cmdstanr/.github/workflows/Test-coverage.yaml at master · stan-dev/cmdstanr · GitHub

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---
# Github Actions workflow to analyze CmdStanR code, test coverage
# yamllint disable rule:line-length

on:
  push:
    branches:
      - master
  pull_request:

name: Test coverage

permissions:
  contents: read
  id-token: write

jobs:
  test-coverage:
    if: "! contains(github.event.head_commit.message, '[ci skip]')"
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }}

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: windows-latest }
          - { os: ubuntu-latest }
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      NOT_CRAN: true

    steps:
      - name: cmdstan env vars
        run: |
          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
        shell: bash

      - uses: n1hility/cancel-previous-runs@v3
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          workflow: Test-coverage.yaml
        if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"

      - uses: actions/checkout@v6

      - uses: r-lib/actions/setup-r@v2
      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, local::., any::covr, any::gridExtra, any::xml2
          needs: coverage

      - name: Install cmdstan
        run: |
          cmdstanr::check_cmdstan_toolchain()
          cmdstanr::install_cmdstan(cores = 2)
        shell: Rscript {0}

      - name: Test coverage (Linux)
        if: runner.os == 'Linux'
        run: |
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
            type = "tests"
          )
          print(cov)
          covr::to_cobertura(cov)
        shell: Rscript {0}

      - name: Test coverage (Windows)
        if: runner.os == 'Windows'
        run: |
          options(covr.gcov = 'C:/rtools44/mingw64/bin/gcov.exe');
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
            type = "tests",
            function_exclusions = "sample_mpi"
          )
          print(cov)
          covr::to_cobertura(cov)
        shell: Rscript {0}

      - uses: codecov/codecov-action@v6
        with:
          # Fail if error if not on PR, or if on PR and token is given
          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
          files: ./cobertura.xml
          plugins: noop
          disable_search: true
          use_oidc: true

      - name: Show testthat output
        if: always()
        run: |
          ## --------------------------------------------------------------------
          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload test results
        if: failure()
        uses: actions/upload-artifact@v7
        with:
          name: coverage-test-failures
          path: ${{ runner.temp }}/package