N: End-to-end automated pipeline test — two countries (Rwanda + Ethiopia), fresh environment

[EBukin]

What to build

An automated end-to-end test that proves the full data preparation pipeline works on a fresh R environment with no pre-existing project data, for two different countries. This test is the definitive quality gate for the entire pipeline redesign (#149).

What it tests

Two country scenarios run in sequence (or in parallel if CI supports it):

1. Rwanda — the default template country; uses get_country_shapes("RWA") + the bundled Rwanda synthetic metadata Excel
2. Ethiopia — a second country with different admin structure; uses get_country_shapes("ETH") + auto-generated metadata skeleton

For each country, the test:

1. Scaffolds a new project into withr::local_tempdir() via create_new_pti(path, app_name = "<Country> PTI", open = FALSE)
2. Verifies all placeholder tokens ({{APP_NAME}}, {{COUNTRY NAME}}) are replaced
3. Calls get_country_shapes(iso3) and verifies the returned list passes validate_geometries()
4. Runs the full 00-master.R pipeline headlessly — via quarto::quarto_render() calls matching the current master script
5. Asserts all expected app-data/ outputs exist and are valid:
   • app-data/shapes.rds — loadable with readRDS(); passes validate_geometries()
   • app-data/metadata.xlsx — loadable with fct_template_reader(); has at least one variable
   • app-data/metadata-hex.xlsx — exists (Step 4 runs by default)
   • app-data/pti-metadata.html — exists and is non-empty
   • docs/index.html — exists (Quarto website rendered)
6. Verifies shiny::testApp() or equivalent headless launch completes without error

Test location

tests/testthat/test-e2e-pipeline.R

Tagged with a custom skip condition so it does not run on every devtools::test() call — only in CI or when explicitly opted in:

skip_if_not(
  identical(Sys.getenv("PTI_RUN_E2E"), "true"),
  "Skipping E2E pipeline test (set PTI_RUN_E2E=true to run)"
)

CI configuration

A separate GitHub Actions workflow e2e-pipeline.yml that:

• Runs on push to main and on a weekly schedule
• Sets PTI_RUN_E2E=true
• Has internet access (fetches live WB parquets and hex data)
• Uses a clean R environment (no cached project data)

Ethiopia metadata note

Ethiopia requires a metadata workbook. For the E2E test, generate a minimal skeleton automatically using the auto-generation path (if #7 lands) or generate a synthetic one from the shapes using a test helper. The test does not need real indicator data — synthetic random values per polygon are sufficient to exercise the pipeline.

Acceptance criteria

• Test runs to completion for both Rwanda and Ethiopia in CI
• All six assertions pass for each country
• Test is skipped by default in devtools::test(); runs with PTI_RUN_E2E=true
• CI workflow file present in .github/workflows/e2e-pipeline.yml
• Test fails loudly with an actionable message if any pipeline step errors
• Rwanda run completes in under 10 minutes on a standard CI runner

Blocked by

#148 (Inf-4 — get_country_shapes() must exist)
Issues A through J of #149 (full pipeline must be in place)