Issue 216: end-to-end CI

.github/workflows/pipeline-run-check.yaml

@@ -0,0 +1,39 @@
+name: Pipeline Run Check
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run-pipeline:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: "Set up R"
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "release"
+          use-public-rspm: true
+      - name: "Install poetry"
+        run: pip install poetry
+      - name: "Install pyrenew-hew"
+        run: poetry install
+      - name: "Set up Quarto"
+        uses: quarto-dev/quarto-actions/setup@v2
+      - name: "Set up dependencies for hewr"
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: hewr
+      - name: "Install extra pkgs"
+        run: |
+            pak::local_install("hewr", ask = FALSE)
+            pak::pkg_install("cmu-delphi/epipredict@main", ask = FALSE)
+            pak::pkg_install("cmu-delphi/epiprocess@main", ask = FALSE)
+        shell: Rscript {0}
+      - name: "Run pipeline"
+        run: poetry run bash pipelines/tests/test_forecast_state.sh pipelines/tests

.gitignore

@@ -403,3 +403,6 @@ private_data/*
 # Test data exceptions to the general data exclusion
 !pipelines/tests/covid-19_r_2024-01-29_f_2023-11-01_t_2024-01-29/model_runs/TD/data/data.tsv
 !pipelines/tests/covid-19_r_2024-01-29_f_2023-11-01_t_2024-01-29/model_runs/TD/data/eval_data.tsv
+
+# Ignore test pipe output
+pipelines/tests/private_data/*

hewr/NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(combine_training_and_eval_data)
+export(generate_exp_growth_pois)
 export(get_all_model_batch_dirs)
 export(make_forecast_figure)
 export(parse_model_batch_dir_path)

hewr/R/generate_exp_growth_process.R

@@ -0,0 +1,26 @@
+#' Generate Exponential Growth Process with Poisson Noise
+#'
+#' This function generates a sequence of samples from an exponential growth
+#' process through Poisson sampling:
+#' ```math
+#' \begin{aligned}
+#' \( \lambda_t &= I_0 \exp(\sum_{t=1}^{t} r_t) \) \\
+#' I_t &\sim \text{Poisson}(\lambda_t).
+#' ```
+#' @param rt A numeric vector of exponential growth rates.
+#' @param initial A numeric value representing the initial value of the process.
+#'
+#' @return An integer vector of Poisson samples generated from the exponential
+#' growth process.
+#'
+#' @examples
+#' rt <- c(0.1, 0.2, 0.15)
+#' initial <- 10
+#' generate_exp_growth_pois(rt, initial)
+#'
+#' @export
+generate_exp_growth_pois <- function(rt, initial) {
+  means <- initial * exp(cumsum(rt))
+  samples <- stats::rpois(length(means), lambda = means)
+  return(samples)
+}

hewr/tests/testthat/test_generate_exp_growth_process.R

@@ -0,0 +1,30 @@
+test_that("generate_exp_growth_pois generates correct number of samples", {
+  rt <- c(0.1, 0.2, 0.15)
+  initial <- 10
+  samples <- generate_exp_growth_pois(rt, initial)
+  expect_length(samples, length(rt))
+})
+
+test_that("generate_exp_growth_pois returns a vector of integers", {
+  rt <- c(0.1, 0.2, 0.15)
+  initial <- 10
+  samples <- generate_exp_growth_pois(rt, initial)
+  expect_type(samples, "integer")
+})
+
+test_that("generate_exp_growth_pois does not return implausible values", {
+  rt <- c(0.1, 0.2, 0.15)
+  initial <- 10
+  analytic_av <- initial * exp(cumsum(rt))
+  analytic_std <- sqrt(analytic_av)
+  samples <- generate_exp_growth_pois(rt, initial)
+  expect_true(all(samples <= initial + 10 * analytic_std))
+  expect_true(all(samples >= initial - 10 * analytic_std))
+})
+
+test_that("generate_exp_growth_pois handles empty growth rates", {
+  rt <- numeric(0)
+  initial <- 10
+  samples <- generate_exp_growth_pois(rt, initial)
+  expect_equal(samples, numeric(0))
+})