[med-svn] [python-cutadapt] branch upstream updated (7782a43 -> 89cb1e6)

[Kevin Murray]

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

      from  7782a43   Imported Upstream version 1.11
       new  89cb1e6   New upstream version 1.12

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


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 -------------------------
 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 --------------
 28 files changed, 418 insertions(+), 478 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 tests/cut/shortened.fastq
 copy tests/cut/{small.fasta => small-no-trim.fasta} (57%)
 delete mode 100644 tests/testxopen.py

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