[med-svn] [python-cutadapt] branch master updated (191316c -> 471f992)

[Andreas Tille]

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

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

      from  191316c   upload release 1.9.1
       new  c92ba44   More complete information
       new  1f69411   Provide a single user interface based on the Python3 version
       new  01a0b97   Provide a package cutadapt containing just the user interface
       new  250b0dc   Imported Upstream version 1.10
       new  614fb4d   Merge tag 'upstream/1.10'
       new  6277f85   New upstream version
       new  793d92f   We do not have the latest cython version currently but the version even in Jessie-Backports seems to work well
       new  30ca906   Only one single manpage
       new  ce85d0c   Install single executable
       new  7f22735   Remove README.Debian since we now have only one user interface
       new  652f8cb   Better hardening
       new  471f992   Upload to unstable

The 12 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                         |   22 +
 LICENSE                             |    2 +-
 PKG-INFO                            |    2 +-
 cutadapt/__init__.py                |    2 +-
 cutadapt/__main__.py                |   12 -
 cutadapt/_align.c                   | 4016 ++++++++---------------------------
 cutadapt/_align.pyx                 |    1 +
 cutadapt/_align.so                  |  Bin 532496 -> 0 bytes
 cutadapt/_qualtrim.c                |  743 ++++++-
 cutadapt/_qualtrim.pyx              |   36 +
 cutadapt/_qualtrim.so               |  Bin 92136 -> 0 bytes
 cutadapt/_seqio.c                   | 2320 +++++++-------------
 cutadapt/_seqio.pyx                 |   59 +-
 cutadapt/_seqio.so                  |  Bin 397664 -> 0 bytes
 cutadapt/adapters.py                |  264 ++-
 cutadapt/filters.py                 |    8 +-
 cutadapt/modifiers.py               |   63 +-
 cutadapt/qualtrim.py                |   31 +-
 cutadapt/report.py                  |   35 +-
 cutadapt/scripts/cutadapt.py        |  214 +-
 cutadapt/seqio.py                   |  413 ++--
 cutadapt/xopen.py                   |   10 +-
 debian/README.Debian                |    2 -
 debian/changelog                    |    9 +
 debian/control                      |   67 +-
 debian/cutadapt.1                   |  301 +++
 debian/cutadapt.man1                |  307 ---
 debian/cutadapt.manpages            |    1 +
 debian/cutadapt3.man1               |  307 ---
 debian/patches/cython_version.patch |   16 +
 debian/patches/series               |    1 +
 debian/python-cutadapt.manpages     |    1 -
 debian/python3-cutadapt.manpages    |    1 -
 debian/rules                        |    7 +-
 debian/upstream/metadata            |    3 +-
 doc/colorspace.rst                  |   23 +-
 doc/conf.py                         |    2 +-
 doc/guide.rst                       |   59 +-
 doc/ideas.rst                       |   14 +-
 doc/installation.rst                |   72 +-
 setup.py                            |   57 +-
 tests/cut/linked.fasta              |   10 +
 tests/cut/nextseq.fastq             |    8 +
 tests/cut/small.fasta               |    6 +
 tests/data/linked.fasta             |   10 +
 tests/data/nextseq.fastq            |    8 +
 tests/testadapters.py               |   43 +-
 tests/testpaired.py                 |   11 +-
 tests/testqualtrim.py               |   14 +
 tests/tests.py                      |   30 +-
 tests/testseqio.py                  |   53 +-
 tests/utils.py                      |    2 +-
 52 files changed, 3705 insertions(+), 5993 deletions(-)
 delete mode 100755 cutadapt/__main__.py
 delete mode 100755 cutadapt/_align.so
 delete mode 100755 cutadapt/_qualtrim.so
 delete mode 100755 cutadapt/_seqio.so
 delete mode 100644 debian/README.Debian
 create mode 100644 debian/cutadapt.1
 delete mode 100644 debian/cutadapt.man1
 create mode 100644 debian/cutadapt.manpages
 delete mode 100644 debian/cutadapt3.man1
 create mode 100644 debian/patches/cython_version.patch
 create mode 100644 debian/patches/series
 delete mode 100644 debian/python-cutadapt.manpages
 delete mode 100644 debian/python3-cutadapt.manpages
 create mode 100644 tests/cut/linked.fasta
 create mode 100644 tests/cut/nextseq.fastq
 create mode 100644 tests/cut/small.fasta
 create mode 100644 tests/data/linked.fasta
 create mode 100644 tests/data/nextseq.fastq
 create mode 100644 tests/testqualtrim.py

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