Merge upstream

mlpack · Feb 21, 2021 · f36c858 · f36c858
2 parents 733db6a + 9b91a08
commit f36c858
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diff --git a/.appveyor.yml b/.appveyor.yml
@@ -1,17 +1,11 @@
 clone_depth: 10
 
 environment:
-  BOOST_PROG_OPTION : "C:/projects/mlpack/\
-  boost_program_options-vc140.1.60.0.0/lib/native/address-model-64/lib/*.*"
   BOOST_MATH : "C:/projects/mlpack/\
   boost_math_c99-vc140.1.60.0.0/lib/native/address-model-64/lib/*.*"
   BOOST_RANDOM : "C:/projects/mlpack/\
   boost_random-vc140.1.60.0.0/lib/native/address-model-64/lib/*.*"
-  BOOST_SERIALIZATION : "C:/projects/mlpack/\
-  boost_serialization-vc140.1.60.0.0/lib/native/address-model-64/lib/*.*"
-  BOOST_UNIT_TEST : "C:/projects/mlpack/\
-  boost_unit_test_framework-vc140.1.60.0.0/lib/native/address-model-64/lib/*.*"
-  ARMADILLO_DOWNLOAD : "http://ftp.fau.de/macports/distfiles/armadillo/armadillo-8.400.0.tar.xz"
+  ARMADILLO_DOWNLOAD : "https://data.kurg.org/armadillo-8.400.0.tar.xz"
   ARMADILLO_LIBRARY : "C:/projects/mlpack/armadillo-8.400.0/\
   build/Debug/armadillo.lib"
   BLAS_LIBRARY : "%APPVEYOR_BUILD_FOLDER%/OpenBLAS.0.2.14.1/lib/native/lib/x64/\
@@ -22,50 +16,36 @@ environment:
   JENKINS_DOC : "C:/projects/mlpack/dist/win-installer/jenkinsdoc.zip"
   GIT_VERSION_FILE : "C:/projects/mlpack/src/mlpack/core/util/gitversion.hpp"
   matrix:
-    - APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2015
-      VSVER: Visual Studio 14 2015 Win64
-      MSBUILD: C:\Program Files (x86)\MSBuild\14.0\bin\MSBuild.exe
-    - APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
-      VSVER: Visual Studio 15 2017 Win64
-      MSBUILD: C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\MSBuild\15.0\Bin\MSBuild.exe
-# Currently, the VS2019 build seems to always time out.  This seems to be an
-# AppVeyor issue.
-#    - APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
-#      VSVER: Visual Studio 16 2019
-#      MSBUILD: C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\MSBuild\Current\Bin\MSBuild.exe
+    - APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
+      VSVER: Visual Studio 16 2019
+      MSBUILD: C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\MSBuild\Current\Bin\MSBuild.exe
 
+# We have removed the VS studio 15 2017 build since it is not possible to complete
+# or finish the build due to the `compiler out of heap space issues`.
+# Therefore, in the meanwhile, we are only doing the installation for VS 16 2019.
 
 configuration: Release
 
-os: Visual Studio 2015
+os: Visual Studio 2019
 
 install:
   - ps: nuget install boost -o "${env:APPVEYOR_BUILD_FOLDER}" -Version 1.60.0
-  - ps: >
-      nuget install boost_unit_test_framework-vc140
-      -o "${env:APPVEYOR_BUILD_FOLDER}" -Version 1.60.0
-  - ps: >
-      nuget install boost_program_options-vc140
-      -o "${env:APPVEYOR_BUILD_FOLDER}" -Version 1.60.0
   - ps: >
       nuget install boost_random-vc140
       -o "${env:APPVEYOR_BUILD_FOLDER}" -Version 1.60.0
-  - ps: >
-      nuget install boost_serialization-vc140
-      -o "${env:APPVEYOR_BUILD_FOLDER}" -Version 1.60.0
   - ps: >
       nuget install boost_math_c99-vc140
       -o "${env:APPVEYOR_BUILD_FOLDER}" -Version 1.60.0
+  - ps: >
+      nuget install unofficial-flayan-cereal
+      -o "${env:APPVEYOR_BUILD_FOLDER}"
   - ps: nuget install OpenBLAS -o "${env:APPVEYOR_BUILD_FOLDER}"
   - set path=C:\Program Files (x86)\WiX Toolset v3.11\bin;%path%
 
 build_script:
   - mkdir boost_libs
-  - ps: cp ${env:BOOST_PROG_OPTION} C:\projects\mlpack\boost_libs\
   - ps: cp ${env:BOOST_MATH} C:\projects\mlpack\boost_libs\
   - ps: cp ${env:BOOST_RANDOM} C:\projects\mlpack\boost_libs\
-  - ps: cp ${env:BOOST_SERIALIZATION} C:\projects\mlpack\boost_libs\
-  - ps: cp ${env:BOOST_UNIT_TEST} C:\projects\mlpack\boost_libs\
   - echo TEST_ARMA is %ARMADILLO_DOWNLOAD%
   - >
     appveyor DownloadFile %ARMADILLO_DOWNLOAD%
@@ -89,17 +69,20 @@ build_script:
     -DLAPACK_LIBRARIES:FILEPATH=%BLAS_LIBRARY%
     -DARMADILLO_INCLUDE_DIR="C:/projects/mlpack/armadillo-8.400.0/include"
     -DARMADILLO_LIBRARY:FILEPATH=%ARMADILLO_LIBRARY%
+    -DCEREAL_INCLUDE_DIR="C:/projects/mlpack/unofficial-flayan-cereal.1.2.2/build/native/include"
     -DBOOST_INCLUDEDIR:PATH=%BOOST_INCLUDE%
-    -DBOOST_LIBRARYDIR:PATH="C:/projects/mlpack/boost_libs"
     -DDEBUG=OFF
     -DPROFILE=OFF
     -DBUILD_PYTHON_BINDINGS=OFF
+    -DBUILD_GO_BINDINGS=OFF
+    -DBUILD_R_BINDINGS=OFF
+    -DBUILD_TESTS=OFF
     -DCMAKE_BUILD_TYPE=Release ..
   - >
     "%MSBUILD%" "C:\projects\mlpack\build\mlpack.sln"
     /m /verbosity:minimal /nologo /p:BuildInParallel=true
     /p:Configuration=Release;Platform=x64
-  
+
   # Zip Artifacts.
   - >
     7z a mlpack-windows-no-libs.zip
@@ -108,7 +91,7 @@ build_script:
     7z a mlpack-windows.zip
     "%APPVEYOR_BUILD_FOLDER%\build\Release\*.*"
     "%APPVEYOR_BUILD_FOLDER%/OpenBLAS.0.2.14.1/lib/native/lib/x64/*.*"
-  
+
   # Pulling documentation for the installer.
   - ps: >
       try{(new-object net.webclient).DownloadFile(${env:JENKINS_DOC_DOWNLOAD},
@@ -119,7 +102,7 @@ build_script:
       [System.IO.Compression.ZipFile]::ExtractToDirectory(${env:JENKINS_DOC},
       'C:\projects\mlpack\dist\win-installer\staging\doc')}
       catch{Write-Output "Unable to add doc to installer, skipping!"}
-  
+
   # Preparing installer staging.
   - cd C:\projects\mlpack\dist\win-installer\staging && mkdir lib
   - ps: >
@@ -137,9 +120,6 @@ build_script:
   - ps: >
       cp C:\projects\mlpack\OpenBLAS.0.2.14.1\lib\native\bin\x64\*.dll
       C:\projects\mlpack\dist\win-installer\staging\
-  - ps: >
-      cp C:\projects\mlpack\boost_libs\boost_unit_test_framework-vc*.dll
-      C:\projects\mlpack\dist\win-installer\staging\
   - ps: >
       cp C:\projects\mlpack\build\include\mlpack
       C:\projects\mlpack\dist\win-installer\staging -recurse
@@ -149,7 +129,7 @@ build_script:
   - ps: >
       cp C:\projects\mlpack\src\mlpack\tests\data\german.csv
       C:\projects\mlpack\dist\win-installer\staging\examples\sample-ml-app\sample-ml-app\data\
-  
+
   # Checking current gitversion or mlpack version.
   - ps: >
       $ver = (Get-Content
@@ -221,7 +201,7 @@ build_script:
 artifacts:
   - path: 'build\*.zip'
     name: mlpack-windows-zip
-  
+
   - path: 'dist\win-installer\mlpack-win-installer\bin\x64\Release\*.msi'
     name: mlpack-windows-installer
 
@@ -237,20 +217,3 @@ cache:
   - packages -> **\packages.config
   - armadillo.tar.xz -> appveyor.yaml
 
-test_script:
-  # Copy all DLLs into the right place before running the test.
-  - ps: cp C:\projects\mlpack\boost_libs\*.* C:\projects\mlpack\build\
-  - ps: >
-      cp C:\projects\mlpack\OpenBLAS.0.2.14.1\lib\native\bin\x64\*.*
-      C:\projects\mlpack\build\
-  - cd "%APPVEYOR_BUILD_FOLDER%/build/"
-  - >
-    Release\mlpack_test.exe
-    --report_level=detailed
-    --log_level=test_suite --log_format=XML > mlpack_test.xml & exit 0
-  # Attempt to upload results to AppVeyor.
-  - ps: >
-      $wc = New-Object 'System.Net.WebClient';
-      $wc.UploadFile(
-      "https://ci.appveyor.com/api/testresults/xunit/$($env:APPVEYOR_JOB_ID)",
-      (Resolve-Path .\mlpack_test.xml));
diff --git a/.ci/ci.yaml b/.ci/ci.yaml
@@ -15,63 +15,49 @@ jobs:
   strategy:
     matrix:
       Plain:
-        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF'
-        python.version: '2.7'
-      Python27:
-        python.version: '2.7'
-        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DPYTHON_EXECUTABLE=/usr/bin/python'
-      Python37:
+        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
+      Python:
+        binding: 'python'
         python.version: '3.7'
-        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DPYTHON_EXECUTABLE=/usr/bin/python3'
+        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 -DBUILD_GO_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
       Julia:
-        python.version: '2.7'
         julia.version: '1.3.0'
-        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=ON -DJULIA_EXECUTABLE=/opt/julia-1.3.0/bin/julia'
+        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=ON -DBUILD_GO_BINDINGS=OFF -DJULIA_EXECUTABLE=/opt/julia-1.3.0/bin/julia -DBUILD_R_BINDINGS=OFF'
+      Go:
+        binding: 'go'
+        go.version: '1.11.0'
+        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=ON -DBUILD_R_BINDINGS=OFF'
       Markdown:
-        python.version: '2.7'
-        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_MARKDOWN_BINDINGS=ON -DBUILD_PYTHON_BINDINGS=OFF'
+        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_MARKDOWN_BINDINGS=ON -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
 
   steps:
   - template: linux-steps.yaml
 
 - job: macOS
   timeoutInMinutes: 360
   pool:
-    vmImage: macOS-10.14
+    vmImage: macOS-latest
   strategy:
     matrix:
       Plain:
-        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF'
+        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
         python.version: '2.7'
-      Python37:
+      Python:
+        binding: 'python'
         python.version: '3.7'
-        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF'
+        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=ON -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
       Julia:
         python.version: '2.7'
         julia.version: '1.3.0'
-        CMakeArgs: '-DDEBUG=OFF -DPROFILE=OFF -DBUILD_JULIA_BINDINGS=ON -DBUILD_PYTHON_BINDINGS=OFF'
-
-  steps:
-  - template: macos-steps.yaml
-
-- job: WindowsVS15
-  timeoutInMinutes: 360
-  displayName: Windows VS15
-  pool:
-    vmImage: vs2017-win2016
-  strategy:
-    matrix:
-      Plain:
-        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF'
+        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_JULIA_BINDINGS=ON -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
+      Go:
+        binding: 'go'
         python.version: '2.7'
-        CMakeGenerator: '-G "Visual Studio 15 2017 Win64"'
-        MSBuildVersion: '15.0'
-        ArchiveNoLibs: 'mlpack-windows-vs15-no-libs.zip'
-        ArchiveLibs: 'mlpack-windows-vs15.zip'
-        ArchiveTests: 'mlpack_test-vs15.xml'
+        go.version: '1.11.0'
+        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=ON -DBUILD_R_BINDINGS=OFF'
 
   steps:
-  - template: windows-steps.yaml
+  - template: macos-steps.yaml
 
 - job: WindowsVS16
   timeoutInMinutes: 360
@@ -81,7 +67,7 @@ jobs:
   strategy:
     matrix:
       Plain:
-        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF'
+        CMakeArgs: '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF'
         python.version: '2.7'
         CMakeGenerator: '-G "Visual Studio 16 2019"'
         MSBuildVersion: '16.0'

diff --git a/.ci/linux-steps.yaml b/.ci/linux-steps.yaml
@@ -7,7 +7,7 @@ steps:
 # Set python version
 - task: UsePythonVersion@0
   inputs:
-    versionSpec: '$(python.version)'
+    versionSpec: '3.7'
 
 # Install build dependencies
 - script: |
@@ -21,41 +21,48 @@ steps:
     unset BOOST_ROOT
     echo "##vso[task.setvariable variable=BOOST_ROOT]"$BOOST_ROOT
 
-    sudo apt-get install -y --allow-unauthenticated libopenblas-dev liblapack-dev g++ libboost1.70-dev libarmadillo-dev xz-utils
+    sudo apt-get install -y --allow-unauthenticated libopenblas-dev g++ libboost1.70-dev xz-utils
 
-    if [ '$(python.version)' == '2.7' ]; then
-      sudo apt-get install -y --allow-unauthenticated python-pip cython python-numpy python-pandas
-      sudo pip install --upgrade --ignore-installed setuptools cython
-      sudo pip install "zipp<3.1"
+    if [ "$(binding)" == "python" ]; then
+      export PYBIN=$(which python)
+      $PYBIN -m pip install --upgrade pip
+      $PYBIN -m pip install --upgrade --ignore-installed setuptools cython pandas
     fi
 
-    if [ '$(python.version)' == '3.7' ]; then
-      sudo apt-get install -y --allow-unauthenticated python3-pip cython3 python3-numpy
-      sudo pip3 install --upgrade --ignore-installed setuptools cython pandas
-    fi
-
-    if [ 'a$(julia.version)' != 'a' ]; then
+    if [ "a$(julia.version)" != "a" ]; then
       wget https://julialang-s3.julialang.org/bin/linux/x64/1.3/julia-1.3.0-linux-x86_64.tar.gz
       sudo tar -C /opt/ -xvpf julia-1.3.0-linux-x86_64.tar.gz
     fi
 
     # Install armadillo.
-    curl https://ftp.fau.de/macports/distfiles/armadillo/armadillo-8.400.0.tar.xz | tar -xvJ && cd armadillo*
+    curl https://data.kurg.org/armadillo-8.400.0.tar.xz | tar -xvJ && cd armadillo*
     cmake . && make && sudo make install && cd ..
+
+    # Install cereal.
+    wget https://github.com/USCiLab/cereal/archive/v1.3.0.tar.gz
+    tar -xvzpf v1.3.0.tar.gz # Unpack into cereal-1.3.0/.
+    cd cereal-1.3.0/
   displayName: 'Install Build Dependencies'
 
 # Configure mlpack (CMake)
-- script: unset BOOST_ROOT && mkdir build && cd build && cmake $(CMakeArgs) ..
+- script: |
+    unset BOOST_ROOT
+    mkdir build && cd build
+    if [ "$(binding)" == "go" ]; then
+      export GOPATH=$PWD/src/mlpack/bindings/go
+      go get -u -t gonum.org/v1/gonum/...
+    fi
+    cmake $(CMakeArgs) -DPYTHON_EXECUTABLE=`which python` -DCEREAL_INCLUDE_DIR=../cereal-1.3.0/include/ ..
   displayName: 'CMake'
 
 # Build mlpack
 - script: cd build && make
-  condition: eq(variables['CMakeArgs'], '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF')
+  condition: eq(variables['CMakeArgs'], '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF')
   displayName: 'Build'
 
 # Build mlpack
 - script: cd build && make -j2
-  condition: ne(variables['CMakeArgs'], '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF')
+  condition: ne(variables['CMakeArgs'], '-DDEBUG=ON -DPROFILE=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=OFF')
   displayName: 'Build'
 
 # Run tests via ctest.

diff --git a/.ci/macos-steps.yaml b/.ci/macos-steps.yaml
@@ -12,13 +12,17 @@ steps:
 # Install Build Dependencies
 - script: |
     set -e
-    sudo xcode-select --switch /Applications/Xcode_10.1.app/Contents/Developer
+    sudo xcode-select --switch /Applications/Xcode_12.2.app/Contents/Developer
     unset BOOST_ROOT
-    pip install cython numpy pandas zipp configparser
-    brew install openblas armadillo boost
+    brew install openblas armadillo boost cereal
+
+    if [ "$(binding)" == "python" ]; then
+      pip install --upgrade pip
+      pip install cython numpy pandas zipp configparser
+    fi
 
     if [ "a$(julia.version)" != "a" ]; then
-      brew cask install julia
+      brew install --cask julia
     fi
 
     git clone --depth 1 https://github.com/mlpack/jenkins-conf.git conf
@@ -28,8 +32,16 @@ steps:
 - script: |
     unset BOOST_ROOT
     mkdir build && cd build
-    export PYPATH=$(which python)
-    cmake $(CMakeArgs) -DPYTHON_EXECUTABLE=$PYPATH ..
+    if [ "$(binding)" == "go" ]; then
+      export GOPATH=$PWD/src/mlpack/bindings/go
+      go get -u -t gonum.org/v1/gonum/...
+    fi
+    if [ "$(binding)" == "python" ]; then
+      export PYPATH=$(which python)
+      cmake $(CMakeArgs) -DPYTHON_EXECUTABLE=$PYPATH ..
+    else
+      cmake $(CMakeArgs) ..
+    fi
   displayName: 'CMake'
 
 # Build mlpack