run_ecosis_pull_example.yaml

name: run_ecosis_pull_example

on:
  schedule:
    - cron:  '15 1 */5 * *'

env:
  R_LIBS_USER: /usr/local/lib/R/site-library
  LC_ALL: en_US.UTF-8
  NCPUS: 2

jobs:
  run-plsr: 
    # The type of runner that the job will run on
    runs-on: ubuntu-latest

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

    steps:
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

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

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        shell: Rscript {0}
      
      - name: Install dependencies
        run: |
          Rscript -e 'remotes::install_github(repo="TESTgroup-BNL/spectratrait", dependencies=TRUE)'

      # Run R script
      - name: Run EcoSIS API Pull Example
        run: |
          source("inst/scripts/pull_data_from_ecosis.R")
        shell: Rscript {0}