Issue 94: Add R and Stan for analytical Weibull #88
Workflow file for this run
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| name: check-cmdstan | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| paths: | |
| - '**.stan' | |
| branches: | |
| - main | |
| - develop | |
| schedule: | |
| - cron: '5 4 * * 1' | |
| pull_request: | |
| paths: | |
| - '**.stan' | |
| branches: | |
| - main | |
| - develop | |
| merge_group: | |
| workflow_dispatch: | |
| jobs: | |
| check-cmdstan: | |
| if: "! contains(github.event.head_commit.message, '[ci skip]')" | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| extra-repositories: 'https://stan-dev.r-universe.dev' | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: local::. | |
| - name: Install cmdstan | |
| uses: epinowcast/actions/install-cmdstan@v1 | |
| with: | |
| cmdstan-version: 'latest' | |
| num-cores: 2 | |
| - name: Compile model and check syntax | |
| run: | | |
| stan_file <- file.path(tempdir(), "pcd_functions.stan") | |
| primarycensoreddist::pcd_load_stan_functions( | |
| wrap_in_block = TRUE, | |
| write_to_file = TRUE, | |
| output_file = stan_file | |
| ) | |
| model <- cmdstanr::cmdstan_model(stan_file) | |
| # If the model is not syntactically correct above will fail | |
| # however it may be correct enougth to compile but still contain | |
| # soft depreciated syntax and so we check the syntax again below | |
| # and test the output. | |
| message <- capture.output( | |
| model$check_syntax(pedantic = TRUE), | |
| type = "message" | |
| ) | |
| message | |
| # We can't use TRUE here as pendatic check return lots of false | |
| # positives related to our use of functions. | |
| stopifnot( | |
| length(message) != 0 && length(message) < 15 && | |
| any(message == "Stan program is syntactically correct") | |
| ) | |
| shell: Rscript {0} |