Merge pull request #7696 from quarto-dev/feature/spin

Bring support for rendering from R file

src/execute/rmd.ts

@@ -37,9 +37,14 @@ import {
 } from "./types.ts";
 import { postProcessRestorePreservedHtml } from "./engine-shared.ts";
 import { mappedStringFromFile } from "../core/mapped-text.ts";
-import { mappedIndexToLineCol, MappedString } from "../core/lib/mapped-text.ts";
+import {
+  asMappedString,
+  mappedIndexToLineCol,
+  MappedString,
+} from "../core/lib/mapped-text.ts";
 import { lineColToIndex } from "../core/lib/text.ts";
 import { executeInlineCodeHandler } from "../core/execute-inline.ts";
+import { globalTempContext } from "../core/temp.ts";
 
 const kRmdExtensions = [".rmd", ".rmarkdown"];
 
@@ -58,17 +63,26 @@ export const knitrEngine: ExecutionEngine = {
 
   validExtensions: () => kRmdExtensions.concat(kRmdExtensions),
 
-  claimsFile: (_file: string, ext: string) => {
-    return kRmdExtensions.includes(ext.toLowerCase());
+  claimsFile: (file: string, ext: string) => {
+    return kRmdExtensions.includes(ext.toLowerCase()) ||
+      isKnitrSpinScript(file);
   },
 
   claimsLanguage: (language: string) => {
     return language.toLowerCase() === "r";
   },
 
-  target: (file: string, _quiet?: boolean, markdown?: MappedString) => {
+  target: async (
+    file: string,
+    _quiet?: boolean,
+    markdown?: MappedString,
+  ): Promise<ExecutionTarget | undefined> => {
     if (markdown === undefined) {
-      markdown = mappedStringFromFile(file);
+      if (isKnitrSpinScript(file)) {
+        markdown = asMappedString(await markdownFromKnitrSpinScript(file));
+      } else {
+        markdown = mappedStringFromFile(file);
+      }
     }
     let metadata;
     try {
@@ -86,8 +100,12 @@ export const knitrEngine: ExecutionEngine = {
     return Promise.resolve(target);
   },
 
-  partitionedMarkdown: (file: string) => {
-    return Promise.resolve(partitionMarkdown(Deno.readTextFileSync(file)));
+  partitionedMarkdown: async (file: string) => {
+    if (isKnitrSpinScript(file)) {
+      return partitionMarkdown(await markdownFromKnitrSpinScript(file));
+    } else {
+      return partitionMarkdown(Deno.readTextFileSync(file));
+    }
   },
 
   execute: async (options: ExecuteOptions): Promise<ExecuteResult> => {
@@ -353,3 +371,35 @@ function resolveInlineExecute(code: string) {
     (expr) => `${"`"}r .QuartoInlineRender(${expr})${"`"}`,
   )(code);
 }
+
+export function isKnitrSpinScript(file: string) {
+  const ext = extname(file).toLowerCase();
+  if (ext == ".r") {
+    const text = Deno.readTextFileSync(file);
+    // Consider a .R script that can be spinned if it contains a YAML header inside a special `#'` comment
+    return /^\s*#'\s*---[\s\S]+?\s*#'\s*---/.test(text);
+  } else {
+    return false;
+  }
+}
+
+export async function markdownFromKnitrSpinScript(file: string) {
+  // run spin to get .qmd and get markdown from .qmd
+
+  // TODO: implement a caching system because spin is slow and it seems we call this twice for each run
+  // 1. First as part of the target() call
+  // 2. Second as part of renderProject() call to get `partitioned` information to get `resourcesFrom` with `resourceFilesFromRenderedFile()`
+
+  // we need a temp dir for `CallR` to work but we don't have access to usual options.tempDir.
+  const tempDir = globalTempContext().createDir();
+
+  const result = await callR<string>(
+    "spin",
+    { input: file },
+    tempDir,
+    undefined,
+    true,
+  );
+
+  return result;
+}

src/resources/rmd/rmd.R

@@ -7,11 +7,17 @@
   # execute knitr::spin
   spin <- function(input) {
 
+    if (utils::packageVersion("knitr") < "1.44") {
+      stop(
+        "knitr >= 1.44 is required for rendering with Quarto from `.R` files. ",
+        "Please update knitr.", call. = FALSE)
+    }
+
     # read file
     text <- xfun::read_utf8(input)
 
     # spin and return
-    knitr::spin(text = text, knit = FALSE)
+    knitr::spin(text = text, knit = FALSE, format = "qmd")
 
   }
 

tests/docs/knitr-spin.R

@@ -0,0 +1,30 @@
+#' ---
+#' title: "A report generated from a pure R script"
+#' format: html
+#' ---
+#'
+#' This is a report generated by `knitr::spin()`.
+#' 
+#' ## Code block {#block}
+#'
+#' Let's try some **knitr** options:
+
+#| echo: false
+#| fig-with: 7
+#  This is a normal R comment.
+plot(cars)
+
+#' ## Inline value {#inline}
+#' 
+#' Now write an inline value. We know the value of $\pi$ is
+{{ pi }}
+#' .
+#'
+#' Finally please note that all roxygen comments are
+#' optional. You do not need chunk options, either,
+#' unless you want more control over the output
+#' elements such as the size of plots.
+
+# /* Write comments between /* and */ like C comments:
+Sys.sleep(60)
+# */

tests/smoke/render/render-r.test.ts

@@ -7,7 +7,7 @@
 
 import { docs, fileLoader, inTempDirectory } from "../../utils.ts";
 import { join } from "path/mod.ts";
-import { ensureHtmlSelectorSatisfies, fileExists } from "../../verify.ts";
+import { ensureHtmlElements, ensureHtmlSelectorSatisfies, fileExists } from "../../verify.ts";
 import { testRender } from "./render.ts";
 
 inTempDirectory((dir) => {
@@ -72,3 +72,18 @@ testRender(knitrOptions.input, "html", false, [
 
 const sqlEngine = fileLoader()("test-knitr-sql.qmd", "html");
 testRender(sqlEngine.input, "html", false);
+
+
+const toSpin = fileLoader()("knitr-spin.R", "html");
+testRender(toSpin.input, "html", false, [
+  ensureHtmlElements(
+    toSpin.output.outputPath, ["#block img"]
+  ),
+  ensureHtmlSelectorSatisfies(
+    toSpin.output.outputPath,
+    "#inline code",
+    (nodeList) => {
+      return /^3\.14+/.test(nodeList[0].textContent);
+    },
+  ),
+]);