010
  2. Peter Cock

    Close these handles (avoids ResourceWarning on Python 3.2)

    authored December 26, 2010

Aug 03, 2010

  1. Peter Cock

    Update test_Prank_tool.py for recent PRANK v100802 release (see also …

    …Bug 3119)
    authored August 03, 2010

Jul 26, 2010

  1. Peter Cock

    Move os.environ['LANG'] = 'C' into just those unit tests which call e…

    …xternal tools. Having it in run_tests.py was changing the default encoding causing problems on Python 3 with special characters in plain text files
    authored July 26, 2010
  2. Peter Cock

    Make the application wrappers executable as discussed on the dev mail…

    …ing list (cherry-picked from my app-exec3 branch)
    authored July 26, 2010

Jul 19, 2010

  1. Peter Cock

    Hack for Bug 3119, Bio.Nexus can't parse NEXUS output from Prank v100…

    …701 (1 July 2010)
    authored July 19, 2010
  2. Peter Cock

    Problem with test_Prank_tool.py and Prank v.100701 appears to be a bu…

    …g in Prank's output
    authored July 19, 2010
  3. Peter Cock

    prank v.100701 has dropped a lot of output formats (GenBank, EMBL, NB…

    …RF/PIR) so don't use them in our unit test
    authored July 19, 2010

Jul 09, 2010

  1. Peter Cock

    Use universal_readlines=True with subprocess.Popen, important for Pyt…

    …hon 3 to ensure we get the child handles in text mode
    authored July 09, 2010

Jul 05, 2010

  1. Peter Cock

    Use assertTrue in unit tests (added in Python 2.4) since the earlier …

    …assert_ method is deprecated in Python 2.7
    authored July 05, 2010

Dec 06, 2009

  1. Peter Cock

    Don't use the deprecated generic_run function in unit tests (Patch fr…

    …om Cymon Cox via Bug 2961)
    authored December 06, 2009

Nov 11, 2009

  1. Peter Cock

    No code changes. Removing white space before ':' character to match P…

    …EP8. Added a few missing license statements too.
    authored November 11, 2009

Aug 06, 2009

  1. Peter Cock

    Use PRANK conversions to test AlignIO. Also test using PRANK output f…

    …ilenames with spaces
    authored August 06, 2009

Jul 18, 2009

  1. Peter Cock

    Renaming variable: Bio.Application.generic_run does not return stdin

    authored July 18, 2009

Jun 22, 2009

  1. Peter Cock

    Removed trailing space from command line wrapper output

    authored June 22, 2009

May 08, 2009

  1. Peter Cock

    Updating Prank unit test after fixing the realbranches parameter

    authored May 08, 2009

May 04, 2009

  1. Peter Cock

    Explicitly support switch parameters in application wrappers (see Bug…

    … 2822)
    authored May 04, 2009
  2. Peter Cock

    Add properties and keyword argument support to the Bio.Application ba…

    …sed command line wrappers (Bug 2822)
    authored May 04, 2009

Apr 29, 2009

  1. Peter Cock

    Patch from Cymon to use a smaller input file (runtime now 2s instead …

    …of 16s) and check we can parse the NEXUS output (Bug 2815)
    authored April 29, 2009

Apr 28, 2009

  1. Peter Cock

    MUSCLE and PRANK tests work on Windows, try a few sensible install lo…

    …cations then the full path to try to locate the tools.
    authored April 28, 2009
  2. Peter Cock

    Merging fix from Cymon

    authored April 28, 2009
  3. Peter Cock

    PRANK command line wrapper and unit test from Cymon Cox (Bug 2815)

    authored April 28, 2009
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