Issue #221: Add marginal model #114
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: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
- name: cmdstan env vars | |
run: | | |
echo "CMDSTAN_PATH=${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} |