Issue #221: Add marginal model #49
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: cmdstan env vars | |
| run: | | |
| echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV | |
| shell: bash | |
| - uses: actions/checkout@v4 | |
| - name: Install cmdstan Linux system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev || true | |
| sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true | |
| sudo apt-get install -y libpng-dev || true | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| extra-repositories: 'https://stan-dev.r-universe.dev' | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: local::. | |
| - name: Install cmdstan | |
| uses: epinowcast/actions/install-cmdstan@v1 | |
| with: | |
| cmdstan-version: 'latest' | |
| num-cores: 2 | |
| - name: Compile model and check syntax | |
| run: | | |
| dummy_obs <- dplyr::tibble( | |
| pdate_lwr = as.Date("2020-01-01"), | |
| sdate_lwr = as.Date("2020-02-01") | |
| ) | |
| dummy_obs <- epidist::as_epidist_linelist_data(dummy_obs) | |
| dummy_obs <- epidist::as_epidist_latent_model(dummy_obs) | |
| stancode <- epidist::epidist( | |
| data = dummy_obs, fn = brms::make_stancode | |
| ) | |
| mod <- cmdstanr::cmdstan_model( | |
| stan_file = cmdstanr::write_stan_file(stancode), compile = FALSE | |
| ) | |
| message <- capture.output( | |
| mod$check_syntax(pedantic = FALSE), | |
| type = "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 && | |
| all(message == "Stan program is syntactically correct") | |
| ) | |
| shell: Rscript {0} |