Merge branch 'master' into cereal

Signed-off-by: Omar Shrit <omar@shrit.me>

CMake/FindGo.cmake

@@ -14,9 +14,9 @@ if (GO_EXECUTABLE)
        RESULT_VARIABLE RESULT
   )
   if (RESULT EQUAL 0)
-    string(REGEX REPLACE ".*([0-9]+\\.[0-9]+\\.[0-9]+).*" "\\1"
+    string(REGEX REPLACE ".*([0-9]+\\.[0-9]+\(\\.[0-9]+\)?).*" "\\1"
         GO_VERSION_STRING ${GO_VERSION_STRING})
-    endif()
+  endif()
 endif()
 
 include(FindPackageHandleStandardArgs)

COPYRIGHT.txt

@@ -132,6 +132,7 @@ Copyright:
   Copyright 2020, Lakshya Ojha <ojhalakshya@gmail.com>
   Copyright 2020, Bisakh Mondal <bisakhmondal00@gmail.com>
   Copyright 2020, Benson Muite <benson_muite@emailplus.org>
+  Copyright 2020, Sarthak Bhardwaj <7sarthakbhardwaj@gmail.com>   
 
 License: BSD-3-clause
   All rights reserved.

doc/guide/build.hpp

@@ -100,8 +100,8 @@ installed through apt:
 
 @code
 # apt-get install libboost-math-dev libboost-test-dev libcereal-dev
-  libarmadillo-dev binutils-dev python-pandas python-numpy cython
-  python-setuptools
+  libarmadillo-dev binutils-dev python3-pandas python3-numpy cython3
+  python3-setuptools
 @endcode
 
 If you are using Ubuntu 19.10 or newer, you can also install @c libensmallen-dev
@@ -123,7 +123,7 @@ On Fedora, Red Hat, or CentOS, these same dependencies can be obtained via dnf:
 
 @code
 # dnf install boost-devel boost-test boost-math armadillo-devel binutils-devel 
-  python2-Cython python2-setuptools python2-numpy python2-pandas ensmallen-devel 
+  python3-Cython python3-setuptools python3-numpy python3-pandas ensmallen-devel 
   stbi-devel cereal-devel
 @endcode
 

src/mlpack/CMakeLists.txt

@@ -125,68 +125,9 @@ string(REGEX REPLACE ".*#define MLPACK_VERSION_PATCH [\"]?([0-9x]+)[\"]?.*"
 set(PACKAGE_VERSION
   "${MLPACK_VERSION_MAJOR}.${MLPACK_VERSION_MINOR}.${MLPACK_VERSION_PATCH}")
 
-# If we are building Python bindings, we have to configure setup.py but only
-# after we've recursed into methods/.
-if (BUILDING_PYTHON_BINDINGS)
-
-  get_property(CYTHON_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-      PROPERTY INCLUDE_DIRECTORIES)
-  add_custom_target(python_configure
-      COMMAND ${CMAKE_COMMAND}
-          -D SETUP_PY_IN=${CMAKE_SOURCE_DIR}/src/mlpack/bindings/python/setup.py.in
-          -D SETUP_PY_OUT=${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/setup.py
-          -D PACKAGE_VERSION="${PACKAGE_VERSION}"
-          -D Boost_SERIALIZATION_LIBRARY="${Boost_SERIALIZATION_LIBRARY_RELEASE}"
-          -D Boost_LIBRARY_DIRS="${Boost_LIBRARY_DIRS}"
-          -D ARMADILLO_LIBRARIES="${ARMADILLO_LIBRARIES}"
-          -D MLPACK_LIBRARY=$<TARGET_LINKER_FILE:mlpack>
-          -D MLPACK_LIBDIR=$<TARGET_LINKER_FILE_DIR:mlpack>
-          -D MLPACK_PYXS="${MLPACK_PYXS}"
-          -D OpenMP_CXX_FLAGS="${OpenMP_CXX_FLAGS}"
-          -D DISABLE_CFLAGS="${DISABLE_CFLAGS}"
-          -D CYTHON_INCLUDE_DIRECTORIES="${CYTHON_INCLUDE_DIRECTORIES}"
-          -D CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}
-          -D OUTPUT_DIR=${CMAKE_BINARY_DIR}
-          -P "${CMAKE_SOURCE_DIR}/src/mlpack/bindings/python/ConfigureSetup.cmake"
-      BYPRODUCTS "${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/setup.py"
-      COMMENT "Configuring setup.py...")
-  add_dependencies(python_configure python_copy)
-  add_dependencies(python_configured python_configure)
-
-  # Append the package version to __init__.py after all the imports are loaded.
-  file(APPEND ${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/mlpack/__init__.py
-  "__version__='${PACKAGE_VERSION}'\n")
-endif ()
-
-# If we are building Julia bindings, we have to end the 'module' declaration in
-# mlpack.jl
-if (BUILD_JULIA_BINDINGS)
-  file(APPEND
-      "${CMAKE_BINARY_DIR}/src/mlpack/bindings/julia/mlpack/src/mlpack.jl"
-      "\nend\ninclude(\"functions.jl\")\ninclude(\"serialization.jl\")\nend\n")
-endif ()
-
-# If we are building Go bindings, we have to end the 'module' declaration in
-# models.go
-if (BUILD_GO_BINDINGS)
-  file(APPEND
-      "${CMAKE_BINARY_DIR}/src/mlpack/bindings/go/src/mlpack.org/v1/mlpack/models.go"
-      "*/\n"
-      "import \"C\"\n\n"
-      "import (\n"
-      "  \"runtime\"\n"
-      "  \"unsafe\"\n"
-      ")\n\n")
-
-  include("${CMAKE_SOURCE_DIR}/CMake/go/AppendModel.cmake")
-  # Read list content.
-  get_property(MODELS GLOBAL PROPERTY GO_MODELS)
-  foreach (models IN LISTS MODELS)
-    append_model(
-        "${CMAKE_BINARY_DIR}/src/mlpack/bindings/go/src/mlpack.org/v1/mlpack/models.go"
-         ${models})
-  endforeach()
-endif()
+post_python_bindings()
+post_julia_setup()
+post_go_setup()
 
 # If we are building R-bindings, we have to run some setup after we
 # recurse into methods/.  If not, this macro is empty.

src/mlpack/bindings/cli/third_party/CLI/CLI11.hpp

@@ -691,7 +691,7 @@ class CallForVersion : public Success {
         : CallForVersion("This should be caught in your main function, see examples", ExitCodes::Success) {}
 };
 
-/// Does not output a diagnostic in CLI11_PARSE, but allows to return from main() with a specific error code.
+/// Does not output a diagnostic in CLI11_PARSE, but allows main() to return with a specific error code.
 class RuntimeError : public ParseError {
     CLI11_ERROR_DEF(ParseError, RuntimeError)
     explicit RuntimeError(int exit_code = 1) : RuntimeError("Runtime error", exit_code) {}

src/mlpack/bindings/go/CMakeLists.txt

@@ -9,6 +9,29 @@ macro (not_found_return message)
   endif()
 endmacro ()
 
+macro (post_go_setup)
+  if (BUILD_GO_BINDINGS)
+    # Once `GO_MODELS` is populated, generate `models.go`.
+    file(APPEND
+        "${CMAKE_BINARY_DIR}/src/mlpack/bindings/go/src/mlpack.org/v1/mlpack/models.go"
+        "*/\n"
+        "import \"C\"\n\n"
+        "import (\n"
+        "  \"runtime\"\n"
+        "  \"unsafe\"\n"
+        ")\n\n")
+
+    include("${CMAKE_SOURCE_DIR}/CMake/go/AppendModel.cmake")
+    # Read list content.
+    get_property(MODELS GLOBAL PROPERTY GO_MODELS)
+    foreach (models IN LISTS MODELS)
+      append_model(
+        "${CMAKE_BINARY_DIR}/src/mlpack/bindings/go/src/mlpack.org/v1/mlpack/models.go"
+         ${models})
+    endforeach()
+  endif()
+endmacro ()
+
 # If we are not supposed to make Go bindings, define the macro so it does
 # nothing and leave this file.
 if (NOT BUILD_GO_BINDINGS)
@@ -176,7 +199,7 @@ set_property(GLOBAL PROPERTY GO_MODELS "")
 macro (add_go_binding name)
 if (BUILD_GO_BINDINGS)
 
-  # Include all .h that define model to models.go. 
+  # Include all .h that define model to models.go.
   file(READ "${CMAKE_CURRENT_SOURCE_DIR}/${name}_main.cpp" MAIN_FILE)
   if (MAIN_FILE MATCHES "PARAM_MODEL")
     file(APPEND

src/mlpack/bindings/julia/CMakeLists.txt

@@ -7,6 +7,16 @@ macro (not_found_return message)
   return()
 endmacro ()
 
+macro (post_julia_setup)
+  # If we are building Julia bindings, we have to end the 'module' declaration in
+  # mlpack.jl.
+  if (BUILD_JULIA_BINDINGS)
+    file(APPEND
+        "${CMAKE_BINARY_DIR}/src/mlpack/bindings/julia/mlpack/src/mlpack.jl"
+        "\nend\ninclude(\"functions.jl\")\ninclude(\"serialization.jl\")\nend\n")
+  endif ()
+endmacro ()
+
 # If we are not supposed to make Julia bindings, define the macro so it does
 # nothing and leave this file.
 if (NOT BUILD_JULIA_BINDINGS)

src/mlpack/bindings/python/CMakeLists.txt

@@ -7,6 +7,40 @@ macro (not_found_return message)
   return()
 endmacro ()
 
+macro (post_python_bindings)
+  # If we are building Python bindings, we have to configure setup.py but only
+  # after we've recursed into methods/.
+  if (BUILDING_PYTHON_BINDINGS)
+    get_property(CYTHON_INCLUDE_DIRECTORIES DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        PROPERTY INCLUDE_DIRECTORIES)
+    add_custom_target(python_configure
+        COMMAND ${CMAKE_COMMAND}
+            -D SETUP_PY_IN=${CMAKE_SOURCE_DIR}/src/mlpack/bindings/python/setup.py.in
+            -D SETUP_PY_OUT=${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/setup.py
+            -D PACKAGE_VERSION="${PACKAGE_VERSION}"
+            -D Boost_SERIALIZATION_LIBRARY="${Boost_SERIALIZATION_LIBRARY_RELEASE}"
+            -D Boost_LIBRARY_DIRS="${Boost_LIBRARY_DIRS}"
+            -D ARMADILLO_LIBRARIES="${ARMADILLO_LIBRARIES}"
+            -D MLPACK_LIBRARY=$<TARGET_LINKER_FILE:mlpack>
+            -D MLPACK_LIBDIR=$<TARGET_LINKER_FILE_DIR:mlpack>
+            -D MLPACK_PYXS="${MLPACK_PYXS}"
+            -D OpenMP_CXX_FLAGS="${OpenMP_CXX_FLAGS}"
+            -D DISABLE_CFLAGS="${DISABLE_CFLAGS}"
+            -D CYTHON_INCLUDE_DIRECTORIES="${CYTHON_INCLUDE_DIRECTORIES}"
+            -D CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}
+            -D OUTPUT_DIR=${CMAKE_BINARY_DIR}
+            -P "${CMAKE_SOURCE_DIR}/src/mlpack/bindings/python/ConfigureSetup.cmake"
+        BYPRODUCTS "${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/setup.py"
+        COMMENT "Configuring setup.py...")
+    add_dependencies(python_configure python_copy)
+    add_dependencies(python_configured python_configure)
+
+    # Append the package version to __init__.py after all the imports are loaded.
+    file(APPEND ${CMAKE_BINARY_DIR}/src/mlpack/bindings/python/mlpack/__init__.py
+    "__version__='${PACKAGE_VERSION}'\n")
+  endif ()
+endmacro ()
+
 # If we are not supposed to make Python bindings, define the macro so it does
 # nothing and leave this file.
 if (NOT BUILD_PYTHON_BINDINGS)

src/mlpack/core/cv/cv_base_impl.hpp

@@ -23,10 +23,12 @@ CVBase<MLAlgorithm,
        MatType,
        PredictionsType,
        WeightsType>::CVBase() :
-    isDatasetInfoPassed(false)
+    isDatasetInfoPassed(false),
+    numClasses(0)
 {
   static_assert(!MIE::TakesNumClasses,
-      "The given MLAlgorithm requires the numClasses parameter");
+      "The given MLAlgorithm requires the numClasses parameter; "
+      "make sure that you pass numClasses with type size_t!");
 }
 
 template<typename MLAlgorithm,

src/mlpack/methods/bayesian_linear_regression/bayesian_linear_regression_main.cpp

@@ -86,8 +86,8 @@ BINDING_EXAMPLE(
                "predictions", "test_predictions") +
     "\n\n"
     "Because the estimator computes a predictive distribution instead of "
-    "simple point estimate, the " + PRINT_PARAM_STRING("stds") + " parameter "
-    "allows to save the prediction uncertainties: "
+    "a simple point estimate, the " + PRINT_PARAM_STRING("stds") + " parameter "
+    "allows one to save the prediction uncertainties: "
     "\n\n" +
     PRINT_CALL("bayesian_linear_regression", "input_model",
                "blr_model", "test", "test",