This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository unanimity.
commit 17cc0f4201170a80cb88e951a1ec9ba9c78d8317 Merge: 6e8f934 eeb5d26 Author: Afif Elghraoui <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/unanimity.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
