[med-svn] [khmer] branch upstream updated (a119d2c -> 5744859)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Oct 7 17:16:09 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository khmer.
from a119d2c New upstream version 2.1.1+dfsg
adds 5744859 New upstream version 2.1.2+dfsg
No new revisions were added by this update.
Summary of changes:
.gitignore | 1 +
CHANGELOG.md | 18 +
Doxyfile.in | 6 +-
MANIFEST.in | 1 +
Makefile | 52 +-
doc/dev/a-quick-guide-to-testing.rst | 2 +-
doc/dev/codebase-guide.rst | 9 +-
doc/dev/development.rst | 48 +-
doc/dev/guidelines-continued-dev.rst | 28 +
doc/requirements.txt | 1 +
examples/c++-api/Makefile | 19 +-
examples/c++-api/bloom.cc | 6 +-
examples/c++-api/consume.cc | 6 +-
examples/c++-api/exact-counting.cc | 7 +-
{lib => include/khmer}/.gitignore | 0
include/khmer/_cpy_countgraph.hh | 35 +
.../khmer/_cpy_counttable.hh | 30 +-
include/khmer/_cpy_graphlabels.hh | 87 +
include/khmer/_cpy_hashgraph.hh | 274 +
include/khmer/_cpy_hashset.hh | 73 +
include/khmer/_cpy_hashtable.hh | 145 +
include/khmer/_cpy_hllcounter.hh | 81 +
include/khmer/_cpy_khmer.hh | 114 +
include/khmer/_cpy_nodegraph.hh | 42 +
.../khmer/_cpy_nodetable.hh | 35 +-
include/khmer/_cpy_readaligner.hh | 43 +
include/khmer/_cpy_readparsers.hh | 140 +
.../khmer/_cpy_smallcountgraph.hh | 41 +-
.../khmer/_cpy_smallcounttable.hh | 33 +-
include/khmer/_cpy_subsetpartition.hh | 58 +
include/khmer/_cpy_utils.hh | 67 +
{lib => include/oxli}/.gitignore | 0
{lib => include/oxli}/alphabets.hh | 4 +-
{lib => include/oxli}/assembler.hh | 6 +-
{lib => include/oxli}/hashgraph.hh | 12 +-
{lib => include/oxli}/hashtable.hh | 109 +-
{lib => include/oxli}/hllcounter.hh | 4 +-
{lib => include/oxli}/kmer_filters.hh | 4 +-
{lib => include/oxli}/kmer_hash.hh | 8 +-
{lib => include/oxli}/labelhash.hh | 8 +-
{lib => include/oxli}/magic | 6 +-
lib/khmer.hh => include/oxli/oxli.hh | 10 +-
.../oxli/oxli_exception.hh | 50 +-
{lib => include/oxli}/read_aligner.hh | 10 +-
{lib => include/oxli}/read_parsers.hh | 48 +-
{lib => include/oxli}/storage.hh | 16 +-
{lib => include/oxli}/subset.hh | 4 +-
{lib => include/oxli}/traversal.hh | 4 +-
khmer/__init__.py | 7 +-
khmer/_khmer.cc | 4959 ------------
khmer/_oxli/__init__.py | 6 +
khmer/_oxli/assembly.pxd | 75 +
khmer/_oxli/assembly.pyx | 134 +
khmer/_oxli/graphs.pxd | 182 +
khmer/_oxli/graphs.pyx | 20 +
khmer/_oxli/hashing.pxd | 67 +
khmer/_oxli/hashing.pyx | 66 +
khmer/_oxli/hllcounter.pxd | 38 +
khmer/_oxli/oxli_types.pxd | 19 +
khmer/_oxli/parsing.pxd | 164 +
khmer/_oxli/parsing.pyx | 532 ++
khmer/_oxli/traversal.pxd | 19 +
khmer/_oxli/utils.pxd | 14 +
khmer/_oxli/utils.pyx | 42 +
khmer/_version.py | 6 +-
khmer/khmer_args.py | 5 +-
khmer/thread_utils.py | 1 +
khmer/utils.py | 119 +-
oxli/__init__.py | 1 +
oxli/build_graph.py | 1 +
pytest.ini | 4 +
scripts/abundance-dist-single.py | 3 +-
scripts/annotate-partitions.py | 1 +
scripts/count-median.py | 1 +
scripts/do-partition.py | 1 +
scripts/extract-partitions.py | 1 +
scripts/fastq-to-fasta.py | 1 +
scripts/filter-abund-single.py | 2 +-
scripts/filter-stoptags.py | 1 +
scripts/find-knots.py | 1 +
scripts/interleave-reads.py | 1 +
scripts/load-into-counting.py | 2 +-
scripts/make-initial-stoptags.py | 1 +
scripts/partition-graph.py | 1 +
scripts/sample-reads-randomly.py | 1 +
scripts/split-paired-reads.py | 1 +
scripts/unique-kmers.py | 1 +
setup.cfg | 4 +-
setup.py | 97 +-
{lib => src/khmer}/.gitignore | 0
.../khmer/_cpy_countgraph.cc | 220 +-
.../khmer/_cpy_counttable.cc | 56 +-
src/khmer/_cpy_graphlabels.cc | 510 ++
.../khmer/_cpy_hashgraph.cc | 833 +-
src/khmer/_cpy_hashset.cc | 355 +
src/khmer/_cpy_hashtable.cc | 1016 +++
src/khmer/_cpy_hllcounter.cc | 364 +
src/khmer/_cpy_khmer.cc | 441 ++
src/khmer/_cpy_nodegraph.cc | 162 +
.../khmer/_cpy_nodetable.cc | 65 +-
src/khmer/_cpy_readaligner.cc | 242 +
src/khmer/_cpy_readparsers.cc | 639 ++
.../khmer/_cpy_smallcountgraph.cc | 133 +-
.../khmer/_cpy_smallcounttable.cc | 52 +-
src/khmer/_cpy_subsetpartition.cc | 263 +
src/khmer/_cpy_utils.cc | 177 +
{lib => src/oxli}/.check_openmp.cc | 0
{lib => src/oxli}/.gitignore | 0
{lib => src/oxli}/Makefile | 55 +-
{lib => src/oxli}/alphabets.cc | 4 +-
{lib => src/oxli}/assembler.cc | 4 +-
{lib => src/oxli}/hashgraph.cc | 96 +-
{lib => src/oxli}/hashtable.cc | 179 +-
{lib => src/oxli}/hllcounter.cc | 19 +-
{lib => src/oxli}/kmer_filters.cc | 10 +-
{lib => src/oxli}/kmer_hash.cc | 45 +-
{lib => src/oxli}/labelhash.cc | 95 +-
{lib => src/oxli}/oxli.pc.in | 0
{lib => src/oxli}/read_aligner.cc | 10 +-
{lib => src/oxli}/read_parsers.cc | 38 +-
{lib => src/oxli}/storage.cc | 102 +-
{lib => src/oxli}/subset.cc | 146 +-
{lib => src/oxli}/test-Colors.cc | 14 +-
{lib => src/oxli}/test-compile.cc | 4 +-
{lib => src/oxli}/traversal.cc | 14 +-
tests/{test_assembly.py => graph_features.py} | 389 +-
tests/khmer_tst_utils.py | 1 +
tests/test-data/banding-reads.fq | 8000 ++++++++++++++++++++
tests/test-data/bogus.fa | 2 +
tests/test_banding.py | 158 +
tests/test_countgraph.py | 6 -
tests/test_cython_assembly.py | 441 ++
tests/test_cython_parsing.py | 442 ++
tests/test_filter_abund.py | 2 +
tests/test_functions.py | 295 +-
tests/test_scripts.py | 25 +
tests/test_sequence_validation.py | 83 +-
tests/test_subset_graph.py | 2 +
tests/test_tabletype.py | 5 +-
tests/test_threaded_sequence_processor.py | 1 +
140 files changed, 17454 insertions(+), 7168 deletions(-)
copy {lib => include/khmer}/.gitignore (100%)
create mode 100644 include/khmer/_cpy_countgraph.hh
copy lib/alphabets.hh => include/khmer/_cpy_counttable.hh (76%)
create mode 100644 include/khmer/_cpy_graphlabels.hh
create mode 100644 include/khmer/_cpy_hashgraph.hh
create mode 100644 include/khmer/_cpy_hashset.hh
create mode 100644 include/khmer/_cpy_hashtable.hh
create mode 100644 include/khmer/_cpy_hllcounter.hh
create mode 100644 include/khmer/_cpy_khmer.hh
create mode 100644 include/khmer/_cpy_nodegraph.hh
copy lib/alphabets.hh => include/khmer/_cpy_nodetable.hh (73%)
create mode 100644 include/khmer/_cpy_readaligner.hh
create mode 100644 include/khmer/_cpy_readparsers.hh
copy lib/alphabets.hh => include/khmer/_cpy_smallcountgraph.hh (66%)
copy lib/alphabets.hh => include/khmer/_cpy_smallcounttable.hh (72%)
create mode 100644 include/khmer/_cpy_subsetpartition.hh
create mode 100644 include/khmer/_cpy_utils.hh
copy {lib => include/oxli}/.gitignore (100%)
rename {lib => include/oxli}/alphabets.hh (96%)
rename {lib => include/oxli}/assembler.hh (99%)
rename {lib => include/oxli}/hashgraph.hh (97%)
rename {lib => include/oxli}/hashtable.hh (84%)
rename {lib => include/oxli}/hllcounter.hh (99%)
rename {lib => include/oxli}/kmer_filters.hh (98%)
rename {lib => include/oxli}/kmer_hash.hh (98%)
rename {lib => include/oxli}/labelhash.hh (98%)
rename {lib => include/oxli}/magic (91%)
rename lib/khmer.hh => include/oxli/oxli.hh (98%)
rename lib/khmer_exception.hh => include/oxli/oxli_exception.hh (71%)
rename {lib => include/oxli}/read_aligner.hh (98%)
rename {lib => include/oxli}/read_parsers.hh (84%)
rename {lib => include/oxli}/storage.hh (98%)
rename {lib => include/oxli}/subset.hh (99%)
rename {lib => include/oxli}/traversal.hh (99%)
delete mode 100644 khmer/_khmer.cc
create mode 100644 khmer/_oxli/__init__.py
create mode 100644 khmer/_oxli/assembly.pxd
create mode 100644 khmer/_oxli/assembly.pyx
create mode 100644 khmer/_oxli/graphs.pxd
create mode 100644 khmer/_oxli/graphs.pyx
create mode 100644 khmer/_oxli/hashing.pxd
create mode 100644 khmer/_oxli/hashing.pyx
create mode 100644 khmer/_oxli/hllcounter.pxd
create mode 100644 khmer/_oxli/oxli_types.pxd
create mode 100644 khmer/_oxli/parsing.pxd
create mode 100644 khmer/_oxli/parsing.pyx
create mode 100644 khmer/_oxli/traversal.pxd
create mode 100644 khmer/_oxli/utils.pxd
create mode 100644 khmer/_oxli/utils.pyx
copy {lib => src/khmer}/.gitignore (100%)
copy khmer/_cpy_smallcountgraph.hh => src/khmer/_cpy_countgraph.cc (51%)
rename khmer/_cpy_counttable.hh => src/khmer/_cpy_counttable.cc (55%)
create mode 100644 src/khmer/_cpy_graphlabels.cc
rename khmer/_cpy_hashgraph.hh => src/khmer/_cpy_hashgraph.cc (92%)
create mode 100644 src/khmer/_cpy_hashset.cc
create mode 100644 src/khmer/_cpy_hashtable.cc
create mode 100644 src/khmer/_cpy_hllcounter.cc
create mode 100644 src/khmer/_cpy_khmer.cc
create mode 100644 src/khmer/_cpy_nodegraph.cc
rename khmer/_cpy_nodetable.hh => src/khmer/_cpy_nodetable.cc (55%)
create mode 100644 src/khmer/_cpy_readaligner.cc
create mode 100644 src/khmer/_cpy_readparsers.cc
rename khmer/_cpy_smallcountgraph.hh => src/khmer/_cpy_smallcountgraph.cc (65%)
rename khmer/_cpy_smallcounttable.hh => src/khmer/_cpy_smallcounttable.cc (56%)
create mode 100644 src/khmer/_cpy_subsetpartition.cc
create mode 100644 src/khmer/_cpy_utils.cc
rename {lib => src/oxli}/.check_openmp.cc (100%)
rename {lib => src/oxli}/.gitignore (100%)
rename {lib => src/oxli}/Makefile (86%)
rename {lib => src/oxli}/alphabets.cc (95%)
rename {lib => src/oxli}/assembler.cc (99%)
rename {lib => src/oxli}/hashgraph.cc (91%)
rename {lib => src/oxli}/hashtable.cc (80%)
rename {lib => src/oxli}/hllcounter.cc (97%)
rename {lib => src/oxli}/kmer_filters.cc (97%)
rename {lib => src/oxli}/kmer_hash.cc (83%)
rename {lib => src/oxli}/labelhash.cc (89%)
rename {lib => src/oxli}/oxli.pc.in (100%)
rename {lib => src/oxli}/read_aligner.cc (99%)
rename {lib => src/oxli}/read_parsers.cc (91%)
rename {lib => src/oxli}/storage.cc (92%)
rename {lib => src/oxli}/subset.cc (92%)
rename {lib => src/oxli}/test-Colors.cc (88%)
rename {lib => src/oxli}/test-compile.cc (94%)
rename {lib => src/oxli}/traversal.cc (98%)
rename tests/{test_assembly.py => graph_features.py} (53%)
create mode 100644 tests/test-data/banding-reads.fq
create mode 100644 tests/test-data/bogus.fa
create mode 100644 tests/test_banding.py
create mode 100644 tests/test_cython_assembly.py
create mode 100644 tests/test_cython_parsing.py
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git
More information about the debian-med-commit
mailing list