add token #8
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| # Get ss3 releases and run test model with estimation and hessian | |
| name: run-releases-with-test-model | |
| on: | |
| workflow_dispatch: | |
| push: | |
| schedule: | |
| - cron: '0 15 * * 2' # every Tuesday at 3pm UTC (= 1 0am EST or 11am EDT Eastern time) | |
| # Run fast running SS3 test models with estimation | |
| jobs: | |
| run-releases-with-test-model: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest} | |
| - {os: macos-13} | |
| - {os: macos-latest} | |
| - {os: ubuntu-latest} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout models repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'nmfs-ost/ss3-test-models' | |
| path: test-models-repo | |
| - name: Update Ubuntu packages | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
| sudo apt-get update | |
| sudo apt-get install --only-upgrade libstdc++6 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install R packages to run in parallel | |
| run: Rscript -e 'install.packages(c("pak", "remotes"))' | |
| # - name: Install r4ss (for all but ubuntu) | |
| # if: matrix.config.os == 'macos-13' || matrix.config.os == 'macos-latest' || matrix.config.os == 'windows-latest' | |
| # run: Rscript -e 'pak::pkg_install("r4ss/r4ss")' | |
| - name: Install r4ss (ubuntu) | |
| run: Rscript -e 'remotes::install_github("r4ss/r4ss", ref = "more-gh-fixes-for-gha")' | |
| - name: Run test model | |
| run: | | |
| old_dir <- file.path(getwd(), "test-models-repo", "models", "two_morph_seas_areas") | |
| dir <- file.path(getwd(), "two_morph_seas_areas") | |
| dir.create(dir) | |
| file.rename(old_dir, dir) | |
| unlink(old_dir,recursive = TRUE) | |
| r4ss::get_ss3_exe(dir = dir) | |
| r4ss::run(dir = dir) | |
| shell: Rscript {0} | |