check-cmdstan.yaml

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

      - 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(case = 1L, ptime = 1, stime = 2,
            delay_daily = 1, delay_lwr = 1, delay_upr = 2, ptime_lwr = 1,
            ptime_upr = 2, stime_lwr = 1, stime_upr = 2, obs_time = 100,
            censored = "interval", censored_obs_time = 10, ptime_daily = 1,
            stime_daily = 1
          )
          dummy_obs <- epidist::as_latent_individual(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}