[shark] branch debian/sid updated (f4bfcc7 -> 6addea5)
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Thu Dec 10 19:50:03 UTC 2015
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a change to branch debian/sid
in repository shark.
omits f4bfcc7 Release to unstable.
omits 4435e19 Add upstream metadata.
omits e3f20ad Add README.Debian file.
omits 7b43014 Add gbp.conf file.
omits 8b193ae Repack sources to exclude upstream debianization.
omits 3c34654 Add watch file.
omits 2b4fde7 Add autopkgtest testsuite.
omits 1ae89ac Add patch queue.
omits 4967b4d Update d/rules.
omits 7aca993 Add package install files.
omits 660db0c Update d/copyright.
omits 386521f Update d/control.
omits 526073d d/changelog: closes #595485.
omits d7222ed Add debmake debianization.
adds d576bf7 updated documentation to reflect 3.0 release
adds 39ed32e updated installation page for windows
adds 97954f0 typo corrected
adds bd47297 typos
adds 05e8333 addet travis-ci buildfile
adds a4f2cd7 whitespaces matter..
adds 187081a boost is named differently
adds d429fbf default boost on travis-ci is too old, trying backports...
adds 628fcb2 used aydins config
adds 140043f DIRECTORY replaced by PATH as it is unknown prior cmake 2.8.12 which does not exist on travis
adds 7baa1cf standard travis command requires configure...
adds a60941c yaml error...i begin to hate thi trial& error approach
adds 5f0dd47 added multithreaded build as time limit exceeded
adds 3f06e8b removed potentially hazardeous print-outs of iteration status which make up quite a big portion of runtime
adds fcff956 set openmp threads to a sane number for the virtualized environment of travis
adds ae56b67 trying out osx travis support
adds 71eb300 syntax error
adds c1e26f1 troubleshooting: somehow build process gets killed..
adds fac1f91 improved indent
adds bffb22e Create appveyor.yml
adds 0baec0b Update appveyor.yml
adds ab2357f Update appveyor.yml
adds b53238a Update appveyor.yml
adds 2d73e92 Update appveyor.yml
adds 66d6904 Update appveyor.yml
adds b2dc9c3 Update appveyor.yml
adds 395945c Update appveyor.yml
adds bd43092 Update appveyor.yml
adds a9a1568 Update appveyor.yml
adds da54a41 Update appveyor.yml
adds 90b2325 Update appveyor.yml
adds f632251 new website frontpage
adds 199a522 one line added to the css
adds 2c61366 added icon to front page, changed links in sub-pages to new front page
adds 081337e added missing include to Shark.h which prevented the define sto get through to the DLL macros. Fixes #10
adds b437aae Merge branch 'master' of https://github.com/Shark-ML/Shark
adds 7393006 Update appveyor.yml
adds 92da03e Update CMakeLists.txt
adds 7bb4193 Update CMakeLists.txt
adds 5998a76 Update appveyor.yml
adds 9da1946 Update appveyor.yml
adds 881cbb7 Update MultiNomialDistribution.h
adds 4a356ba Update appveyor.yml
adds f8875a6 Update MultiNomialDistribution.h
adds 56b6369 Update MultiNomialDistribution.h
adds 710da04 Update MultiNomialDistribution.h
adds ce99bfe Update appveyor.yml
adds 17c9711 Update appveyor.yml
adds 912095d BUILD_SHARED_LIBS=ON
adds c962e02 Update appveyor.yml
adds d6dc915 Merge pull request #13 from Shark-ML/appveyor
adds 3ce327f Update appveyor.yml
adds e56f12d Update appveyor.yml
adds c181701 appveyor added to homepage
adds 2659421 removed same_closure, it is never going to work well
adds 2b9bd3a reorganized asignment operators by centralizing them through freestanding operators. also theoretical upport for blockwie expression is added albeit no expression is declared blockwise right now
adds 69c14fe fixed unused variable warning
adds dfecdec added const_expression template which produces the const expression type (which is the same as const_closure except for container types for which it is const ContainerType). This is necessary to simplify expression generation as it is virtually impossible to write a non-const-> const conversion when the types are Proxy<Matrix> -> Proxy<matrix_reference<const Matrix> >. This is going to be used in the typedefs for const_closure
adds 58ee65b added missing special case for gemv when the matrix orientation is unknown (which very rarely happens)
adds 54cf77f fixed a small bug in proxy assignment and added a template function eval_block which checks at compile time whether the expression is a block expression. If yes, it is evaluated and a temporary is returned, otherwise the expression is returned untouched
adds 9b91378 rewrote const_closure_Type generation of proxies. This is now by default Proxy<M> -> Proxy<const_expression<M>::type >. The old behaviour was Proxy<M>->Proxy<M const> const which, for nested proxies does not enforce read-onlyness due to proxy semantics (which behave more like references or pointers)
adds 1b43f7c made the matrix-vector prod a block expression which internally uses kernels::gemv. this required a lot of changes in vector_expression to be able to write stuff like 2*prod(A,v)+b efficiently. namely two new expressions vector_scalar_multiply which multiplies a vector by a scalar and vector_addition which adds two vectors. This is because scalar multiplication can be carried out by gemv efficiently so it makes sense to have plus_assign_to or assign_to take an additi [...]
adds 58304c5 type
adds d83bd6a added the same proxy changes to the vector proxies
adds d94cfee replaced axpy_prod with prod for all matrix-vector multiplications. the code is now much simpler in many cases
adds d094fb2 added matrix-matrix prod() as well as required matrix-expressions matrix_scalar_prod and matrix_addition
adds 669bc58 removed accidentally included file
adds 62dec7c removed almost all uses of axpy_prod
adds b0c7cf0 typo
adds fc2a185 fixed some typos
adds cd733f5 various bugfixes
adds 241e77b clang error on travis-ci lead me to the path of a much simpler implementation of eval_block - a simple implicit cast/copy
adds 3ac7e4d rwrote operator+/- for vector/matrix +- scalar operations. they now use the more efficient block interface
adds 87653fe fixed typo
adds 063ec6d made scalar_expressions a vector expression which prevents dangling reference problems...
adds d2a34bc reimplemented the outer_product class so that it is easier to understand.
adds 9645832 Merge pull request #12 from Shark-ML/blas
adds 97b1c54 unused variable removed (and hence a warning)
adds 384186a Update Pgm.h
adds 83829e9 documentation bug fixed
adds d51ee74 Fix HDF5 detection.
adds dd28d83 Merge pull request #23 from ghisvail/fix/hdf5-detection
adds 3595484 fixed issue #26
adds 925f872 moved the non-atlas specific cblas interface to kernels/cblas
adds 74ec2bf restructured finding ATLAS/Accelerate a little to make it easier to add future CBLAS packages
adds 80b817c added support for generic cblas libraries
adds 57e553b added support for Generic and OpenBLAS. compiles
adds f92111b Merge pull request #20 from Shark-ML/blas
adds eca36c6 added copyright information to files to fix issue #25
adds 7664b7d fix of #24
adds a1a68fd added SOVERSION recommendiation of issue #21
new 3ea73d1 updating cmake version to 2.8.12 in travis, hope this works
new a36fb32 fixed a broken check that a HDF5 file was opened correctly. Also fixed the buildscript to copy the test files in the build directory. fixes #22
new 7ef1b1f Merge branch 'master' of ssh://github.com/Shark-ML/Shark
new 76adba3 Revert "added SOVERSION recommendiation of issue #21"
new 3252eae Use public SHARK_[SO]VERSION variables in library target.
new 7df87be Merge pull request #29 from ghisvail/fix/soversion-management
new 74f2f4e Replace non-ascii characters.
new 1240cd8 Merge pull request #28 from ghisvail/fix/cmsa-files-encoding
new b1fa7e6 fixed issue #30
new c6fcc64 Merge tag 'upstream/v3.0.1' into upstream
new f2afcc3 Add debmake debianization.
new 9130c7d d/changelog: closes #595485.
new b9cf153 Update d/control.
new 01c7fdc Update d/copyright.
new a775666 Add package install files.
new 95fb7c6 Update d/rules.
new bca8ff0 Add patch queue.
new 4881f94 Add autopkgtest testsuite.
new e294c6b Add watch file.
new 3e141b3 Repack sources to exclude upstream debianization.
new e730f8f Add gbp.conf file.
new 96b6d25 Add README.Debian file.
new 75378c9 Add upstream metadata.
new 6addea5 Release to unstable.
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Summary of changes:
.travis.yml | 36 +
CMakeLists.txt | 128 ++-
README.txt | 6 +-
Test/Algorithms/DirectSearch/MOCMA.cpp | 2 +-
Test/Algorithms/DirectSearch/RealCodedNSGAII.cpp | 3 +-
Test/Algorithms/DirectSearch/SteadyStateMOCMA.cpp | 2 +-
Test/CMakeLists.txt | 6 +-
Test/Data/HDF5Tests.cpp | 7 +-
appveyor.yml | 48 +
cBlasCheck.cpp | 9 +
debian/changelog | 2 +-
debian/control | 1 +
.../patches/Disable-doxygen-generate-tagfile.patch | 21 +
.../Disable-override-of-CMAKE_BUILD_TYPE.patch | 22 -
.../Disable-privacy-breaching-content.patch | 39 +
debian/patches/Fix-CMake-package-creation.patch | 6 +-
debian/patches/Fix-examples-install-target.patch | 21 +-
debian/patches/Fix-library-install-target.patch | 2 +-
debian/patches/Fix-typo-in-tutorials.patch | 21 -
debian/patches/Set-soversion-to-zero.patch | 21 -
debian/patches/Use-GNUInstallDirs.patch | 6 +-
debian/patches/Use-system-MathJax.patch | 2 +-
debian/patches/series | 5 +-
doc/{sphinx_pages/static => }/SharkLogo.png | Bin
doc/download.png | Bin 2892 -> 320 bytes
doc/doxygen_pages/templates/header.html | 3 +-
doc/frontpage.css | 278 ++++++
doc/index.html | 318 +++++-
.../about_shark/images => }/lgplv3-147x51.png | Bin
doc/{sphinx_pages/static => }/shark16.ico | Bin
doc/sphinx_pages/index.rst | 5 -
.../rest_sources/about_shark/copyright.rst | 3 +
doc/sphinx_pages/rest_sources/about_shark/news.rst | 8 +-
.../rest_sources/downloads/downloads.rst | 10 +-
.../rest_sources/getting_started/installation.rst | 48 +-
.../tutorials/concepts/data/datasets.tut | 4 +-
.../tutorials/concepts/library_design/kernels.rst | 4 +-
.../tutorials/concepts/library_design/models.rst | 4 +-
.../tutorials/concepts/misc/statistics.rst | 96 +-
.../tutorials/concepts/misc/statistics.tut | 2 +-
.../tutorials/first_steps/shark_layout.rst | 9 +-
.../rest_sources/tutorials/tutorials.rst | 1 -
doc/sphinx_pages/templates/layout.html | 2 +-
examples/CMakeLists.txt | 8 +-
include/shark/Algorithms/DirectSearch/CMSA.h | 4 +-
.../Algorithms/DirectSearch/FastNonDominatedSort.h | 27 +
include/shark/Algorithms/DirectSearch/Grid.h | 27 +
include/shark/Algorithms/DirectSearch/LMCMA.h | 4 +-
.../Algorithms/GradientDescent/Impl/dlinmin.inl | 44 +-
.../Algorithms/GradientDescent/Impl/wolfecubic.inl | 42 +-
include/shark/Algorithms/QP/QpMcLinear.h | 3 +-
.../shark/Algorithms/Trainers/KernelSGDTrainer.h | 3 +-
.../Trainers/NormalizeComponentsWhitening.h | 4 +-
include/shark/Core/DLLSupport.h | 1 +
include/shark/Core/Shark.h.in | 41 +-
include/shark/Data/HDF5.h | 10 +-
include/shark/Data/Impl/CVDatasetTools.inl | 28 +-
include/shark/Data/Impl/Dataset.inl | 34 +-
include/shark/Data/Impl/Statistics.inl | 27 +
include/shark/Data/Pgm.h | 4 +-
include/shark/LinAlg/BLAS/assignment.hpp | 606 ++++++++++++
include/shark/LinAlg/BLAS/detail/functional.hpp | 27 +
include/shark/LinAlg/BLAS/detail/iterator.hpp | 32 +-
include/shark/LinAlg/BLAS/detail/traits.hpp | 35 +-
include/shark/LinAlg/BLAS/expression_types.hpp | 121 +--
include/shark/LinAlg/BLAS/fwd.hpp | 27 +
include/shark/LinAlg/BLAS/io.hpp | 27 +
include/shark/LinAlg/BLAS/kernels/atlas/potrf.hpp | 5 +-
.../BLAS/kernels/{atlas => cblas}/cblas_inc.hpp | 40 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/dot.hpp | 16 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/gemm.hpp | 24 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/gemv.hpp | 24 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/tpmv.hpp | 12 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/trmm.hpp | 16 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/trmv.hpp | 12 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/trsm.hpp | 16 +-
.../LinAlg/BLAS/kernels/{atlas => cblas}/trsv.hpp | 12 +-
include/shark/LinAlg/BLAS/kernels/default/gemv.hpp | 12 +
include/shark/LinAlg/BLAS/kernels/dot.hpp | 10 +-
include/shark/LinAlg/BLAS/kernels/gemm.hpp | 4 +-
include/shark/LinAlg/BLAS/kernels/gemv.hpp | 4 +-
.../shark/LinAlg/BLAS/kernels/gotoblas/cblas_inc.h | 36 -
include/shark/LinAlg/BLAS/kernels/gotoblas/gemm.h | 164 ----
include/shark/LinAlg/BLAS/kernels/gotoblas/gemv.h | 137 ---
include/shark/LinAlg/BLAS/kernels/gotoblas/syrk.h | 133 ---
include/shark/LinAlg/BLAS/kernels/gotoblas/trsm.h | 128 ---
include/shark/LinAlg/BLAS/kernels/gotoblas/trsv.h | 112 ---
.../shark/LinAlg/BLAS/kernels/matrix_assign.hpp | 45 +-
include/shark/LinAlg/BLAS/kernels/potrf.hpp | 2 +-
include/shark/LinAlg/BLAS/kernels/syev.hpp | 2 +-
include/shark/LinAlg/BLAS/kernels/tpmv.hpp | 4 +-
include/shark/LinAlg/BLAS/kernels/traits.hpp | 2 +-
include/shark/LinAlg/BLAS/kernels/trmm.hpp | 6 +-
include/shark/LinAlg/BLAS/kernels/trmv.hpp | 4 +-
include/shark/LinAlg/BLAS/kernels/trsm.hpp | 4 +-
include/shark/LinAlg/BLAS/kernels/trsv.hpp | 4 +-
.../shark/LinAlg/BLAS/kernels/vector_assign.hpp | 29 +-
include/shark/LinAlg/BLAS/lu.hpp | 31 +-
include/shark/LinAlg/BLAS/matrix.hpp | 166 +---
include/shark/LinAlg/BLAS/matrix_expression.hpp | 1030 +++++++++++++-------
include/shark/LinAlg/BLAS/matrix_proxy.hpp | 890 ++++-------------
include/shark/LinAlg/BLAS/matrix_set.hpp | 27 +
include/shark/LinAlg/BLAS/matrix_sparse.hpp | 94 +-
include/shark/LinAlg/BLAS/operation.hpp | 27 +
include/shark/LinAlg/BLAS/permutation.hpp | 27 +
include/shark/LinAlg/BLAS/triangular_matrix.hpp | 145 +--
include/shark/LinAlg/BLAS/vector.hpp | 252 +----
include/shark/LinAlg/BLAS/vector_expression.hpp | 387 +++++++-
include/shark/LinAlg/BLAS/vector_proxy.hpp | 291 +-----
include/shark/LinAlg/BLAS/vector_sparse.hpp | 124 ++-
include/shark/LinAlg/Impl/Cholesky.inl | 49 +-
include/shark/LinAlg/Impl/eigensymm.inl | 31 +-
include/shark/LinAlg/Impl/pivotingRQ.inl | 48 +-
include/shark/LinAlg/Impl/solveSystem.inl | 94 +-
include/shark/LinAlg/Impl/solveTriangular.inl | 43 +-
include/shark/LinAlg/Impl/svd.inl | 43 +-
include/shark/LinAlg/Metrics.h | 4 +-
include/shark/LinAlg/rotations.h | 13 +-
include/shark/LinAlg/solveSystem.h | 4 +-
include/shark/Models/Autoencoder.h | 10 +-
include/shark/Models/ConvexCombination.h | 7 +-
include/shark/Models/FFNet.h | 10 +-
include/shark/Models/Impl/LinearModel.inl | 264 -----
include/shark/Models/Kernels/CSvmDerivative.h | 7 +-
include/shark/Models/Kernels/GaussianRbfKernel.h | 2 +-
include/shark/Models/Kernels/KernelExpansion.h | 2 +-
include/shark/Models/Kernels/LinearKernel.h | 4 +-
include/shark/Models/Kernels/MonomialKernel.h | 8 +-
include/shark/Models/Kernels/PolynomialKernel.h | 9 +-
include/shark/Models/LinearClassifier.h | 27 +
include/shark/Models/LinearModel.h | 6 +-
include/shark/Models/LinearNorm.h | 27 +
include/shark/Models/RecurrentStructure.h | 54 +-
include/shark/Models/SigmoidModel.h | 27 +
include/shark/Models/TiedAutoencoder.h | 12 +-
include/shark/Models/Trees/KDTree.h | 2 +-
include/shark/ObjectiveFunctions/Benchmarks/GSP.h | 27 +
.../Benchmarks/RotatedErrorFunction.h | 3 +-
.../ObjectiveFunctions/Impl/ErrorFunction.inl | 31 +-
.../ObjectiveFunctions/Impl/NoisyErrorFunction.inl | 32 +-
.../Impl/SparseAutoencoderError.inl | 33 +-
.../NegativeGaussianProcessEvidence.h | 3 +-
.../Distributions/MultiNomialDistribution.h | 14 +-
.../Distributions/MultiVariateNormalDistribution.h | 3 +-
.../shark/Statistics/Tests/WilcoxonRankSumTest.h | 27 +
.../Unsupervised/RBM/Impl/AverageEnergyGradient.h | 31 +-
.../RBM/Impl/ConvolutionalEnergyGradient.h | 27 +
include/shark/Unsupervised/RBM/Impl/analytics.h | 4 +-
.../Unsupervised/RBM/Neuronlayers/BinaryLayer.h | 13 +-
.../Unsupervised/RBM/Neuronlayers/BipolarLayer.h | 53 +-
.../Unsupervised/RBM/Neuronlayers/GaussianLayer.h | 7 +-
.../RBM/Neuronlayers/TruncatedExponentialLayer.h | 4 +-
.../Unsupervised/RBM/Problems/BarsAndStripes.h | 27 +
.../shark/Unsupervised/RBM/Problems/DistantModes.h | 27 +
include/shark/Unsupervised/RBM/Problems/MNIST.h | 27 +
include/shark/Unsupervised/RBM/Problems/Shifter.h | 27 +
include/shark/Unsupervised/RBM/RBM.h | 4 +-
src/Algorithms/DirectSearch/CMSA.cpp | 2 +-
src/Algorithms/FisherLDA.cpp | 4 +-
src/Algorithms/GradientDescent/BFGS.cpp | 6 +-
.../GradientDescent/TrustRegionNewton.cpp | 2 +-
src/Algorithms/LinearRegression.cpp | 2 +-
src/Algorithms/PCA.cpp | 11 +-
src/CMakeLists.txt | 8 +-
src/Models/OnlineRNNet.cpp | 20 +-
src/Models/RBFLayer.cpp | 3 +-
src/Models/RNNet.cpp | 11 +-
167 files changed, 4385 insertions(+), 3822 deletions(-)
create mode 100644 .travis.yml
create mode 100644 appveyor.yml
create mode 100644 cBlasCheck.cpp
create mode 100644 debian/patches/Disable-doxygen-generate-tagfile.patch
delete mode 100644 debian/patches/Disable-override-of-CMAKE_BUILD_TYPE.patch
create mode 100644 debian/patches/Disable-privacy-breaching-content.patch
delete mode 100644 debian/patches/Fix-typo-in-tutorials.patch
delete mode 100644 debian/patches/Set-soversion-to-zero.patch
copy doc/{sphinx_pages/static => }/SharkLogo.png (100%)
create mode 100644 doc/frontpage.css
copy doc/{sphinx_pages/rest_sources/about_shark/images => }/lgplv3-147x51.png (100%)
copy doc/{sphinx_pages/static => }/shark16.ico (100%)
create mode 100644 include/shark/LinAlg/BLAS/assignment.hpp
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/cblas_inc.hpp (73%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/dot.hpp (87%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/gemm.hpp (86%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/gemv.hpp (85%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/tpmv.hpp (92%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/trmm.hpp (90%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/trmv.hpp (91%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/trsm.hpp (89%)
rename include/shark/LinAlg/BLAS/kernels/{atlas => cblas}/trsv.hpp (90%)
delete mode 100644 include/shark/LinAlg/BLAS/kernels/gotoblas/cblas_inc.h
delete mode 100644 include/shark/LinAlg/BLAS/kernels/gotoblas/gemm.h
delete mode 100644 include/shark/LinAlg/BLAS/kernels/gotoblas/gemv.h
delete mode 100644 include/shark/LinAlg/BLAS/kernels/gotoblas/syrk.h
delete mode 100644 include/shark/LinAlg/BLAS/kernels/gotoblas/trsm.h
delete mode 100644 include/shark/LinAlg/BLAS/kernels/gotoblas/trsv.h
delete mode 100644 include/shark/Models/Impl/LinearModel.inl
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