Issue #400: Rename to naive model and latent model #39
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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: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: cmdstan env vars | |
| run: | | |
| echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV | |
| shell: bash | |
| - uses: actions/checkout@v4 | |
| - name: Install cmdstan Linux system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev || true | |
| sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true | |
| sudo apt-get install -y libpng-dev || true | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| extra-repositories: 'https://stan-dev.r-universe.dev' | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: local::. | |
| - name: Install cmdstan | |
| uses: epinowcast/actions/install-cmdstan@v1 | |
| with: | |
| cmdstan-version: 'latest' | |
| num-cores: 2 | |
| - name: Compile model and check syntax | |
| run: | | |
| dummy_data <- data.frame( | |
| pdate_lwr = as.POSIXct("2024-01-01 00:00:00"), | |
| pdate_upr = as.POSIXct("2024-01-02 00:00:00"), | |
| sdate_lwr = as.POSIXct("2024-01-03 00:00:00"), | |
| sdate_upr = as.POSIXct("2024-01-04 00:00:00"), | |
| obs_date = as.POSIXct("2024-01-05 00:00:00") | |
| ) | |
| linelist <- epidist::as_epidist_linelist(dummy_data) | |
| latent_model <- epidist::as_latent_model(linelist) | |
| stancode <- epidist::epidist( | |
| data = latent_model, fn = brms::make_stancode | |
| ) | |
| mod <- cmdstanr::cmdstan_model( | |
| stan_file = cmdstanr::write_stan_file(stancode), compile = FALSE | |
| ) | |
| message <- capture.output( | |
| mod$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} |