[med-svn] [khmer] branch master updated (370587c -> a5cdb20)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Jun 25 16:46:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from 370587c better cleanup
new cb1975f New upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12
new a8ded0e update changelog
new f39ef7b refresh patches
new b246f2e add new dependencies
new 85afb20 fix fatal pytest.skip usage
new 66dc7df fix patch
new bc6d873 reflect move of CONTRIBUTING.md
new ef6ee8d reflect removal of TODO as well
new f51fd1f New upstream version 2.1.1+dfsg
new a5cdb20 new upstream release
The 10 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:
.dictionary | 155 +
doc/dev/details.rst => .github/CONTRIBUTING.md | 24 +-
.github/PULL_REQUEST_TEMPLATE.md | 16 +
.gitignore | 5 +-
.mailmap | 10 +-
.travis.yml | 91 +
CHANGELOG.md | 79 +
CITATION | 12 +-
CONTRIBUTING.md | 42 -
IDEAS | 18 -
MANIFEST.in | 5 +-
Makefile | 223 +-
README.rst | 117 +-
TODO | 80 -
author-skips.txt | 15 +
authors.csv | 68 +
ci_scripts/install.sh | 31 +
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 | 17 +
debian/clean | 4 +-
debian/control | 7 +-
debian/copyright | 2 +-
debian/docs | 2 -
debian/patches/amend-skip | 24 +
debian/patches/cpython-bug-empty-exceptions | 8 +-
debian/patches/disable_google_analytics | 2 +-
debian/patches/get_version | 27 +-
debian/patches/local-libs | 2 +-
debian/patches/older-setuptools | 6 +-
debian/patches/pkg-config | 12 -
debian/patches/series | 6 +-
debian/patches/setup.py-py3 | 23 +
debian/patches/silence-mt-bug | 6 +-
debian/patches/update-manifest | 11 +
debian/rules | 9 +-
debian/tests/control | 2 +-
doc/conf.py | 31 +-
doc/contributors.rst | 51 +-
doc/dev/a-quick-guide-to-testing.rst | 50 +-
doc/dev/binary-file-formats.rst | 14 +-
doc/dev/codebase-guide.rst | 23 +-
doc/dev/coding-guidelines-and-review.rst | 189 -
doc/dev/development.rst | 95 +-
doc/dev/for-khmer-developers.rst | 33 +-
doc/dev/getting-started.rst | 399 +-
doc/dev/guidelines-continued-dev.rst | 269 +
doc/dev/index.rst | 16 +-
doc/dev/python-api.rst | 152 +
doc/dev/release.rst | 127 +-
doc/dev/scripts-and-sandbox.rst | 47 +-
doc/index.rst | 53 +-
doc/introduction.rst | 115 +-
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 | 5 +-
doc/roadmap.rst | 16 +-
doc/{dev/crazy-ideas.rst => user/api-examples.rst} | 31 +-
doc/user/blog-posts.rst | 22 +-
doc/user/choosing-table-sizes.rst | 53 +-
doc/user/guide.rst | 16 +-
doc/user/index.rst | 16 +-
doc/user/install.rst | 43 +-
doc/user/known-issues.rst | 23 +-
doc/whats-new-2.0.rst | 197 -
examples/README.txt | 5 -
examples/c++-api/.gitignore | 3 +
examples/c++-api/Makefile | 20 +
examples/c++-api/bloom.cc | 38 +
examples/c++-api/consume.cc | 39 +
examples/c++-api/exact-counting.cc | 40 +
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 +-
khmer/__init__.py | 172 +-
khmer/_cpy_counttable.hh | 128 +
khmer/_cpy_hashgraph.hh | 1587 +
khmer/_cpy_nodetable.hh | 131 +
khmer/_cpy_smallcountgraph.hh | 181 +
khmer/_cpy_smallcounttable.hh | 127 +
khmer/_khmer.cc | 6100 +-
khmer/_version.py | 488 +-
khmer/kfile.py | 38 +-
khmer/khmer_args.py | 368 +-
khmer/khmer_logger.py | 13 +-
khmer/thread_utils.py | 68 +-
khmer/{khmer_logger.py => trimming.py} | 66 +-
khmer/utils.py | 115 +-
ChangeLog => legacy/ChangeLog | 662 +-
jenkins-build.sh => legacy/jenkins-build.sh | 12 +-
lib/.gitignore | 1 +
lib/Makefile | 18 +-
lib/{test-compile.cc => alphabets.cc} | 21 +-
lib/{.check_openmp.cc => alphabets.hh} | 23 +-
lib/assembler.cc | 533 +
lib/assembler.hh | 177 +
lib/counting.cc | 1041 -
lib/counting.hh | 348 -
lib/get_version.py | 52 -
lib/hashbits.cc | 215 -
lib/hashbits.hh | 215 -
lib/{hashtable.cc => hashgraph.cc} | 760 +-
lib/hashgraph.hh | 298 +
lib/hashtable.cc | 1168 +-
lib/hashtable.hh | 490 +-
lib/hllcounter.cc | 39 +-
lib/hllcounter.hh | 33 +-
lib/khmer.hh | 22 +-
lib/kmer_filters.cc | 159 +
lib/{test-Colors.cc => kmer_filters.hh} | 42 +-
lib/kmer_hash.cc | 47 +-
lib/kmer_hash.hh | 98 +-
lib/labelhash.cc | 198 +-
lib/labelhash.hh | 110 +-
lib/magic | 61 +-
lib/oxli.pc.in | 4 +-
lib/read_aligner.cc | 24 +-
lib/read_aligner.hh | 8 +-
lib/read_parsers.cc | 407 +-
lib/read_parsers.hh | 189 +-
lib/storage.cc | 916 +
lib/storage.hh | 651 +
lib/subset.cc | 339 +-
lib/subset.hh | 31 +-
lib/test-Colors.cc | 2 +-
lib/test-compile.cc | 4 +-
lib/traversal.cc | 325 +-
lib/traversal.hh | 253 +-
oxli/__init__.py | 15 +-
oxli/build_graph.py | 14 +-
oxli/functions.py | 21 +-
oxli/partition.py | 49 +
papers/paper-v2.1.md | 121 +
pylintrc | 384 +
pytest.ini | 4 +
sandbox/Makefile.read_aligner_training | 26 +-
sandbox/README.rst | 16 +-
sandbox/abundance-hist-by-position.py | 70 -
sandbox/assemble-and-track.py | 139 +
sandbox/assemble-on-the-go.py | 118 +
sandbox/assembly-diff.py | 4 +-
sandbox/assemstats3.py | 3 +-
sandbox/bloom-count.py | 3 +
sandbox/collect-reads.py | 3 +-
sandbox/collect-variants.py | 3 +-
sandbox/count-kmers-single.py | 5 +-
sandbox/count-kmers.py | 3 +-
sandbox/extract-compact-dbg.py | 230 +
sandbox/extract-unassembled-reads-2.py | 72 +
sandbox/extract-unassembled-reads.py | 86 +
sandbox/fasta-to-abundance-hist.py | 57 -
sandbox/find-high-abund-kmers.py | 107 -
sandbox/graph-size.py | 2 +-
sandbox/hi-lo-abundance-by-position.py | 65 -
sandbox/link-compact-dbg.py | 198 +
sandbox/optimal_args_hashbits.py | 5 +-
sandbox/readaligner_pairhmm_train.py | 14 +-
sandbox/reassemble-contigs.py | 51 +
sandbox/saturate-by-median.py | 3 +-
sandbox/stoptag-abundance-hist.py | 2 +
sandbox/streaming-assembly-simple.py | 145 +
sandbox/sweep-out-reads-with-contigs.py | 2 +-
sandbox/sweep-reads2.py | 63 +-
sandbox/sweep-reads3.py | 5 +-
scripts/abundance-dist-single.py | 83 +-
scripts/abundance-dist.py | 60 +-
scripts/annotate-partitions.py | 13 +-
scripts/count-median.py | 16 +-
scripts/do-partition.py | 54 +-
scripts/extract-long-sequences.py | 11 +-
scripts/extract-paired-reads.py | 32 +-
scripts/extract-partitions.py | 308 +-
scripts/fastq-to-fasta.py | 20 +-
scripts/filter-abund-single.py | 103 +-
scripts/filter-abund.py | 100 +-
scripts/filter-stoptags.py | 19 +-
scripts/find-knots.py | 13 +-
scripts/interleave-reads.py | 46 +-
scripts/load-graph.py | 6 +-
scripts/load-into-counting.py | 63 +-
scripts/make-initial-stoptags.py | 14 +-
scripts/merge-partitions.py | 15 +-
scripts/normalize-by-median.py | 65 +-
scripts/partition-graph.py | 52 +-
scripts/readstats.py | 26 +-
scripts/sample-reads-randomly.py | 38 +-
scripts/split-paired-reads.py | 36 +-
scripts/trim-low-abund.py | 544 +-
scripts/unique-kmers.py | 35 +-
setup.cfg | 24 +-
setup.py | 88 +-
sort-authors-list.py | 22 +-
tests/__init__.py | 1 +
tests/khmer_tst_utils.py | 109 +-
tests/test-data/README.rst | 10 +
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
...ed-mixed.fa.pe => paired-mixed-witherror.fa.pe} | 2 +-
tests/test-data/{paired.fq => paired.malformat.fq} | 6 +-
.../{paired.fq.1 => paired.malformat.fq.2} | 6 +-
tests/test-data/simple-genome-reads.fa | 2000 +
tests/test-data/simple-genome.fa | 2 +
tests/test-data/single-read.fa | 2 +
tests/test-data/unclean-reads.fastq | 8 +
tests/test-data/valid-read-testing.fq | 36 +
tests/test_assembly.py | 906 +
tests/test_countgraph.py | 357 +-
tests/test_counting_single.py | 60 +-
tests/{test_filter.py => test_counttable.py} | 85 +-
.../test_cpython_hierarchy.py | 74 +-
tests/test_filter_abund.py | 432 +
tests/test_functions.py | 280 +-
tests/test_graph.py | 32 +-
tests/test_hashset.py | 169 +
tests/test_hll.py | 73 +-
tests/test_labelhash.py | 78 +-
tests/test_lump.py | 31 +-
tests/test_nibblestorage.py | 131 +
tests/test_nodegraph.py | 489 +-
tests/test_normalize_by_median.py | 254 +-
tests/test_oxli_functions.py | 9 +-
tests/test_read_aligner.py | 127 +-
tests/test_read_handling.py | 789 +
tests/test_read_parsers.py | 156 +-
tests/test_sandbox_scripts.py | 128 +-
tests/test_script_arguments.py | 265 +-
tests/test_script_output.py | 184 +
tests/test_scripts.py | 1653 +-
tests/test_sequence_validation.py | 335 +
tests/test_streaming_io.py | 92 +-
tests/test_subset_graph.py | 143 +-
tests/test_tabletype.py | 448 +
tests/test_threaded_sequence_processor.py | 47 +-
tests/test_version.py | 11 +-
third-party/seqan/ChangeLog | 5 +
.../core/include/seqan/basic/debug_test_system.h | 2 +-
versioneer.py | 1905 +-
254 files changed, 25965 insertions(+), 366088 deletions(-)
create mode 100644 .dictionary
rename doc/dev/details.rst => .github/CONTRIBUTING.md (86%)
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
create mode 100644 .travis.yml
create mode 100644 CHANGELOG.md
delete mode 100644 CONTRIBUTING.md
delete mode 100644 IDEAS
delete mode 100644 TODO
create mode 100644 author-skips.txt
create mode 100644 authors.csv
create mode 100644 ci_scripts/install.sh
delete mode 100644 data/16s+23s.fa
delete mode 100644 data/16s.fa
delete mode 100644 data/1m-bigpart.fa
delete mode 100644 data/23s.fa
delete mode 100644 data/MSB2-part.group1.fa
delete mode 100644 data/MSB2-part.group10.fa
delete mode 100644 data/MSB2-part.group31.fa
delete mode 100644 data/high-sodd.fa
delete mode 100644 data/mda-test.fa
delete mode 100644 data/primers.fa
create mode 100644 debian/patches/amend-skip
delete mode 100644 debian/patches/pkg-config
create mode 100644 debian/patches/setup.py-py3
create mode 100644 debian/patches/update-manifest
delete mode 100644 doc/dev/coding-guidelines-and-review.rst
create mode 100644 doc/dev/guidelines-continued-dev.rst
create mode 100644 doc/dev/python-api.rst
create mode 100644 doc/release-notes/release-2.1.md
create mode 100644 doc/release-notes/release-2.1.rst
rename doc/{dev/crazy-ideas.rst => user/api-examples.rst} (63%)
delete mode 100644 doc/whats-new-2.0.rst
delete mode 100644 examples/README.txt
create mode 100644 examples/c++-api/.gitignore
create mode 100644 examples/c++-api/Makefile
create mode 100644 examples/c++-api/bloom.cc
create mode 100644 examples/c++-api/consume.cc
create mode 100644 examples/c++-api/exact-counting.cc
create mode 100644 examples/c++-api/reads.fastq
create mode 100755 examples/python-api/bloom.py
create mode 100755 examples/python-api/consume.py
create mode 100755 examples/python-api/exact-counting.py
create mode 100644 khmer/_cpy_counttable.hh
create mode 100644 khmer/_cpy_hashgraph.hh
create mode 100644 khmer/_cpy_nodetable.hh
create mode 100644 khmer/_cpy_smallcountgraph.hh
create mode 100644 khmer/_cpy_smallcounttable.hh
copy khmer/{khmer_logger.py => trimming.py} (61%)
rename ChangeLog => legacy/ChangeLog (83%)
rename jenkins-build.sh => legacy/jenkins-build.sh (91%)
copy lib/{test-compile.cc => alphabets.cc} (84%)
copy lib/{.check_openmp.cc => alphabets.hh} (85%)
create mode 100644 lib/assembler.cc
create mode 100644 lib/assembler.hh
delete mode 100644 lib/counting.cc
delete mode 100644 lib/counting.hh
delete mode 100755 lib/get_version.py
delete mode 100644 lib/hashbits.cc
delete mode 100644 lib/hashbits.hh
copy lib/{hashtable.cc => hashgraph.cc} (55%)
create mode 100644 lib/hashgraph.hh
create mode 100644 lib/kmer_filters.cc
copy lib/{test-Colors.cc => kmer_filters.hh} (67%)
create mode 100644 lib/storage.cc
create mode 100644 lib/storage.hh
mode change 100644 => 100755 oxli/build_graph.py
mode change 100644 => 100755 oxli/functions.py
create mode 100755 oxli/partition.py
create mode 100644 papers/paper-v2.1.md
create mode 100644 pylintrc
create mode 100644 pytest.ini
delete mode 100755 sandbox/abundance-hist-by-position.py
create mode 100755 sandbox/assemble-and-track.py
create mode 100755 sandbox/assemble-on-the-go.py
mode change 100644 => 100755 sandbox/count-kmers.py
create mode 100755 sandbox/extract-compact-dbg.py
create mode 100755 sandbox/extract-unassembled-reads-2.py
create mode 100755 sandbox/extract-unassembled-reads.py
delete mode 100755 sandbox/fasta-to-abundance-hist.py
delete mode 100755 sandbox/find-high-abund-kmers.py
delete mode 100755 sandbox/hi-lo-abundance-by-position.py
create mode 100755 sandbox/link-compact-dbg.py
mode change 100644 => 100755 sandbox/optimal_args_hashbits.py
mode change 100644 => 100755 sandbox/readaligner_pairhmm_train.py
create mode 100755 sandbox/reassemble-contigs.py
create mode 100755 sandbox/streaming-assembly-simple.py
create mode 100644 tests/test-data/README.rst
copy tests/test-data/{paired-mixed.fa.pe => paired-mixed-witherror.fa.pe} (92%)
copy tests/test-data/{paired.fq => paired.malformat.fq} (95%)
copy tests/test-data/{paired.fq.1 => paired.malformat.fq.2} (90%)
create mode 100644 tests/test-data/simple-genome-reads.fa
create mode 100644 tests/test-data/simple-genome.fa
create mode 100644 tests/test-data/single-read.fa
create mode 100644 tests/test-data/unclean-reads.fastq
create mode 100644 tests/test-data/valid-read-testing.fq
create mode 100644 tests/test_assembly.py
rename tests/{test_filter.py => test_counttable.py} (53%)
copy sandbox/stoptag-abundance-hist.py => tests/test_cpython_hierarchy.py (58%)
mode change 100755 => 100644
create mode 100644 tests/test_filter_abund.py
create mode 100644 tests/test_hashset.py
create mode 100644 tests/test_nibblestorage.py
create mode 100644 tests/test_read_handling.py
create mode 100644 tests/test_script_output.py
create mode 100644 tests/test_sequence_validation.py
create mode 100644 tests/test_tabletype.py
mode change 100755 => 100644 versioneer.py
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