[med-svn] [unanimity] 04/04: Merge tag 'upstream/2.0.4+20161206+dfsg'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository unanimity.

commit 17cc0f4201170a80cb88e951a1ec9ba9c78d8317
Merge: 6e8f934 eeb5d26
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Dec 18 01:15:25 2016 -0800

    Merge tag 'upstream/2.0.4+20161206+dfsg'
    
    Upstream version 2.0.4+20161206+dfsg

 .gitignore                                         |    3 +
 .gitmodules                                        |    4 -
 CMakeLists.txt                                     |    2 +-
 cmake/uny-compilerflags.cmake                      |    4 +-
 cmake/uny-dependencies.cmake                       |   32 +-
 cmake/uny-gitsha1.cmake                            |    2 +-
 .../ZScoreMath.rst                                 |  354 +++----
 .../img/ZScore-HMM-figures.jpeg                    |  Bin 0 -> 105415 bytes
 .../{ => img}/pacbioHMM.svg.png                    |  Bin
 include/pacbio/Version.h.in                        |    1 +
 include/pacbio/ccs/Consensus.h                     |   25 +-
 include/pacbio/ccs/ConsensusSettings.h             |    3 +-
 include/pacbio/consensus/AbstractIntegrator.h      |   24 +-
 include/pacbio/consensus/Evaluator.h               |   11 +-
 include/pacbio/consensus/MonoMolecularIntegrator.h |    5 +
 include/pacbio/data/State.h                        |    6 +-
 include/pacbio/denovo/PoaGraph.h                   |    2 +
 include/pacbio/denovo/SparsePoa.h                  |    2 +-
 .../InvalidEvaluatorException.h}                   |   28 +-
 include/pacbio/log/Logging.h                       |  406 --------
 build.sh => scripts/ci/build.sh                    |   12 +-
 scripts/ci/checkout-submodules.sh                  |   13 +
 scripts/makeChangeLog.py                           |   31 -
 scripts/nightly/build.sh                           |   42 +
 scripts/nightly/checkout-submodules.sh             |   13 +
 scripts/nightly/test.sh                            |   20 +
 setup.py                                           |   26 +-
 src/AbstractIntegrator.cpp                         |   42 +-
 src/CMakeLists.txt                                 |    4 -
 src/ConsensusSettings.cpp                          |   59 +-
 src/Evaluator.cpp                                  |   25 +-
 src/Polish.cpp                                     |   56 +-
 src/SparsePoa.cpp                                  |    5 +-
 src/Template.cpp                                   |   32 +-
 src/Utility.cpp                                    |    7 +-
 src/main/ccs.cpp                                   |  146 +--
 src/models/S_P1C1v2_Model.cpp                      |    2 +-
 src/models/S_P2C2_Model.cpp                        |  395 ++++++++
 src/poa/PoaGraph.cpp                               |    2 +
 src/poa/PoaGraphImpl.cpp                           |   22 +
 src/poa/PoaGraphImpl.h                             |   16 +-
 src/poa/PoaGraphTraversals.cpp                     |    8 +-
 swig/CMakeLists.txt                                |   11 +-
 swig/ConsensusCore2.py                             |    1 +
 tests/cram/100zmws.t                               |   64 +-
 tests/cram/100zmws_byStrand.t                      |  134 +--
 tests/cram/force.t                                 |   14 +
 tests/cram/internal/big.t                          |   20 +
 tests/cram/logfile.t                               |   14 +
 tests/cram/tiny.t                                  |    4 +-
 tests/cram/tiny_noPolish.t                         |   33 +
 tests/data/params/SP2C2.json                       | 1026 ++++++++++++++++++++
 tests/python/test_tool_contract.py                 |    2 +-
 tests/unit/TestLoadModels.cpp                      |   27 +-
 tests/unit/TestPoaConsensus.cpp                    |   45 +-
 tests/unit/TestTemplate.cpp                        |    2 +-
 56 files changed, 2293 insertions(+), 996 deletions(-)

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