R-CMD-check.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

# R cmd check for singleCellTK
on:
  push:
    branches: [master, devel]
  pull_request:
    branches: [master, devel]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,   r: 'release'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v3

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

      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: '3.8'

      - name: Pip Installer
        uses: BSFishy/pip-action@v1
        with:
          packages: |
            bbknn
            pandas
            scanorama
            scipy
            numpy
            astroid
            six
            scrublet
            scanpy

      - name: isPythonInstalled
        if: always()
        run: |
          python3 --version
          which python
        shell: bash

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: false

      - name: Install fftw3 on Linux
        if: runner.os == 'Linux'
        run: sudo apt-get install libfftw3-dev

      - name: Install fftw3 on macOS
        if: runner.os == 'macOS'
        run: brew install fftw

      - name: Manual Install
        run: |
          install.packages("BiocManager")
          BiocManager::install("ggtree")
          install.packages("remotes")
          install.packages("magick")
          remotes::install_version("assertive.properties", version = "0.0.5", repos = "http://cran.us.r-project.org", upgrade = "never")
          remotes::install_version("assertive.types", version = "0.0.3", repos = "http://cran.us.r-project.org", upgrade = "never")
          remotes::install_version("multipanelfigure", version = "2.1.2", repos = "http://cran.us.r-project.org", upgrade = "never")
          remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never")
          BiocManager::install("celda")

        shell: Rscript {0}

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache: false
          extra-packages: |
            any::rcmdcheck
          needs: check

      - name: Install XQuartz on macOS
        if: runner.os == 'macOS'
        run: brew install xquartz --cask

      - name: Install Old Seurat
        run: |
          remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never")
          remotes::install_version("SeuratObject", version = "4.1.4", repos = "http://cran.us.r-project.org", upgrade = "never")
          remotes::install_version("Seurat", version = "4.4.0", repos = "http://cran.us.r-project.org", upgrade = "never")
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_: false
        run: |
          options(crayon.enabled = TRUE)
          if (Sys.info()[1] == "Windows") {
            reticulate::use_python(system('where python', intern=TRUE)[1])
          } else {
            reticulate::use_python(system('which python', intern=TRUE))
          }
          reticulate::py_config()
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

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

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check


      - name: Run codecov
        run: |
          install.packages("covr")
          library(covr)
          codecov()
        shell: Rscript {0}

      - name: Upload codecov
        uses: codecov/codecov-action@v2.1.0