Merge branch 'release/6.1.0'

Author: vigsterkr

.clang-format

@@ -0,0 +1,44 @@
+#
+# Shogun clang-format configuration file
+#
+Language:        Cpp
+AccessModifierOffset: -4
+AlignAfterOpenBracket: AlwaysBreak
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterClass:      true
+  AfterControlStatement: true
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  true
+  AfterObjCDeclaration: false
+  AfterStruct:     true
+  AfterUnion:      true
+  BeforeCatch:     true
+  BeforeElse:      true
+  IndentBraces:    false
+ColumnLimit: 80
+ContinuationIndentWidth: 4
+IndentWidth: 4
+NamespaceIndentation: All
+PenaltyBreakComment: 10000
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 10000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+ReflowComments: true
+SortIncludes:    true
+Standard:        Cpp11
+TabWidth:        4
+UseTab:          ForIndentation

.gitignore

@@ -52,53 +52,6 @@ cpplint.py
 /src/configure-*-*.c*
 /src/build-local
 
-# modular interfaces
-/src/interfaces/*_modular/*.doxy
-/src/interfaces/*_modular/Evaluation.i
-/src/interfaces/*_modular/Regression.i
-/src/interfaces/*_modular/Library.i
-/src/interfaces/*_modular/Distribution.i
-/src/interfaces/*_modular/Structure.i
-/src/interfaces/*_modular/Classifier.i
-/src/interfaces/*_modular/Features.i
-/src/interfaces/*_modular/Kernel.i
-/src/interfaces/*_modular/Preprocessor.i
-/src/interfaces/*_modular/Distance.i
-/src/interfaces/*_modular/Clustering.i
-/src/interfaces/*_modular/SGBase.i
-/src/interfaces/*_modular/IO.i
-/src/interfaces/*_modular/Mathematics.i
-/src/interfaces/*_modular/ModelSelection.i
-/src/interfaces/*_modular/modshogun.i
-/src/interfaces/*_modular/modshogun_ignores.i
-/src/interfaces/*_modular/*_includes.i
-/src/interfaces/*_modular/Makefile
-/src/interfaces/*_modular/Converter.i
-/src/interfaces/*_modular/Multiclass.i
-/src/interfaces/*_modular/Machine.i
-/src/interfaces/*_modular/Transfer.i
-/src/interfaces/*_modular/Loss.i
-/src/interfaces/*_modular/Statistics.i
-/src/interfaces/*_modular/Latent.i
-/src/interfaces/*_modular/GaussianProcess.i
-
-# particular modular ones
-/src/interfaces/csharp_modular/*.cs
-/src/interfaces/csharp_modular/abstract_types_extension.i
-/src/interfaces/csharp_modular/modshogun.dll
-/src/interfaces/java_modular/*.java
-/src/interfaces/java_modular/*.jar
-/src/interfaces/java_modular/*.class
-/src/interfaces/java_modular/org/*
-/src/interfaces/java_modular/shogun/*
-/src/interfaces/python_modular/*.py
-/src/interfaces/python_modular/abstract_types_extension.i
-/src/interfaces/r_modular/*.R
-/src/interfaces/r_modular/*.RData
-/src/interfaces/perl_modular/*.pm
-/src/interfaces/octave_modular/abstract_types_extension.i
-/.duped_py_pl.pb
-
 # /examples/
 *.log
 *.exe
@@ -108,9 +61,9 @@ cpplint.py
 !/examples/undocumented/libshogun/*.cpp
 !/examples/undocumented/libshogun/CMakeLists.txt
 !/examples/undocumented/libshogun/tools/
-!examples/undocumented/python_modular/graphical/
-!examples/undocumented/python_modular/*.py
-!examples/undocumented/python_modular/CMakeLists.txt
+!examples/undocumented/python/graphical/
+!examples/undocumented/python/*.py
+!examples/undocumented/python/CMakeLists.txt
 
 # /tests
 /tests/unit/shogun-unit-test
@@ -120,12 +73,8 @@ cpplint.py
 /tests/unit/*.json
 /tests/unit/combined_kernel.weights
 Testing/
-examples/undocumented/python_modular/serialized_svm.bz2
-examples/undocumented/python_modular/tmp/blaah.asc
-examples/undocumented/python_modular/tmp/blaah.h5
-examples/undocumented/python_modular/tmp/blaah.json
-examples/undocumented/python_modular/tmp/blaah.xml
-examples/undocumented/python_modular/vw_cache.dat.cache
+examples/undocumented/python/serialized_svm.bz2
+examples/undocumented/python/vw_cache.dat.cache
 
 # cmake
 /CMakeFiles/
@@ -262,6 +211,7 @@ local.properties
 
 # CDT-specific (C/C++ Development Tooling)
 .cproject
+.idea
 
 # JDT-specific (Eclipse Java Development Tools)
 .classpath

.gitmodules

@@ -5,3 +5,6 @@
 [submodule "debian"]
 	path = debian
 	url = git://github.com/shogun-toolbox/shogun-debian.git
+[submodule "gpl"]
+	path = src/gpl
+	url = git://github.com/shogun-toolbox/shogun-gpl.git

.travis.yml

@@ -1,5 +1,6 @@
 sudo: required
 language: cpp
+cache: ccache
 notifications:
   email: false
   irc:
@@ -16,63 +17,74 @@ matrix:
       services: docker
     - compiler: clang
       services: docker
+    - compiler: gcc
+      services: docker
+      env:
+        - CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE=Debug -DENABLE_COVERAGE=ON -DENABLE_CCACHE=OFF"
+        - CODE_COVERAGE=1
     - compiler: clang
       services: docker
-      python: "2.7_with_system_site_packages"
-      language: python
       env:
-        - CMAKE_OPTIONS="-DPythonModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - CMAKE_OPTIONS="-DINTERFACE_PYTHON=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
         - CC=clang
         - CXX=clang++
     - compiler: clang
       services: docker
-      language: ruby
       env:
-        - CMAKE_OPTIONS="-DRubyModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - CMAKE_OPTIONS="-DINTERFACE_RUBY=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
         - CC=clang
         - CXX=clang++
     - compiler: clang
       services: docker
-      language: java
       env:
-        - CMAKE_OPTIONS="-DJavaModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - CMAKE_OPTIONS="-DINTERFACE_JAVA=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
         - CC=clang
         - CXX=clang++
     - compiler: clang
       services: docker
       env:
-        - CMAKE_OPTIONS="-DCSharpModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - CMAKE_OPTIONS="-DINTERFACE_CSHARP=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
         - CC=clang
         - CXX=clang++
     - compiler: clang
       services: docker
       env:
-        - CMAKE_OPTIONS="-DLuaModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - CMAKE_OPTIONS="-DINTERFACE_LUA=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
         - CC=clang
         - CXX=clang++
     - compiler: gcc
       services: docker
       env:
-        - CMAKE_OPTIONS="-DOctaveModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
-    - compiler: clang
-      services: docker
-      env:
-        - CMAKE_OPTIONS="-DRModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
-        - CC=clang
-        - CXX=clang++
+        - CMAKE_OPTIONS="-DINTERFACE_OCTAVE=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - INTERFACE_OCTAVE=true
     - compiler: clang
       services: docker
       env:
-        - CMAKE_OPTIONS="-DScalaModular=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+        - CMAKE_OPTIONS="-DINTERFACE_R=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
         - CC=clang
         - CXX=clang++
+#    - compiler: clang
+#      services: docker
+#      env:
+#        - CMAKE_OPTIONS="-DScala=ON -DTRAVIS_DISABLE_UNIT_TESTS=ON -DTRAVIS_DISABLE_LIBSHOGUN_TESTS=ON"
+#        - CC=clang
+#        - CXX=clang++
 before_install:
   - docker pull shogun/shogun-dev
-  - echo $CC; echo $CXX
-  - docker run -t -d -P -e "JAVA_HOME=/usr/lib/jvm/java-8-oracle" -e "CC=$CC" -e "CXX=$CXX" --name devenv -v $PWD:/opt/shogun shogun/shogun-dev /bin/sh -c "mkdir /opt/shogun/build;bash"
+  - perl -pe 's/\$(\w+)/$ENV{$1}/g' configs/shogun-sdk/travis.env.in > travis.env
+  - docker run -t -d -P --env-file travis.env --name devenv -v $HOME/.ccache:/root/.ccache -v $PWD:/opt/shogun shogun/shogun-dev /bin/sh -c "mkdir /opt/shogun/build;bash"
 before_script:
   - docker exec -t devenv /bin/sh -c "cd /opt/shogun/build; cmake -DCMAKE_INSTALL_PREFIX=$HOME/shogun-build -DENABLE_TESTING=ON $CMAKE_OPTIONS .."
 script:
+  - |
+    if [ $CC == "gcc" ] && [ -z ${INTERFACE_OCTAVE} ]; then
+      docker exec -t devenv /bin/sh -c "cd /opt/shogun/;  if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then ./scripts/check_format.sh "$TRAVIS_PULL_REQUEST_BRANCH" "$TRAVIS_BRANCH"; fi"
+    fi
   - docker exec -t devenv /bin/sh -c "cd /opt/shogun/build; make -j2"
   - docker exec -t devenv /bin/sh -c "cd /opt/shogun/build; make install"
   - docker exec -t devenv /bin/sh -c "cd /opt/shogun/build; ctest --output-on-failure -j 2"
+after_success:
+  - |
+    if [ $CODE_COVERAGE ] ; then
+      docker exec -t devenv /bin/sh -c "cd /opt/shogun/build; lcov --directory src/shogun/ --capture --output-file all_coverage.info; lcov --remove all_coverage.info '/usr/*' > coverage.info; rm all_coverage.info; codecov -X gcov"
+    fi