run-pollock-tests-by-fleet.yml

name: Run pollock tests (by fleet)

on:
  workflow_dispatch:
  push:

jobs:
  build-deploy:
    runs-on: macos-latest
    env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Check out repository
        uses: actions/checkout@v2 
        
      - name: Set up R (needed for Rmd)
        uses: r-lib/actions/setup-r@v2

      - name: Run pollock tests 
        run: |
          # Names of required packages
          packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "devtools", "lubridate")

          # Install packages not yet installed
          installed_packages <- packages %in% rownames(installed.packages())
          if (any(installed_packages == FALSE)) {
            install.packages(packages[!installed_packages], repos = "http://cran.us.r-project.org")
          }
          
          # install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org"))
          devtools::install_github("NOAA-FIMS/FIMS")
          
          # Load packages
          invisible(lapply(packages, library, character.only = TRUE))

          source(file.path(getwd(), "content", "run_pollock_tests_by_fleet.R"))
        shell: Rscript {0}