migrate from Appveyor to GitHub Actions (#338)

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RGF-team · Mar 6, 2021 · ab328a0 · ab328a0
1 parent cd99ce8
commit ab328a0
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Showing 7 changed files with 152 additions and 189 deletions.
diff --git a/.appveyor.yml b/.appveyor.yml
diff --git a/.ci/.R.appveyor.ps1 b/.ci/.R.appveyor.ps1
diff --git a/.ci/python_tests_windows.ps1 b/.ci/python_tests_windows.ps1
@@ -0,0 +1,25 @@
+function Check-Output {
+ param( [bool]$Success )
+ if (!$Success) {
+ $host.SetShouldExit(-1)
+ Exit -1
+ }
+}
+
+
+$ProgressPreference = "SilentlyContinue" # progress bar bug extremely slows down download speed
+$InstallerName = "$env:GITHUB_WORKSPACE\Miniconda3-latest-Windows-x86_64.exe"
+Invoke-WebRequest -Uri "https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe" -OutFile $InstallerName
+Start-Process -FilePath $InstallerName -ArgumentList "/InstallationType=JustMe /RegisterPython=0 /S /D=$env:CONDA_PATH" -Wait
+conda init powershell
+Invoke-Expression -Command "$env:USERPROFILE\Documents\WindowsPowerShell\profile.ps1"
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+conda create -q -n $env:CONDA_ENV python=$env:PYTHON_VERSION joblib numpy scikit-learn scipy pandas pytest
+conda activate $env:CONDA_ENV
+cd $env:GITHUB_WORKSPACE\python-package
+python setup.py sdist --formats gztar ; Check-Output $?
+pip install dist\rgf_python-$env:RGF_VER.tar.gz -v ; Check-Output $?
+if ($env:TASK -ne "R_PACKAGE") {
+ pytest tests -v ; Check-Output $?
+}
diff --git a/.ci/r_tests_windows.ps1 b/.ci/r_tests_windows.ps1
@@ -0,0 +1,78 @@
+function Check-Output {
+ param( [bool]$Success )
+ if (!$Success) {
+ $host.SetShouldExit(-1)
+ Exit -1
+ }
+}
+
+
+conda activate $env:CONDA_ENV
+
+tzutil /s "GMT Standard Time"
+
+$env:R_LIB_PATH = "$env:USERPROFILE\R"
+$env:CTAN_PACKAGE_ARCHIVE = "https://ctan.math.illinois.edu/systems/win32/miktex/tm/packages/"
+$env:PATH += ";$env:R_LIB_PATH\Rtools\usr\bin" + ";$env:R_LIB_PATH\Rtools\mingw64\bin" + ";$env:R_LIB_PATH\R\bin\x64" + ";$env:R_LIB_PATH\miktex\texmfs\install\miktex\bin\x64"
+cd $env:GITHUB_WORKSPACE
+
+[Void][System.IO.Directory]::CreateDirectory($env:R_LIB_PATH)
+Remove-Item C:\rtools40 -Force -Recurse -ErrorAction Ignore
+
+# ignore R CMD CHECK NOTE checking how long it has
+# been since the last submission
+$env:_R_CHECK_CRAN_INCOMING_ = 0
+$env:_R_CHECK_CRAN_INCOMING_REMOTE_ = 0
+
+$R_VER = "4.0.3"
+$ProgressPreference = "SilentlyContinue" # progress bar bug extremely slows down download speed
+Invoke-WebRequest -Uri https://cloud.r-project.org/bin/windows/base/old/$R_VER/R-$R_VER-win.exe -OutFile R-win.exe
+Start-Process -FilePath R-win.exe -NoNewWindow -Wait -ArgumentList "/VERYSILENT /DIR=$env:R_LIB_PATH\R /COMPONENTS=main,x64" ; Check-Output $?
+
+Invoke-WebRequest -Uri https://cran.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe -OutFile Rtools.exe
+Start-Process -FilePath Rtools.exe -NoNewWindow -Wait -ArgumentList "/VERYSILENT /SUPPRESSMSGBOXES /DIR=$env:R_LIB_PATH\Rtools" ; Check-Output $?
+
+Invoke-WebRequest -Uri https://miktex.org/download/win/miktexsetup-x64.zip -OutFile miktexsetup-x64.zip
+Add-Type -AssemblyName System.IO.Compression.FileSystem
+[System.IO.Compression.ZipFile]::ExtractToDirectory("miktexsetup-x64.zip", "miktex")
+.\miktex\miktexsetup_standalone.exe --remote-package-repository="$env:CTAN_PACKAGE_ARCHIVE" --local-package-repository=.\miktex\download --package-set=essential --quiet download ; Check-Output $?
+.\miktex\download\miktexsetup_standalone.exe --remote-package-repository="$env:CTAN_PACKAGE_ARCHIVE" --portable="$env:R_LIB_PATH\miktex" --quiet install ; Check-Output $?
+
+initexmf --set-config-value [MPM]AutoInstall=1
+echo yes | pacman -S mingw-w64-x86_64-qpdf
+
+cd "$env:GITHUB_WORKSPACE\R-package"
+Add-Content .Renviron "R_LIBS=$env:R_LIB_PATH"
+Add-Content .Rprofile "options(repos = 'https://cran.r-project.org')"
+Add-Content .Rprofile "options(pkgType = 'binary')"
+Add-Content .Rprofile "options(install.packages.check.source = 'no')"
+Add-Content .Rprofile "Sys.setenv(RETICULATE_PYTHON = '$([RegEx]::Escape($env:CONDA_PREFIX))/python.exe')"
+
+Rscript -e "install.packages('devtools', dependencies = TRUE)"
+Rscript -e "devtools::install_deps(pkg = '.', dependencies = TRUE)"
+
+R.exe CMD build . ; Check-Output $?
+
+$PKG_FILE_NAME = Get-Item *.tar.gz
+$PKG_NAME = $PKG_FILE_NAME.BaseName.split("_")[0]
+$LOG_FILE_NAME = "$PKG_NAME.Rcheck/00check.log"
+$COVERAGE_FILE_NAME = "$PKG_NAME.Rcheck/coverage.log"
+
+R.exe CMD check "${PKG_FILE_NAME}" --as-cran ; Check-Output $?
+
+if (Get-Content "$LOG_FILE_NAME" | Select-String -Pattern "NOTE|WARNING|ERROR" -CaseSensitive -Quiet) {
+ echo "NOTEs, WARNINGs or ERRORs have been found by R CMD check"
+ Check-Output $False
+}
+
+$ActualErrorPreference = $ErrorActionPreference
+$ErrorActionPreference = "Continue"
+Rscript -e "covr::codecov(quiet = FALSE)" *>&1 | Tee-Object "$COVERAGE_FILE_NAME" ; $LastExitCode = 0
+$ErrorActionPreference = $ActualErrorPreference
+$Coverage = 0
+$Match = Get-Content "$COVERAGE_FILE_NAME" | Select-String -Pattern "RGF Coverage:" | Select-Object -First 1
+$Coverage = [float]$Match.Line.Trim().Split(" ")[-1].Replace("%", "")
+if ($Coverage -le 50) {
+ echo "Code coverage is extremely small!"
+ Check-Output $False
+}
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -25,35 +25,50 @@ jobs:
  python_version: 3.6
  - os: macos-latest
  python_version: 3.6
+ - os: windows-2016
+ python_version: 3.6
  - os: ubuntu-latest
  container: ubuntu:trusty
  python_version: 3.7
  - os: macos-latest
  python_version: 3.7
+ - os: windows-2016
+ python_version: 3.7
  - os: ubuntu-latest
  container: ubuntu:trusty
  python_version: 3.8
  - os: macos-latest
  python_version: 3.8
+ - os: windows-2016
+ python_version: 3.8
  - os: ubuntu-latest
  container: ubuntu:trusty
  python_version: 3.9
  - os: macos-latest
  python_version: 3.9
+ - os: windows-2016
+ python_version: 3.9
  - os: ubuntu-latest
  container: rocker/verse:latest
  python_version: 3.9
  task: R_PACKAGE
  - os: macos-latest
  python_version: 3.9
  task: R_PACKAGE
+ - os: windows-2016
+ python_version: 3.9
+ task: R_PACKAGE
  container: ${{ matrix.container }}
  steps:
  - name: Checkout repository
  uses: actions/checkout@v2
  with:
  fetch-depth: 5
- - name: Setup and run tests
+ - name: Install pandoc
+ if: matrix.task == 'R_PACKAGE' && startsWith(matrix.os, 'windows')
+ uses: r-lib/actions/setup-pandoc@v1
+ - name: Setup and run tests on Linux and macOS
+ if: matrix.os == 'macOS-latest' || matrix.os == 'ubuntu-latest'
  shell: bash
  run: |
  export OS_NAME="${{ matrix.os }}"
@@ -73,8 +88,26 @@ jobs:
  if [[ $TASK == "R_PACKAGE" ]]; then
  $GITHUB_WORKSPACE/.ci/r_tests.sh || exit -1
  fi
- - name: Create Wheel
- if: matrix.python_version == 3.9 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
+ - name: Setup and run tests on Windows
+ if: startsWith(matrix.os, 'windows')
+ run: |
+ $env:OS_NAME = "${{ matrix.os }}"
+ $env:PYTHON_VERSION = "${{ matrix.python_version }}"
+ $env:CONDA_ENV = "test-env"
+ echo "CONDA_ENV=$env:CONDA_ENV" >> $env:GITHUB_ENV
+ $env:CONDA_PATH = "$env:USERPROFILE\miniconda"
+ echo "CONDA_PATH=$env:CONDA_PATH" >> $env:GITHUB_ENV
+ $env:PATH += ";$env:CONDA_PATH\Scripts"
+ $env:PATH += ";C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\MSBuild\15.0\Bin"
+ $env:TASK = "${{ matrix.task }}"
+ $env:RGF_VER = (Get-Content $env:GITHUB_WORKSPACE\python-package\rgf\VERSION).trim()
+ echo "RGF_VER=$env:RGF_VER" >> $env:GITHUB_ENV
+ & "$env:GITHUB_WORKSPACE\.ci\python_tests_windows.ps1"
+ if ($env:TASK -eq "R_PACKAGE") {
+ & "$env:GITHUB_WORKSPACE\.ci\r_tests_windows.ps1"
+ }
+ - name: Create wheel for Linux and macOS
+ if: (matrix.os == 'macOS-latest' || matrix.os == 'ubuntu-latest') && matrix.python_version == 3.9 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
  shell: bash
  run: |
  export PATH="${{ env.CONDA_PATH }}/bin:$PATH"
@@ -91,6 +124,14 @@ jobs:
  else
  python setup.py bdist_wheel --plat-name=manylinux1_x86_64 --python-tag py3;
  fi
+ - name: Create wheel for Windows
+ if: startsWith(matrix.os, 'windows') && matrix.python_version == 3.9 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
+ run: |
+ $env:PATH += ";${{ env.CONDA_PATH }}\Scripts"
+ $env:PATH += ";C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\MSBuild\15.0\Bin"
+ conda activate ${{ env.CONDA_ENV }}
+ cd $env:GITHUB_WORKSPACE\python-package
+ python setup.py bdist_wheel --plat-name=win-amd64 --python-tag py3
  - name: Create GitHub Release
  if: matrix.python_version == 3.9 && matrix.task != 'R_PACKAGE' && startsWith(github.ref, 'refs/tags/')
  uses: softprops/action-gh-release@v1
@@ -101,7 +142,9 @@ jobs:
  name: ${{ env.RGF_VER }}
  draft: true
  prerelease: false
- files: ${{ github.workspace }}/python-package/dist/*.whl
+ files: |
+ ${{ github.workspace }}/python-package/dist/*.whl
+ ${{ github.workspace }}/python-package/compile/RGF/bin/*.exe
  all-successful:
  # https://github.community/t/is-it-possible-to-require-all-github-actions-tasks-to-pass-without-enumerating-them/117957/4?u=graingert
  runs-on: ubuntu-latest