dev_workflow.yml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.


name: Dev Workflow - Test and check
on:
  push:
    branches: [ "dev" ]

permissions:
  contents: read

jobs:
  R-CMD-check:
    name: R CMD Check
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    runs-on: ubuntu-latest

    steps:

      - name: Remove vignettes dir
        run: rm -rf 'vignettes/'
        shell: bash

      - name: Checkout repo for workflow access
        uses: actions/checkout@v3

      - name: Set up R environment
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Set up dependencies (general)
        uses: r-lib/actions/setup-r-dependencies@v2
        env:
          _R_CHECK_FORCE_SUGGESTS: false
          _R_CHECK_RD_XREFS: false
        with:
          dependencies: '"hard"' # do not use suggested dependencies
          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes

      - name: Set up dependencies (GiottoData)
        run: |
          suppressWarnings({
            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
          })
        shell: Rscript {0}

      - name: Run R CMD check
        uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          error-on: '"error"' # workflow errors on error only, can change to include warnings

      # show testthat output for ease of access
      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash


  test-coverage:
    name: Code coverage
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:

      - name: Checkout repo for workflow access
        uses: actions/checkout@v3

      - name: Set up R environment
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Set up dependencies (general)
        uses: r-lib/actions/setup-r-dependencies@v2
        env:
          _R_CHECK_FORCE_SUGGESTS: false
          _R_CHECK_RD_XREFS: false
        with:
          dependencies: '"hard"' # do not use suggested dependencies
          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
          needs: coverage

      - name: Set up dependencies (GiottoData)
        run: |
          suppressWarnings({
            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
          })
        shell: Rscript {0}

      - name: Test coverage
        run: |
          covr::codecov(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
          )
        shell: Rscript {0}

      # add code cov
      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v3
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}



  lint:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repo for workflow access
        uses: actions/checkout@v3

      - name: Set up R environment
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Set up dependencies (general)
        uses: r-lib/actions/setup-r-dependencies@v2
        env:
          _R_CHECK_FORCE_SUGGESTS: false
          _R_CHECK_RD_XREFS: false
        with:
          dependencies: '"hard"' # do not use suggested dependencies
          extra-packages: any::lintr, local::.
          needs: lint

      - name: Lint
        run: lintr::lint_package()
        shell: Rscript {0}
        env:
          LINTR_ERROR_ON_LINT: false