tests/testthat/test-package.R

In mrc-ide/odin.dust: Compile Odin to Dust

context("package")

test_that("validate package", {
  skip_if_not_installed("pkgload")
  path <- tempfile()
  dir.create(path)
  dir.create(file.path(path, "inst/odin"), FALSE, TRUE)

  name <- "pkg"
  data <- list(name = name)
  writeLines(sub_package_name(readLines("examples/pkg/DESCRIPTION"), name),
             file.path(path, "DESCRIPTION"))
  writeLines(sub_package_name(readLines("examples/pkg/NAMESPACE"), name),
             file.path(path, "NAMESPACE"))
  file.copy("examples/array.R", file.path(path, "inst/odin"))
  file.copy("examples/sir.R", file.path(path, "inst/odin"))

  odin_dust_package(path)

  ## No whitespace in generated files:
  files <- list.files(path, recursive = TRUE, all.files = TRUE,
                      include.dirs = FALSE, no.. = TRUE,
                      full.names = TRUE)
  txt <- unlist(lapply(files, readLines))
  expect_false(any(grepl("\\s+$", txt)))

  pkg <- pkgload::load_all(path, quiet = TRUE)

  r <- matrix(runif(10), 2, 5)
  x0 <- matrix(runif(10), 2, 5)

  mod <- pkg$env$array$new(list(x0 = x0, r = r), 0, 1)
  expect_equal(
    mod$transform_variables(mod$state()),
    list(x = array(x0, c(2, 5, 1))))
  expect_identical(mod$info(), list(dim = list(x = c(2L, 5L)),
                                    len = 10L,
                                    index = list(x = seq_len(10))))
})


test_that("Fail if no odin models found", {
  path <- tempfile()
  dir.create(path)
  dir.create(file.path(path, "inst/odin"), FALSE, TRUE)
  expect_error(
    odin_dust_package(path),
    "Did not find any files in inst/odin")
})


test_that("Do not overwrite files that are not ours", {
  skip_if_not_installed("pkgload")
  path <- tempfile()
  dir.create(path)
  dir.create(file.path(path, "inst/odin"), FALSE, TRUE)

  name <- "pkg"
  data <- list(name = name)
  writeLines(sub_package_name(readLines("examples/pkg/DESCRIPTION"), name),
             file.path(path, "DESCRIPTION"))
  writeLines(sub_package_name(readLines("examples/pkg/NAMESPACE"), name),
             file.path(path, "NAMESPACE"))
  file.copy("examples/array.R", file.path(path, "inst/odin"))
  file.copy("examples/sir.R", file.path(path, "inst/odin"))

  odin_dust_package(path)

  ## Empty file
  file.create(file.path(path, "inst/dust/array.cpp"))
  expect_error(
    odin_dust_package(path),
    "Refusing to overwrite edited file")

  ## File with content
  writeLines("// ignore me", (file.path(path, "inst/dust/array.cpp")))
  expect_error(
    odin_dust_package(path),
    "Refusing to overwrite edited file")
})


test_that("include user support in package", {
  skip_if_not_installed("pkgload")
  path <- tempfile()
  dir.create(path)
  dir.create(file.path(path, "inst/odin"), FALSE, TRUE)

  code <- c(
    'config(include) <- "include.cpp"',
    "n <- 5",
    "x[] <- user()",
    "initial(y[]) <- 0",
    "update(y[]) <- cumulative_to_i(i, x)",
    "dim(x) <- n",
    "dim(y) <- n")

  name <- "pkg2"
  data <- list(name = name)
  writeLines(sub_package_name(readLines("examples/pkg/DESCRIPTION"), name),
             file.path(path, "DESCRIPTION"))
  writeLines(sub_package_name(readLines("examples/pkg/NAMESPACE"), name),
             file.path(path, "NAMESPACE"))
  writeLines(code, file.path(path, "inst/odin/example.R"))
  file.copy("include.cpp", file.path(path, "inst/odin"))

  odin_dust_package(path)

  pkg <- pkgload::load_all(path, quiet = TRUE)

  x <- runif(5)
  mod <- pkg$env$example$new(list(x = x), 0, 1)
  y <- mod$run(1)
  expect_equal(y[, 1], cumsum(x))
})


test_that("use compiled compare function in package", {
  skip_if_not_installed("pkgload")
  path <- tempfile()
  dir.create(path)
  dir.create(file.path(path, "inst/odin"), FALSE, TRUE)

  code <- c("initial(y) <- 0",
            "update(y) <- y + rnorm(0, 1)",
            "scale <- user(1) # ignore.unused",
            'config(compare) <- "compare_simple.cpp"')

  name <- "pkg3"
  data <- list(name = name)
  writeLines(sub_package_name(readLines("examples/pkg/DESCRIPTION"), name),
             file.path(path, "DESCRIPTION"))
  writeLines(sub_package_name(readLines("examples/pkg/NAMESPACE"), name),
             file.path(path, "NAMESPACE"))
  writeLines(code, file.path(path, "inst/odin/example.R"))
  file.copy("examples/compare_simple.cpp", file.path(path, "inst/odin"))

  odin_dust_package(path)

  ## No whitespace in generated files:
  files <- list.files(path, recursive = TRUE, all.files = TRUE,
                      include.dirs = FALSE, no.. = TRUE,
                      full.names = TRUE)
  txt <- unlist(lapply(files, readLines))
  expect_false(any(grepl("\\s+$", txt)))

  pkg <- pkgload::load_all(path, quiet = TRUE)

  np <- 10
  mod <- pkg$env$example$new(list(), 0, np, seed = 1L)
  expect_null(mod$compare_data())

  t <- seq(0, 20, by = 2)
  d <- dust::dust_data(
    data.frame(time = t,
               observed = runif(length(t), 0, sqrt(t)),
               another = 1L))
  mod$set_data(d)

  y <- mod$run(1)
  expect_null(mod$compare_data())
  y <- mod$run(2)
  expect_equal(
    mod$compare_data(),
    drop(y) - d[[2]][[2]]$observed)
})


test_that("Can't compile gpu into package", {
  path <- tempfile()
  dir.create(path)
  dir.create(file.path(path, "inst/odin"), FALSE, TRUE)

  name <- "pkg"
  data <- list(name = name)
  writeLines(sub_package_name(readLines("examples/pkg/DESCRIPTION"), name),
             file.path(path, "DESCRIPTION"))
  writeLines(sub_package_name(readLines("examples/pkg/NAMESPACE"), name),
             file.path(path, "NAMESPACE"))
  file.copy("examples/array.R", file.path(path, "inst/odin"))
  file.copy("examples/sir.R", file.path(path, "inst/odin"))

  expect_error(
    odin_dust_package(path, options = odin_dust_options(gpu = TRUE)),
    "Can't compile gpu models into a package")
})