Merge pull request #249 from mrc-ide/i248

Generate js code directly from odin code

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: odin
 Title: ODE Generation and Integration
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Thibaut", "Jombart", role = "ctb"),

R/js_bundle.R

@@ -1,10 +1,13 @@
-##' Create a JavaScript bundle of odin models
+##' Create a JavaScript bundle of an odin model
 ##'
-##' @title Create a bundle of odin models
+##' @section Warning:
 ##'
-##' @param filenames Filenames with odin source code
+##' The interface and generated code here are subject to change.
 ##'
-##' @param dest Destination file for the generated javascript
+##' @title Create a bundle of an odin model
+##'
+##' @param code An expression, string or path to a file containing
+##'   odin code (as for [odin::odin_parse_]
 ##'
 ##' @param include Optional vector of paths of filenames to include
 ##'   into the javascript bundle
@@ -13,57 +16,37 @@
 ##'   should be included as well.
 ##'
 ##' @export
-odin_js_bundle <- function(filenames, dest = tempfile(),
+##' @examples
+##' js <- odin::odin_js_bundle(quote({
+##'   deriv(x) <- 1
+##'   initial(x) <- 1
+##' }), include_dopri = FALSE)
+##' head(js)
+odin_js_bundle <- function(code,
                            include = NULL,
                            include_dopri = TRUE) {
-  ## The two options here seem to be: use a vector of paths to source
-  ## files or use a path to a directory.  The rest of the interface is
-  ## also totally subject to change because we might want to move
-  ## those options into the general options interface.  The option to
-  ## directly minify from R via V8 would be nice too but probably is
-  ## not possible because of the way that the minification process
-  ## involves the disk.
-  err <- !file.exists(filenames)
-  if (any(err)) {
-    stop(sprintf("%s not exist: %s",
-                 ngettext(sum(err), "File does", "Files do"),
-                 paste(squote(filenames[err]), collapse = ", ")))
-  }
-
   options <- odin_options(target = "js")
+  ir <- odin_parse_(code, options)
+  dat <- generate_js(ir, options)
 
-  f <- function(file) {
-    ir <- odin_parse_(file, options)
-    generate_js(ir, options)
-  }
-  dat <- lapply(filenames, f)
-
-  nms <- vcapply(dat, "[[", "name")
-  err <- duplicated(nms)
-  if (any(err)) {
-    stop(sprintf("Duplicate model names: %s",
-                 paste(squote(unique(nms[err])), collapse = ", ")))
-  }
-
-  needed <- apply(do.call(cbind, lapply(dat, "[[", "include")), 1, any)
   support <- c(
     if (include_dopri) "dopri.js",
     "support.js",
-    names(which(needed)))
+    names(which(dat$include)))
+  support_js <- lapply(odin_file(file.path("js", support)),
+                       readLines, warn = FALSE)
 
   if (!is.null(include)) {
     include <- js_flatten_eqs(lapply(include, readLines))
   }
-  support_js <- lapply(odin_file(file.path("js", support)),
-                       readLines, warn = FALSE)
-
-  code <- c(js_flatten_eqs(support_js),
-            sprintf("var %s = {};", JS_GENERATORS),
-            js_flatten_eqs(lapply(dat, "[[", "code")),
-            include)
 
-  writeLines(code, dest)
-  dest
+  ## TODO: Revisit this now that there's only one generator and work
+  ## out what a sensible return type would be. This depends to a
+  ## degree on how things want to be pushed around in wodin.
+  c(js_flatten_eqs(support_js),
+    sprintf("var %s = {};", JS_GENERATORS),
+    dat$code,
+    include)
 }
 
 
@@ -84,7 +67,9 @@ odin_js_example <- function(filename, dest = tempfile()) {
   html <- dir(path, pattern = "\\.html$", full.names = TRUE)
 
   dir.create(dest, FALSE, TRUE)
-  odin_js_bundle(filename, file.path(dest, "odin.js"), include = include)
+  writeLines(
+    odin_js_bundle(filename, include = include),
+    file.path(dest, "odin.js"))
   file.copy(html, dest, overwrite = TRUE)
   dest
 }

tests/testthat/test-js-bundle.R

@@ -6,20 +6,14 @@ test_that("bundle works", {
             "N0 <- user(1)",
             "K <- 100",
             "r <- user()")
-  p <- tempfile()
-  dir.create(p)
-  filename <- file.path(p, "odin.R")
-  writeLines(code, filename)
-
-  res <- odin_js_bundle(filename)
+  bundle <- odin_js_bundle(code)
 
   ## Keep unwanted bits out:
-  txt <- readLines(res)
-  expect_false(any(grepl("odinSum2", txt)))
-  expect_false(any(grepl("interpolateCheckY", txt)))
+  expect_false(any(grepl("odinSum2", bundle)))
+  expect_false(any(grepl("interpolateCheckY", bundle)))
 
   ct <- V8::v8()
-  invisible(ct$source(res))
+  invisible(ct$eval(bundle))
 
   t <- 0:10
   res <- call_odin_bundle(ct, "odin", list(r = 0.5), t)
@@ -31,27 +25,6 @@ test_that("bundle works", {
 })
 
 
-test_that("bundle fails with missing files", {
-  path1 <- file.path(tempdir(), "myfile1.R")
-  path2 <- file.path(tempdir(), "myfile2.R")
-  expect_error(odin_js_bundle(path1), "File does not exist:")
-  expect_error(odin_js_bundle(c(path1, path2)), "Files do not exist:")
-})
-
-
-test_that("unique model names", {
-  path1 <- tempfile()
-  path2 <- tempfile()
-
-  code <- c("deriv(y) <- 1", "initial(y) <- 1", 'config(base) <- "test"')
-  writeLines(code, path1)
-  writeLines(code, path2)
-
-  expect_error(odin_js_bundle(c(path1, path2)),
-               "Duplicate model names: 'test'")
-})
-
-
 test_that("include interpolate", {
   code <- c("deriv(y) <- pulse",
             "initial(y) <- 0",
@@ -62,15 +35,10 @@ test_that("include interpolate", {
             "dim(zp) <- user()",
             "output(p) <- pulse")
 
-  p <- tempfile()
-  dir.create(p)
-  filename <- file.path(p, "odin.R")
-  writeLines(code, filename)
-
-  res <- odin_js_bundle(filename)
+  res <- odin_js_bundle(code)
 
   ct <- V8::v8()
-  invisible(ct$source(res))
+  invisible(ct$eval(res))
 
   tt <- seq(0, 3, length.out = 301)
   tp <- c(0, 1, 2)
@@ -93,14 +61,11 @@ test_that("include sum", {
             "output(y2[]) <- y[i] * 2",
             "dim(y2) <- length(y)")
 
-  p <- tempfile()
-  dir.create(p)
-  filename <- file.path(p, "odin.R")
-  writeLines(code, filename)
-  res <- odin_js_bundle(filename)
+
+  res <- odin_js_bundle(code)
 
   ct <- V8::v8()
-  invisible(ct$source(res))
+  invisible(ct$eval(res))
   tt <- seq(0, 10, length.out = 101)
   yy <- call_odin_bundle(ct, "odin", NULL, tt)
   res <- list(y = unname(yy[, 2:4]),
@@ -130,11 +95,7 @@ test_that("include fancy sum", {
     "dim(a) <- c(n_spp, n_spp)",
     "dim(ay) <- c(n_spp, n_spp)")
 
-  p <- tempfile()
-  dir.create(p)
-  filename <- file.path(p, "odin.R")
-  writeLines(code, filename)
-  res <- odin_js_bundle(filename)
+  res <- odin_js_bundle(code)
 
   user <- list(r = c(1.00, 0.72, 1.53, 1.27),
                a = rbind(c(1.00, 1.09, 1.52, 0.00),
@@ -144,7 +105,7 @@ test_that("include fancy sum", {
                y0 = c(0.3013, 0.4586, 0.1307, 0.3557))
 
   ct <- V8::v8()
-  invisible(ct$source(res))
+  invisible(ct$eval(res))
 
   tt <- seq(0, 50, length.out = 101)
   yy <- call_odin_bundle(ct, "odin", user, tt)
@@ -159,14 +120,10 @@ test_that("simple stochastic model in a bundle", {
     "initial(x) <- 0",
     "update(x) <- x + norm_rand()")
 
-  p <- tempfile()
-  dir.create(p)
-  filename <- file.path(p, "odin.R")
-  writeLines(code, filename)
-  res <- odin_js_bundle(filename)
+  res <- odin_js_bundle(code)
 
   ct <- V8::v8()
-  invisible(ct$source(res))
+  invisible(ct$eval(res))
   ct$call("setSeed", 1)
   tt <- 0:20
   yy <- call_odin_bundle(ct, "odin", NULL, tt)