Merge pull request #278 from mrc-ide/odin-mrc-3745

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: odin
 Title: ODE Generation and Integration
-Version: 1.4.1
+Version: 1.4.2
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Thibaut", "Jombart", role = "ctb"),

inst/js/test-discrete.js

@@ -1,3 +1,4 @@
 function call_odin_bundle(Model, pars, tStart, tEnd, dt, nParticles) {
-    return dust.wodinRunDiscrete(Model, pars, tStart, tEnd, dt, nParticles)
+    const solution = dust.wodinRunDiscrete(Model, pars, tStart, tEnd, dt, nParticles);
+    return solution({mode: "grid", tStart, tEnd, nPoints: Infinity});
 }

tests/testthat/helper-js.R

@@ -14,9 +14,8 @@ call_odin_bundle_continuous <- function(bundle, user, t0, t1, tn,
   } else {
     control_js <- V8::JS(jsonlite::toJSON(control, auto_unbox = TRUE))
   }
-  res <- ct$call("call_odin_bundle", odin_js, user_js, t0, t1, tn, control_js)
-  res$y <- t(res$y)
-  res
+
+  ct$call("call_odin_bundle", odin_js, user_js, t0, t1, tn, control_js)
 }
 
 
@@ -74,3 +73,7 @@ skip_if_no_js <- function() {
   ## behaves poorly.
   skip_on_cran()
 }
+
+list_to_matrix <- function(x) {
+  matrix(unlist(x), ncol = length(x))
+}

tests/testthat/test-js-bundle.R

@@ -22,9 +22,9 @@ test_that("bundle works", {
   sol <- with(list(K = 100, r = 0.5, y0 = 1),
               K / (1 + (K / y0 - 1) * exp(-r * t)))
 
-  expect_equal(res$names, "N")
   expect_equal(res$x, t)
-  expect_equal(drop(res$y), sol, tolerance = 1e-6)
+  expect_equal(res$values$name, "N")
+  expect_equal(res$values$y[[1]], sol, tolerance = 1e-6)
 })
 
 
@@ -52,9 +52,9 @@ test_that("include interpolate", {
 
   tt <- seq(t0, t1, length.out = tn)
 
-  expect_equal(res$names, c("y", "p"))
+  expect_equal(res$values$name, c("y", "p"))
   zz <- ifelse(tt < 1, 0, ifelse(tt > 2, 1, tt - 1))
-  expect_equal(res$y[, 1], zz, tolerance = 2e-5)
+  expect_equal(res$values$y[[1]], zz, tolerance = 2e-5)
 })
 
 
@@ -78,12 +78,12 @@ test_that("include sum", {
 
   res <- call_odin_bundle_continuous(bundle, NULL, t0, t1, tn)
   expect_equal(
-    res$names,
+    res$values$name,
     c("y[1]", "y[2]", "y[3]", "ytot", "y2[1]", "y2[2]", "y2[3]"))
 
-  y <- res$y[, 1:3]
-  ytot <- res$y[, 4]
-  y2 <- res$y[, 5:7]
+  y <- list_to_matrix(res$values$y[1:3])
+  ytot <- res$values$y[[4]]
+  y2 <- list_to_matrix(res$values$y[5:7])
 
   expect_equal(ytot, rowSums(y))
   expect_equal(y2, y * 2)
@@ -127,8 +127,10 @@ test_that("include fancy sum", {
   tt <- seq(t0, t1, length.out = tn)
   cmp <- odin::odin_(code, target = "r")$new(user = user)$run(tt)
 
-  expect_equal(res$names, c("y[1]", "y[2]", "y[3]", "y[4]"))
-  expect_equal(res$y, unname(cmp[, -1]), tolerance = 1e-5)
+  expect_equal(res$values$name, c("y[1]", "y[2]", "y[3]", "y[4]"))
+
+  expect_equal(list_to_matrix(res$values$y),
+               unname(cmp[, -1]), tolerance = 1e-5)
 })