[med-svn] [khmer] branch experimental-2.1 updated (2e45ec4 -> 4f0fab4)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jun 23 13:36:19 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch experimental-2.1
in repository khmer.
from 2e45ec4 reflect removal of TODO as well
new a119d2c New upstream version 2.1.1+dfsg
new 6683f81 Merge tag 'upstream/2.1.1+dfsg' into experimental-2.1
new 4f0fab4 new upstream release
The 3 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:
.github/CONTRIBUTING.md | 2 -
.gitignore | 1 +
.mailmap | 7 +
.travis.yml | 7 +-
.ycm_extra_conf.py | 105 -
CHANGELOG.md | 18 +-
MANIFEST.in | 5 +-
Makefile | 75 +-
README.rst | 123 +-
author-skips.txt | 15 +
authors.csv | 68 +
data/16s+23s.fa | 800 -
data/16s.fa | 714 -
data/1m-bigpart.fa | 44872 --------
data/23s.fa | 86 -
data/MSB2-part.group1.fa | 100806 -----------------
data/MSB2-part.group10.fa | 101128 -----------------
data/MSB2-part.group31.fa | 103446 ------------------
data/high-sodd.fa | 384 -
data/mda-test.fa | 28 -
data/primers.fa | 4 -
debian/changelog | 4 +-
debian/control | 2 +-
debian/patches/amend-skip | 20 +-
debian/patches/disable_google_analytics | 2 +-
debian/patches/get_version | 6 +-
debian/patches/older-setuptools | 2 +-
debian/patches/series | 1 +
debian/patches/setup.py-py3 | 23 +
debian/patches/update-manifest | 6 +-
doc/conf.py | 18 +-
doc/contributors.rst | 37 +-
doc/dev/a-quick-guide-to-testing.rst | 42 +-
doc/dev/binary-file-formats.rst | 14 +-
doc/dev/codebase-guide.rst | 7 +-
doc/dev/crazy-ideas.rst | 47 -
doc/dev/details.rst | 42 -
doc/dev/development.rst | 33 +-
doc/dev/for-khmer-developers.rst | 33 +-
doc/dev/getting-started.rst | 379 +-
...and-review.rst => guidelines-continued-dev.rst} | 170 +-
doc/dev/index.rst | 16 +-
doc/dev/release.rst | 107 +-
doc/index.rst | 31 +-
doc/introduction.rst | 101 +-
doc/release-notes/release-1.2.md | 64 +-
doc/release-notes/release-1.2.rst | 25 +-
doc/release-notes/release-1.4.md | 10 +-
doc/release-notes/release-1.4.rst | 12 +-
doc/release-notes/release-2.0.md | 4 +-
doc/release-notes/release-2.0.rst | 4 +-
doc/release-notes/release-2.1.md | 47 +
doc/release-notes/release-2.1.rst | 78 +
doc/requirements.txt | 1 +
doc/user/api-examples.rst | 58 +-
doc/user/choosing-table-sizes.rst | 53 +-
doc/user/install.rst | 29 +-
doc/user/known-issues.rst | 23 +-
doc/whats-new-2.0.rst | 197 -
examples/c++-api/.gitignore | 4 +-
examples/c++-api/Makefile | 18 +-
examples/c++-api/bloom.cc | 38 +
examples/c++-api/consume.cc | 39 +
.../c++-api/{count-demo.cc => exact-counting.cc} | 23 +-
examples/c++-api/reads.fastq | 532 +
examples/python-api/bloom.py | 26 +
examples/python-api/consume.py | 20 +
examples/python-api/exact-counting.py | 39 +
examples/stamps/do.sh | 8 +-
ez_setup.py | 332 -
khmer/__init__.py | 13 +
khmer/_khmer.cc | 2 +-
khmer/_version.py | 118 +-
khmer/khmer_args.py | 38 +-
lib/assembler.cc | 64 +-
lib/assembler.hh | 16 +-
lib/hashtable.cc | 46 -
lib/hashtable.hh | 130 +-
lib/khmer.hh | 1 -
lib/kmer_filters.cc | 2 +-
lib/kmer_filters.hh | 2 +-
lib/magic | 1 -
lib/read_parsers.cc | 5 +-
lib/read_parsers.hh | 8 +-
lib/traversal.cc | 69 +-
lib/traversal.hh | 42 +-
papers/paper-v2.1.md | 121 +
sandbox/memusg | 46 -
scripts/abundance-dist-single.py | 18 +-
scripts/annotate-partitions.py | 2 +-
scripts/do-partition.py | 10 +-
scripts/extract-paired-reads.py | 4 +-
scripts/extract-partitions.py | 8 +-
scripts/filter-abund-single.py | 6 +-
scripts/filter-abund.py | 6 +-
scripts/filter-stoptags.py | 4 +-
scripts/load-into-counting.py | 2 +-
scripts/make-initial-stoptags.py | 4 +-
scripts/merge-partitions.py | 2 +-
scripts/normalize-by-median.py | 15 +-
scripts/partition-graph.py | 8 +-
scripts/readstats.py | 1 -
scripts/trim-low-abund.py | 73 +-
scripts/unique-kmers.py | 8 +-
setup.py | 42 +-
sort-authors-list.py | 22 +-
tests/khmer_tst_utils.py | 5 +-
tests/test-data/goodversion-k12.ht | Bin 16 -> 28 bytes
tests/test-data/goodversion-k12.ht.gz | Bin 38 -> 56 bytes
tests/test-data/goodversion-k32.stoptags | Bin 1174 -> 1354 bytes
tests/test-data/valid-read-testing.fq | 36 +
tests/test_assembly.py | 20 +
tests/test_counttable.py | 19 +
tests/test_nibblestorage.py | 14 +-
tests/test_nodegraph.py | 29 +-
tests/test_read_parsers.py | 22 +-
tests/test_sandbox_scripts.py | 32 +-
tests/test_script_arguments.py | 32 +-
tests/test_scripts.py | 70 +-
tests/test_sequence_validation.py | 335 +
tests/test_tabletype.py | 4 +-
third-party/bzip2/.gitignore | 2 -
third-party/bzip2/CHANGES | 327 -
third-party/bzip2/LICENSE | 42 -
third-party/bzip2/Makefile | 217 -
third-party/bzip2/Makefile-libbz2_so | 59 -
third-party/bzip2/README | 215 -
third-party/bzip2/README.COMPILATION.PROBLEMS | 58 -
third-party/bzip2/README.XML.STUFF | 45 -
third-party/bzip2/blocksort.c | 1094 -
third-party/bzip2/bz-common.xsl | 39 -
third-party/bzip2/bz-fo.xsl | 276 -
third-party/bzip2/bz-html.xsl | 20 -
third-party/bzip2/bzdiff | 76 -
third-party/bzip2/bzdiff.1 | 47 -
third-party/bzip2/bzgrep | 75 -
third-party/bzip2/bzgrep.1 | 56 -
third-party/bzip2/bzip.css | 74 -
third-party/bzip2/bzip2.1 | 454 -
third-party/bzip2/bzip2.1.preformatted | 399 -
third-party/bzip2/bzip2.c | 2034 -
third-party/bzip2/bzip2.txt | 391 -
third-party/bzip2/bzip2recover.c | 514 -
third-party/bzip2/bzlib.c | 1572 -
third-party/bzip2/bzlib.h | 282 -
third-party/bzip2/bzlib_private.h | 509 -
third-party/bzip2/bzmore | 61 -
third-party/bzip2/bzmore.1 | 152 -
third-party/bzip2/compress.c | 672 -
third-party/bzip2/crctable.c | 104 -
third-party/bzip2/decompress.c | 646 -
third-party/bzip2/dlltest.c | 175 -
third-party/bzip2/dlltest.dsp | 93 -
third-party/bzip2/entities.xml | 9 -
third-party/bzip2/format.pl | 68 -
third-party/bzip2/huffman.c | 205 -
third-party/bzip2/libbz2.def | 27 -
third-party/bzip2/libbz2.dsp | 130 -
third-party/bzip2/makefile.msc | 63 -
third-party/bzip2/manual.html | 2540 -
third-party/bzip2/manual.pdf | Bin 256905 -> 0 bytes
third-party/bzip2/manual.ps | 72843 ------------
third-party/bzip2/manual.xml | 2964 -
third-party/bzip2/mk251.c | 31 -
third-party/bzip2/randtable.c | 84 -
third-party/bzip2/sample1.bz2 | Bin 32348 -> 0 bytes
third-party/bzip2/sample1.ref | Bin 98696 -> 0 bytes
third-party/bzip2/sample2.bz2 | Bin 73732 -> 0 bytes
third-party/bzip2/sample2.ref | Bin 212340 -> 0 bytes
third-party/bzip2/sample3.bz2 | Bin 235 -> 0 bytes
third-party/bzip2/sample3.ref | 30007 -----
third-party/bzip2/spewG.c | 54 -
third-party/bzip2/unzcrash.c | 141 -
third-party/bzip2/words0 | 9 -
third-party/bzip2/words1 | 4 -
third-party/bzip2/words2 | 5 -
third-party/bzip2/words3 | 30 -
third-party/bzip2/xmlproc.sh | 114 -
third-party/zlib/.gitignore | 5 -
third-party/zlib/CMakeLists.txt | 249 -
third-party/zlib/ChangeLog | 1472 -
third-party/zlib/FAQ | 368 -
third-party/zlib/INDEX | 68 -
third-party/zlib/Makefile.in | 288 -
third-party/zlib/Makefile.pic | 3 -
third-party/zlib/README | 115 -
third-party/zlib/adler32.c | 179 -
third-party/zlib/compress.c | 80 -
third-party/zlib/configure | 831 -
third-party/zlib/crc32.c | 425 -
third-party/zlib/crc32.h | 441 -
third-party/zlib/deflate.c | 1967 -
third-party/zlib/deflate.h | 346 -
third-party/zlib/doc/algorithm.txt | 209 -
third-party/zlib/doc/rfc1950.txt | 619 -
third-party/zlib/doc/rfc1951.txt | 955 -
third-party/zlib/doc/rfc1952.txt | 675 -
third-party/zlib/doc/txtvsbin.txt | 107 -
third-party/zlib/gzclose.c | 25 -
third-party/zlib/gzguts.h | 209 -
third-party/zlib/gzlib.c | 634 -
third-party/zlib/gzread.c | 594 -
third-party/zlib/gzwrite.c | 577 -
third-party/zlib/infback.c | 640 -
third-party/zlib/inffast.c | 340 -
third-party/zlib/inffast.h | 11 -
third-party/zlib/inffixed.h | 94 -
third-party/zlib/inflate.c | 1512 -
third-party/zlib/inflate.h | 122 -
third-party/zlib/inftrees.c | 306 -
third-party/zlib/inftrees.h | 62 -
third-party/zlib/make_vms.com | 867 -
third-party/zlib/test/example.c | 601 -
third-party/zlib/test/infcover.c | 671 -
third-party/zlib/test/minigzip.c | 651 -
third-party/zlib/treebuild.xml | 116 -
third-party/zlib/trees.c | 1226 -
third-party/zlib/trees.h | 128 -
third-party/zlib/uncompr.c | 59 -
third-party/zlib/win32/DLL_FAQ.txt | 397 -
third-party/zlib/win32/Makefile.bor | 110 -
third-party/zlib/win32/Makefile.gcc | 182 -
third-party/zlib/win32/Makefile.msc | 163 -
third-party/zlib/win32/README-WIN32.txt | 103 -
third-party/zlib/win32/VisualC.txt | 3 -
third-party/zlib/win32/zlib.def | 86 -
third-party/zlib/win32/zlib1.rc | 40 -
third-party/zlib/zconf.h.cmakein | 513 -
third-party/zlib/zconf.h.in | 511 -
third-party/zlib/zlib.3 | 151 -
third-party/zlib/zlib.3.pdf | Bin 8734 -> 0 bytes
third-party/zlib/zlib.h | 1768 -
third-party/zlib/zlib.map | 83 -
third-party/zlib/zlib.pc.cmakein | 13 -
third-party/zlib/zlib.pc.in | 13 -
third-party/zlib/zlib2ansi | 152 -
third-party/zlib/zutil.c | 324 -
third-party/zlib/zutil.h | 253 -
versioneer.py | 525 +-
239 files changed, 3134 insertions(+), 498309 deletions(-)
delete mode 100644 .ycm_extra_conf.py
create mode 100644 author-skips.txt
create mode 100644 authors.csv
delete mode 100644 data/16s+23s.fa
delete mode 100644 data/16s.fa
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delete mode 100644 data/MSB2-part.group31.fa
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create mode 100644 debian/patches/setup.py-py3
delete mode 100644 doc/dev/crazy-ideas.rst
delete mode 100644 doc/dev/details.rst
rename doc/dev/{coding-guidelines-and-review.rst => guidelines-continued-dev.rst} (52%)
create mode 100644 doc/release-notes/release-2.1.md
create mode 100644 doc/release-notes/release-2.1.rst
delete mode 100644 doc/whats-new-2.0.rst
create mode 100644 examples/c++-api/bloom.cc
create mode 100644 examples/c++-api/consume.cc
rename examples/c++-api/{count-demo.cc => exact-counting.cc} (55%)
create mode 100644 examples/c++-api/reads.fastq
create mode 100755 examples/python-api/bloom.py
create mode 100755 examples/python-api/consume.py
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