[med-svn] [khmer] branch master updated (4cfbd03 -> a5add3e)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Sep 4 23:11:49 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from 4cfbd03 drop two more files
new 381599a Imported Upstream version 2.0~rc6+dfsg
new 936f879 Merge tag 'upstream/2.0_rc6+dfsg'
new 4ec6263 version bump for rc6
new a5add3e refresh patches
The 4 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:
.mailmap | 9 +-
CITATION | 119 +++++--
CODE_OF_CONDUCT.rst | 38 ++
CONTRIBUTING.md | 39 ++
ChangeLog | 176 +++++++++
Doxyfile.in | 21 +-
LICENSE | 141 ++++++--
MANIFEST.in | 2 +-
Makefile | 74 +++-
README.rst | 38 ++
bink.ipynb | 535 ----------------------------
debian/changelog | 2 +-
debian/patches/cpython-bug-empty-exceptions | 10 +-
debian/patches/install-prefix | 41 +--
debian/patches/older-setuptools | 4 +-
debian/patches/setup-py-py3 | 10 +-
doc/LICENSE.rst | 3 +-
doc/_static/labibi.css | 2 +-
doc/conf.py | 7 +-
doc/contributors.rst | 53 ++-
doc/dev/a-quick-guide-to-testing.rst | 38 ++
doc/dev/binary-file-formats.rst | 44 ++-
doc/dev/codebase-guide.rst | 50 ++-
doc/dev/coding-guidelines-and-review.rst | 47 ++-
doc/dev/crazy-ideas.rst | 39 +-
doc/dev/details.rst | 37 +-
doc/dev/development.rst | 59 ++-
doc/dev/for-khmer-developers.rst | 42 ++-
doc/dev/getting-started.rst | 157 +++++++-
doc/dev/hackathon.rst | 37 ++
doc/dev/index.rst | 38 ++
doc/dev/release.rst | 42 ++-
doc/dev/scripts-and-sandbox.rst | 58 ++-
doc/index.rst | 144 ++++++--
doc/introduction.rst | 63 +++-
doc/release-notes/index.rst | 39 ++
doc/release-notes/release-1.0.1.md | 38 ++
doc/release-notes/release-1.0.1.rst | 40 +++
doc/release-notes/release-1.0.md | 38 ++
doc/release-notes/release-1.0.rst | 40 +++
doc/release-notes/release-1.1.md | 38 ++
doc/release-notes/release-1.1.rst | 40 +++
doc/release-notes/release-1.2.md | 38 ++
doc/release-notes/release-1.2.rst | 40 +++
doc/release-notes/release-1.3.md | 37 ++
doc/release-notes/release-1.3.rst | 40 +++
doc/release-notes/release-1.4.md | 39 +-
doc/release-notes/release-1.4.rst | 40 +++
doc/release-notes/release-2.0.md | 340 ++++++++++++++++++
doc/release-notes/release-2.0.rst | 386 ++++++++++++++++++++
doc/requirements.txt | 2 +-
doc/roadmap.rst | 38 +-
doc/run-corn-50m.sh | 41 ++-
doc/user/biblio.rst | 72 +++-
doc/user/blog-posts.rst | 40 ++-
doc/user/choosing-table-sizes.rst | 73 +++-
doc/user/examples.rst | 55 ++-
doc/user/galaxy.rst | 48 ++-
doc/user/getting-help.rst | 43 ++-
doc/user/guide.rst | 159 +++++----
doc/user/index.rst | 38 ++
doc/user/install.rst | 46 ++-
doc/user/known-issues.rst | 47 ++-
doc/user/partitioning-big-data.rst | 42 ++-
doc/user/scripts.rst | 61 +++-
doc/whats-new-2.0.rst | 184 ++++++++--
examples/stamps/do.sh | 34 +-
ez_setup.py | 332 -----------------
jenkins-build.sh | 34 ++
khmer/__init__.py | 37 +-
khmer/_khmer.cc | 60 +++-
khmer/_version.py | 4 +-
khmer/kfile.py | 37 +-
khmer/khmer_args.py | 60 +++-
khmer/khmer_logger.py | 37 +-
khmer/thread_utils.py | 49 ++-
khmer/utils.py | 43 ++-
lib/.check_openmp.cc | 42 ++-
lib/Makefile | 58 ++-
lib/counting.cc | 52 ++-
lib/counting.hh | 50 ++-
lib/get_version.py | 42 ++-
lib/graphtest.cc | 80 -----
lib/hashbits.cc | 44 ++-
lib/hashbits.hh | 48 ++-
lib/hashtable.cc | 102 ++++--
lib/hashtable.hh | 51 ++-
lib/hllcounter.cc | 52 ++-
lib/hllcounter.hh | 46 ++-
lib/khmer.hh | 44 ++-
lib/khmer_exception.hh | 44 ++-
lib/kmer_hash.cc | 48 ++-
lib/kmer_hash.hh | 75 ++--
lib/labelhash.cc | 44 ++-
lib/labelhash.hh | 46 ++-
lib/primes.hh | 75 ----
lib/read_aligner.cc | 42 ++-
lib/read_aligner.hh | 43 ++-
lib/read_aligner_test.sh | 1 -
lib/read_parsers.cc | 44 ++-
lib/read_parsers.hh | 44 ++-
lib/subset.cc | 70 +++-
lib/subset.hh | 44 ++-
lib/test-Colors.cc | 42 ++-
lib/test-compile.cc | 46 ++-
lib/test-read-aligner.cc | 63 ----
lib/traversal.cc | 47 ++-
lib/traversal.hh | 48 ++-
oxli/__init__.py | 55 ++-
oxli/build_graph.py | 39 +-
oxli/functions.py | 43 ++-
sandbox/Makefile.read_aligner_training | 35 ++
sandbox/README.rst | 38 ++
sandbox/abundance-hist-by-position.py | 36 +-
sandbox/assembly-diff-2.py | 36 +-
sandbox/assembly-diff.py | 36 +-
sandbox/assemstats3.py | 48 ++-
sandbox/bloom-count.py | 40 ++-
sandbox/build-sparse-graph.py | 39 +-
sandbox/calc-best-assembly.py | 35 +-
sandbox/calc-error-profile.py | 37 +-
sandbox/calc-median-distribution.py | 36 +-
sandbox/collect-reads.py | 39 +-
sandbox/collect-variants.py | 36 +-
sandbox/correct-reads.py | 45 ++-
sandbox/count-kmers-single.py | 37 +-
sandbox/count-kmers.py | 37 +-
sandbox/error-correct-pass2.py | 38 +-
sandbox/estimate_optimal_hash.py | 42 ++-
sandbox/extract-single-partition.py | 36 +-
sandbox/fasta-to-abundance-hist.py | 36 +-
sandbox/filter-below-abund.py | 36 +-
sandbox/filter-median-and-pct.py | 36 +-
sandbox/filter-median.py | 36 +-
sandbox/find-high-abund-kmers.py | 39 +-
sandbox/graph-size.py | 36 +-
sandbox/hi-lo-abundance-by-position.py | 36 +-
sandbox/make-coverage.py | 37 +-
sandbox/memusg | 46 ---
sandbox/multi-rename.py | 37 +-
sandbox/normalize-by-median-pct.py | 38 +-
sandbox/optimal_args_hashbits.py | 38 +-
sandbox/print-stoptags.py | 36 +-
sandbox/print-tagset.py | 36 +-
sandbox/readaligner_pairhmm_train.py | 34 ++
sandbox/renumber-partitions.py | 36 +-
sandbox/saturate-by-median.py | 43 ++-
sandbox/shuffle-reverse-rotary.py | 38 +-
sandbox/slice-reads-by-coverage.py | 35 +-
sandbox/split-fasta.py | 36 +-
sandbox/split-sequences-by-length.py | 38 +-
sandbox/stoptag-abundance-hist.py | 36 +-
sandbox/stoptags-by-position.py | 38 +-
sandbox/strip-partition.py | 36 +-
sandbox/subset-report.py | 36 +-
sandbox/sweep-files.py | 40 ++-
sandbox/sweep-out-reads-with-contigs.py | 37 +-
sandbox/sweep-reads.py | 42 ++-
sandbox/sweep-reads2.py | 36 +-
sandbox/sweep-reads3.py | 36 +-
sandbox/write-trimmomatic.py | 37 +-
scripts/README.txt | 1 -
scripts/abundance-dist-single.py | 58 ++-
scripts/abundance-dist.py | 58 ++-
scripts/annotate-partitions.py | 62 +++-
scripts/count-median.py | 59 ++-
scripts/do-partition.py | 63 +++-
scripts/extract-long-sequences.py | 52 ++-
scripts/extract-paired-reads.py | 59 ++-
scripts/extract-partitions.py | 59 ++-
scripts/fastq-to-fasta.py | 46 ++-
scripts/filter-abund-single.py | 50 ++-
scripts/filter-abund.py | 52 ++-
scripts/filter-stoptags.py | 60 +++-
scripts/find-knots.py | 59 ++-
scripts/interleave-reads.py | 57 ++-
scripts/load-graph.py | 39 +-
scripts/load-into-counting.py | 61 +++-
scripts/make-initial-stoptags.py | 55 ++-
scripts/merge-partitions.py | 55 ++-
scripts/normalize-by-median.py | 75 ++--
scripts/oxli | 35 +-
scripts/partition-graph.py | 63 +++-
scripts/readstats.py | 55 ++-
scripts/sample-reads-randomly.py | 66 +++-
scripts/split-paired-reads.py | 53 ++-
scripts/trim-low-abund.py | 58 ++-
scripts/unique-kmers.py | 57 ++-
setup.py | 73 +++-
sort-authors-list.py | 92 +++++
tests/__init__.py | 35 +-
tests/khmer_tst_utils.py | 42 ++-
tests/test_countgraph.py | 40 ++-
tests/test_counting_single.py | 41 ++-
tests/test_filter.py | 40 ++-
tests/test_functions.py | 40 ++-
tests/test_graph.py | 40 ++-
tests/test_hll.py | 40 ++-
tests/test_labelhash.py | 40 ++-
tests/test_lump.py | 38 +-
tests/test_nodegraph.py | 36 +-
tests/test_normalize_by_median.py | 49 ++-
tests/test_oxli_functions.py | 42 ++-
tests/test_read_aligner.py | 40 ++-
tests/test_read_parsers.py | 42 ++-
tests/test_sandbox_scripts.py | 36 +-
tests/test_script_arguments.py | 36 +-
tests/test_scripts.py | 195 ++++++----
tests/test_streaming_io.py | 39 +-
tests/test_subset_graph.py | 40 ++-
tests/test_threaded_sequence_processor.py | 66 +++-
tests/test_version.py | 38 +-
versioneer.py | 0
213 files changed, 8758 insertions(+), 2694 deletions(-)
delete mode 100644 bink.ipynb
create mode 100644 doc/release-notes/release-2.0.md
create mode 100644 doc/release-notes/release-2.0.rst
delete mode 100644 ez_setup.py
delete mode 100644 lib/graphtest.cc
delete mode 100644 lib/primes.hh
delete mode 100755 lib/read_aligner_test.sh
delete mode 100644 lib/test-read-aligner.cc
delete mode 100755 sandbox/memusg
delete mode 100644 scripts/README.txt
create mode 100755 sort-authors-list.py
mode change 100644 => 100755 versioneer.py
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