[med-svn] [python-cutadapt] branch master updated (e2c0774 -> 14dfa8a)
Andreas Tille
tille at debian.org
Sat Feb 10 12:31:42 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository python-cutadapt.
from e2c0774 upload new upstream 1.13
new 500335b New upstream version 1.15
new 5400201 Update upstream source from tag 'upstream/1.15'
new 4e072b1 New upstream release
new e487501 cme fix dpkg-control
new 0c6665c debhelper 11
new a4e9a3d hardening=+all
new a032c8c Update quilt patches
new 14dfa8a Versioned Build-Depends: python-xopen (>= 0.3.2)
The 8 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 | 35 +-
MANIFEST.in | 14 +-
PKG-INFO | 2 +-
cutadapt.egg-info/entry_points.txt | 3 -
cutadapt.egg-info/requires.txt | 1 -
cutadapt/scripts/__init__.py | 0
debian/changelog | 10 +
debian/compat | 2 +-
debian/control | 9 +-
.../0002-Fix-encoding-issue-in-setup.py.patch | 23 -
debian/patches/0003_fixtest.patch | 37 -
debian/patches/cython_version.patch | 8 +-
debian/patches/series | 2 -
debian/rules | 5 +-
doc/conf.py | 6 +-
doc/develop.rst | 124 +
doc/guide.rst | 289 +-
doc/ideas.rst | 16 +-
doc/index.rst | 1 +
doc/installation.rst | 69 +-
doc/recipes.rst | 86 +
setup.cfg | 4 +-
setup.py | 45 +-
.../cutadapt.egg-info}/PKG-INFO | 2 +-
.../cutadapt.egg-info}/SOURCES.txt | 81 +-
.../cutadapt.egg-info}/dependency_links.txt | 0
src/cutadapt.egg-info/entry_points.txt | 3 +
src/cutadapt.egg-info/requires.txt | 1 +
.../cutadapt.egg-info}/top_level.txt | 0
{cutadapt => src/cutadapt}/__init__.py | 0
.../cutadapt.py => src/cutadapt/__main__.py | 674 +--
{cutadapt => src/cutadapt}/_align.c | 1580 ++---
{cutadapt => src/cutadapt}/_align.pyx | 5 +
{cutadapt => src/cutadapt}/_qualtrim.c | 266 +-
{cutadapt => src/cutadapt}/_qualtrim.pyx | 0
{cutadapt => src/cutadapt}/_seqio.c | 6265 ++++++++++++++------
{cutadapt => src/cutadapt}/_seqio.pyx | 98 +
{cutadapt => src/cutadapt}/_version.py | 4 +-
{cutadapt => src/cutadapt}/adapters.py | 165 +-
{cutadapt => src/cutadapt}/align.py | 0
{cutadapt => src/cutadapt}/colorspace.py | 0
{cutadapt => src/cutadapt}/compat.py | 0
{cutadapt => src/cutadapt}/filters.py | 183 +-
{cutadapt => src/cutadapt}/modifiers.py | 61 +-
src/cutadapt/pipeline.py | 651 ++
{cutadapt => src/cutadapt}/qualtrim.py | 0
{cutadapt => src/cutadapt}/report.py | 254 +-
{cutadapt => src/cutadapt}/seqio.py | 226 +-
tests/cut/demultiplexed.first.1.fastq | 4 +
tests/cut/demultiplexed.first.2.fastq | 4 +
tests/cut/demultiplexed.second.1.fastq | 4 +
...-short.2.fastq => demultiplexed.second.2.fastq} | 0
...d-m27.1.fastq => demultiplexed.unknown.1.fastq} | 8 -
...immed.2.fastq => demultiplexed.unknown.2.fastq} | 4 +
...d-not-anchored.fasta => linked-discard-g.fasta} | 6 -
tests/cut/linked-discard.fasta | 6 +
tests/cut/linked-not-anchored.fasta | 4 +-
tests/data/block1.fastq.bz2 | Bin 87 -> 0 bytes
tests/data/block2.fastq.bz2 | Bin 206 -> 0 bytes
tests/{testadapters.py => test_adapters.py} | 76 +-
tests/{testalign.py => test_align.py} | 0
tests/{testcolorspace.py => test_colorspace.py} | 4 +-
tests/{tests.py => test_commandline.py} | 52 +-
tests/{testfilters.py => test_filters.py} | 9 +-
tests/{testmodifiers.py => test_modifiers.py} | 0
tests/{testpaired.py => test_paired.py} | 257 +-
tests/{testqualtrim.py => test_qualtrim.py} | 1 +
tests/{testseqio.py => test_seqio.py} | 81 +-
tests/test_trim.py | 57 +
tests/testtrim.py | 28 -
tests/utils.py | 28 +-
71 files changed, 7699 insertions(+), 4244 deletions(-)
delete mode 100644 cutadapt.egg-info/entry_points.txt
delete mode 100644 cutadapt.egg-info/requires.txt
delete mode 100644 cutadapt/scripts/__init__.py
delete mode 100644 debian/patches/0002-Fix-encoding-issue-in-setup.py.patch
delete mode 100644 debian/patches/0003_fixtest.patch
create mode 100644 doc/develop.rst
rename {cutadapt.egg-info => src/cutadapt.egg-info}/PKG-INFO (99%)
rename {cutadapt.egg-info => src/cutadapt.egg-info}/SOURCES.txt (78%)
rename {cutadapt.egg-info => src/cutadapt.egg-info}/dependency_links.txt (100%)
create mode 100644 src/cutadapt.egg-info/entry_points.txt
create mode 100644 src/cutadapt.egg-info/requires.txt
rename {cutadapt.egg-info => src/cutadapt.egg-info}/top_level.txt (100%)
rename {cutadapt => src/cutadapt}/__init__.py (100%)
rename cutadapt/scripts/cutadapt.py => src/cutadapt/__main__.py (63%)
rename {cutadapt => src/cutadapt}/_align.c (88%)
rename {cutadapt => src/cutadapt}/_align.pyx (99%)
rename {cutadapt => src/cutadapt}/_qualtrim.c (94%)
rename {cutadapt => src/cutadapt}/_qualtrim.pyx (100%)
rename {cutadapt => src/cutadapt}/_seqio.c (59%)
rename {cutadapt => src/cutadapt}/_seqio.pyx (64%)
rename {cutadapt => src/cutadapt}/_version.py (82%)
rename {cutadapt => src/cutadapt}/adapters.py (83%)
rename {cutadapt => src/cutadapt}/align.py (100%)
rename {cutadapt => src/cutadapt}/colorspace.py (100%)
rename {cutadapt => src/cutadapt}/compat.py (100%)
rename {cutadapt => src/cutadapt}/filters.py (57%)
rename {cutadapt => src/cutadapt}/modifiers.py (78%)
create mode 100644 src/cutadapt/pipeline.py
rename {cutadapt => src/cutadapt}/qualtrim.py (100%)
rename {cutadapt => src/cutadapt}/report.py (50%)
rename {cutadapt => src/cutadapt}/seqio.py (80%)
create mode 100644 tests/cut/demultiplexed.first.1.fastq
create mode 100644 tests/cut/demultiplexed.first.2.fastq
create mode 100644 tests/cut/demultiplexed.second.1.fastq
copy tests/cut/{paired-too-short.2.fastq => demultiplexed.second.2.fastq} (100%)
copy tests/cut/{paired-m27.1.fastq => demultiplexed.unknown.1.fastq} (52%)
copy tests/cut/{paired-untrimmed.2.fastq => demultiplexed.unknown.2.fastq} (62%)
copy tests/cut/{linked-not-anchored.fasta => linked-discard-g.fasta} (57%)
create mode 100644 tests/cut/linked-discard.fasta
delete mode 100644 tests/data/block1.fastq.bz2
delete mode 100644 tests/data/block2.fastq.bz2
rename tests/{testadapters.py => test_adapters.py} (59%)
rename tests/{testalign.py => test_align.py} (100%)
rename tests/{testcolorspace.py => test_colorspace.py} (98%)
rename tests/{tests.py => test_commandline.py} (91%)
rename tests/{testfilters.py => test_filters.py} (80%)
rename tests/{testmodifiers.py => test_modifiers.py} (100%)
rename tests/{testpaired.py => test_paired.py} (56%)
rename tests/{testqualtrim.py => test_qualtrim.py} (99%)
rename tests/{testseqio.py => test_seqio.py} (75%)
create mode 100644 tests/test_trim.py
delete mode 100644 tests/testtrim.py
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