Add GitHub action for cmdstanr (#201)

* Copy check-cmdstan.yaml from epinowcast

* Try making epidist specific

* Remove epinowcast related code

* Use epidist:: and cmdstanr::

* Corrections for this to run

---------

Co-authored-by: Sam Abbott <[email protected]>

.github/workflows/check-cmdstan.yaml

@@ -0,0 +1,85 @@
+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" >> $GITHUB_ENV
+        shell: bash
+
+      - uses: actions/checkout@v4
+
+      - name: Install cmdstan Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev || true
+          sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
+          sudo apt-get install -y libpng-dev || true
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with: 
+          extra-packages: local::.
+
+      - name: Install cmdstan
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: 'latest'
+          num-cores: 2
+
+      - name: Compile model and check syntax
+        run: |
+          dummy_obs <- data.table::data.table(case = 1L, ptime = 1, stime = 2,
+            delay_daily = 1, delay_lwr = 1, delay_upr = 2, ptime_lwr = 1,
+            ptime_upr = 2, stime_lwr = 1, stime_upr = 2, obs_at = 100,
+            censored = "interval", censored_obs_time = 10, ptime_daily = 1,
+            stime_daily = 1
+          )
+          dummy_obs <- epidist::as_latent_individual(dummy_obs)
+          stancode <- epidist::epidist(
+            data = dummy_obs, fn = brms::make_stancode
+          )
+          mod <- cmdstanr::cmdstan_model(
+            stan_file = cmdstanr::write_stan_file(stancode), compile = FALSE
+          )
+          message <- capture.output(
+            mod$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}