[med-svn] [python-ruffus] 05/12: Merge tag 'upstream/2.5+dfsg'

Andreas Tille tille at debian.org
Thu Feb 5 21:24:29 UTC 2015


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-ruffus.

commit 47a06c539de84711490acd20c079edeba9deaf1b
Merge: 9a0cf80 f6c05d5
Author: Andreas Tille <tille at debian.org>
Date:   Thu Feb 5 19:18:12 2015 +0100

    Merge tag 'upstream/2.5+dfsg'
    
    Upstream version 2.5+dfsg

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