#!/usr/bin/env bash

# Run the current learning project workflow end to end.
#
# This is intentionally simpler than a targets pipeline.
# It gives us one command that runs the simulation smoke check and renders the
# Quarto notebooks while the project is still small.

set -euo pipefail

# Make the script work even if it is called from another directory.
script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$script_dir"

mkdir -p "outputs/reports"

Rscript "scripts/01_simulate_icu_data.R"

quarto render "notebooks/01_target_trial_basics.qmd" --output-dir "../outputs/reports"
quarto render "notebooks/02_explore_simulated_data.qmd" --output-dir "../outputs/reports"

printf '\nWorkflow complete. Reports are in outputs/reports/.\n'