This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to tag debian/2.1.2+dfsg-1 in repository khmer.
commit f2b168335bdb572a70ec1da3d0e5a2e5c8aec48a Merge: 0235101 5744859 Author: Michael R. Crusoe <[email protected]> Date: Thu Oct 5 09:12:14 2017 -0700 Updated version 2.1.2+dfsg from 'upstream/2.1.2+dfsg' with Debian dir 764652a9cbfa1ad17c00ad640bdf1d172020b4a8 .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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
