[med-svn] [python-cutadapt] branch master updated (a148fa4 -> ce0569f)

[Kevin Murray]

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daube-guest pushed a change to branch master
in repository python-cutadapt.

      from  a148fa4   upload upstream release 1.11
       new  89cb1e6   New upstream version 1.12
       new  0ba0917   Merge tag 'upstream/1.12'
       new  65b233e   bump changelog
       new  db0912d   Refresh patches, add patch to fix setup.py encoding issue
       new  1f867cd   Add myself to uploaders
       new  ce0569f   Close bug for new release in d/changelog

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 CHANGES.rst                                        |  11 ++
 PKG-INFO                                           |  45 ++++-
 README.rst                                         |   2 +-
 bin/_preamble.py                                   |  21 ---
 bin/cutadapt                                       |  10 --
 cutadapt.egg-info/PKG-INFO                         |  45 ++++-
 cutadapt.egg-info/SOURCES.txt                      |   8 +-
 cutadapt.egg-info/entry_points.txt                 |   3 +
 cutadapt.egg-info/requires.txt                     |   1 +
 cutadapt/_align.c                                  |  36 ++--
 cutadapt/_seqio.c                                  |   2 +-
 cutadapt/_seqio.pyx                                |   2 +-
 cutadapt/_version.py                               |   4 +-
 cutadapt/adapters.py                               |  12 +-
 cutadapt/filters.py                                |   2 +-
 cutadapt/modifiers.py                              |   9 +
 cutadapt/scripts/cutadapt.py                       | 115 ++++++-------
 cutadapt/seqio.py                                  |   4 +-
 cutadapt/xopen.py                                  | 182 ---------------------
 debian/changelog                                   |   6 +
 debian/control                                     |   3 +-
 .../0002-Fix-encoding-issue-in-setup.py.patch      |  23 +++
 debian/patches/cython_version.patch                |  15 +-
 debian/patches/series                              |   1 +
 doc/colorspace.rst                                 |  26 ++-
 doc/guide.rst                                      | 157 ++++++++++++------
 doc/recipes.rst                                    |  48 ++++--
 setup.py                                           |   7 +-
 tests/cut/shortened.fastq                          |  12 ++
 tests/cut/{small.fasta => small-no-trim.fasta}     |   4 +-
 tests/testmodifiers.py                             |  19 ++-
 tests/tests.py                                     |   8 +
 tests/testxopen.py                                 | 101 ------------
 33 files changed, 460 insertions(+), 484 deletions(-)
 delete mode 100644 bin/_preamble.py
 delete mode 100755 bin/cutadapt
 create mode 100644 cutadapt.egg-info/entry_points.txt
 create mode 100644 cutadapt.egg-info/requires.txt
 delete mode 100644 cutadapt/xopen.py
 create mode 100644 debian/patches/0002-Fix-encoding-issue-in-setup.py.patch
 create mode 100644 tests/cut/shortened.fastq
 copy tests/cut/{small.fasta => small-no-trim.fasta} (57%)
 delete mode 100644 tests/testxopen.py

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