[med-svn] [khmer] branch upstream updated (7483ff8 -> 381599a)

Michael Crusoe misterc-guest at moszumanska.debian.org
Fri Sep 4 23:11:51 UTC 2015


This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a change to branch upstream
in repository khmer.

      from  7483ff8   Imported Upstream version 2.0~rc3+dfsg
       new  381599a   Imported Upstream version 2.0~rc6+dfsg

The 1 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 ------------------------------
 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
 208 files changed, 8744 insertions(+), 2641 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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