Merge branch 'main' into feature/site-nesting

Author: Al Manning

.github/pull_request_template.md

@@ -22,6 +22,6 @@ print("Hello Quarto!")
 
 I have (if applicable):
 
-- [ ] filed a [contributor agreement](../CONTRIBUTING.md).
+- [ ] filed a [contributor agreement](https://github.com/quarto-dev/quarto-cli/blob/main/CONTRIBUTING.md).
 - [ ] referenced the GitHub issue this PR closes
 - [ ] updated the appropriate changelog

.github/workflows/test-smokes.yml

@@ -78,6 +78,8 @@ jobs:
       - uses: ./.github/workflows/actions/quarto-dev
 
       - name: Install Tinytex
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           quarto install tinytex
 

news/changelog-1.3.md

@@ -1,8 +1,11 @@
-## Changes
-
 ## Jupyter Notebooks
 
 - Add support for embedding cell outputs in quarto documents using `{{< embed >}}`. You can address cells by Id, Tag, or label, such as `{{< embed mynotebook.ipynb#fig-output >}}` which would embed the output of a cell with the label `fig-output`). You can also provide a list of ids like `{{< embed mynotebook.ipynb#fig-output,tbl-out >}}`.
+- Only attempt to postprocess `text/plain` output if it's nonempty ([#3896](https://github.com/quarto-dev/quarto-cli/issues/3896)).
+
+## Code Annotation
+
+- Add support for annotation of code cells (executable or non-executable). You can read more about code annotation at [https://www.quarto.org/docs/prerelease/1.3.html](https://www.quarto.org/docs/prerelease/1.3.html).
 
 ## HTML Format
 
@@ -33,6 +36,7 @@
 - Add support for automatically converting SVG images to PDF ([#2575](https://github.com/quarto-dev/quarto-cli/issues/2575))
 - Previously, if the `pdf-engine` was set to `latexmk`, we would bypass many features of Quarto and use Pandoc to produce the PDF output. Starting in in Quarto 1.3, all Quarto features will be enabled for the `latexmk` engine and `latexmk` will be used to run the PDF generation loop.
 - Fix author processing in default PDFs for complex author names (#3483)
+- Remove excessive vertical space between theorem type blocks ([#3776](https://github.com/quarto-dev/quarto-cli/issues/3776)).
 
 ## Beamer Format
 
@@ -64,6 +68,9 @@
 - Listings now support `template-params`, which will be passed to custom EJS templates in a variable called `templateParams` when a listing is rendered.
 - Custom listing objects now resolve `path: ` fields into the metadata that would be generated by standard listings, giving custom listing access to computed metadata like `reading-time`, etc.
 - Improve support for `date-modified` in listings
+- Improve support for `yml` based listings by supporting usage of title and description from `yml`.
+- Allow listings in project to point directly to non-input files (such as `yml` files) to use for contents.
+- Allow `sort: false` to disable any sorting, allowing items to appear in their original / natural order. (#3296)
 
 ## Websites
 
@@ -83,6 +90,10 @@
 
 - `quarto.version()` now returns `Version` object that simplifies comparison (thank you @tarleb)
 
+## HTML Output
+
+- HTML output will not decorate links within source code (for example, from `code-link: true`) with external icons. (#3755)
+
 ## Miscellaneous
 
 - Work around pandoc strict checking of `number-offset` type. ([#3126](https://github.com/quarto-dev/quarto-cli/issues/3126))
@@ -94,3 +105,12 @@
 - Add new `kbd` shortcode, to describe keyboard keys ([#3384](https://github.com/quarto-dev/quarto-cli/issues/3384)). See the [pre-release documentation](https://quarto.org/docs/prerelease/1.3.html) for details.
 - Replace default style for date picker component in OJS ([#2863](https://github.com/quarto-dev/quarto-cli/issues/2863)).
 - `quarto check` now supports `quarto check versions` for checking binary dependency versions in the case of custom binaries ([#3602](https://github.com/quarto-dev/quarto-cli/issues/3602)).
+- the API for shortcode handlers in lua now accepts a fourth parameter `raw_args` which hold the unparsed arguments in a table ([#3833](https://github.com/quarto-dev/quarto-cli/issues/3833)).
+- remove scaffolding div from conditional content in final output ([#3847](https://github.com/quarto-dev/quarto-cli/issues/3847)).
+- ensure proof titles are appended to paragraph nodes ([#3772](https://github.com/quarto-dev/quarto-cli/issues/3772)).
+- Support parsing markdown in table captions in LaTeX and HTML tables ([#2573](https://github.com/quarto-dev/quarto-cli/issues/2573)).
+
+## Pandoc filter changes
+
+- Quarto 1.3 introduces the notion of Custom AST nodes to Pandoc filters. If you use Lua filters for processing callouts, tabsets, or conditional blocks, consult the [pre-release documentation](https://quarto.org/docs/prerelease/1.3.html) for how to change your filters to support the new syntax.
+- Quarto 1.3 now processes HTML tables (in Markdown input) into Pandoc AST nodes, which can be processed by user filters and output into non-HTML formats. In addition, it supports "embedded Markdown content" which will be resolved by quarto's processing, including shortcode and crossref resolution. See the [prerelease documentation](https://quarto.org/docs/prerelease/1.3.html) for more.

package/src/common/package-filters.ts

@@ -26,18 +26,22 @@ export function buildFilter(
     return "";
   }).trimStart();
 
+  const importSrcs = [];
   // append imports to src
   const importRe = /^import\("(.*)?"\)$/gm;
   let match = importRe.exec(imports);
   while (match) {
     const importFilePath = join(filterDir, match[1]);
+    console.log(`Inlining ${match[1]} from ${importFilePath}`);
     let importSrc = Deno.readTextFileSync(importFilePath);
     if (!importSrc.endsWith("\n")) {
       importSrc += "\n";
     }
-    src = `${importSrc}\n` + src;
+    importSrcs.push(importSrc);
     match = importRe.exec(imports);
   }
+  importSrcs.push(src);
+  src = importSrcs.join("");
 
   // write src to dist
   info(`Writing inlined file ${output}`);

package/src/common/prepare-dist.ts

@@ -143,14 +143,10 @@ function inlineFilters(config: Configuration) {
   info("Building inlined filters");
   const outDir = join(config.directoryInfo.share, "filters");
   const filtersToInline: Filter[] = [
+    { name: "main", dir: "." },
+    { name: "pagebreak", dir: "rmarkdown" },
     { name: "quarto-init" },
-    { name: "normalize" },
-    { name: "quarto-pre" },
     { name: "crossref" },
-    { name: "layout" },
-    { name: "quarto-post" },
-    { name: "pagebreak", dir: "rmarkdown" },
-    { name: "quarto-finalize" },
   ];
 
   filtersToInline.forEach((filter) => {

quarto-cli.code-workspace

@@ -27,6 +27,13 @@
     },
     "[ejs]": {
       "editor.formatOnSave": false
-    }
+    },
+    "deno.inlayHints.enumMemberValues.enabled": false,
+    "deno.inlayHints.functionLikeReturnTypes.enabled": false,
+    "deno.inlayHints.parameterNames.enabled": "none",
+    "deno.inlayHints.parameterTypes.enabled": false,
+    "deno.inlayHints.propertyDeclarationTypes.enabled": false,
+    "deno.inlayHints.variableTypes.enabled": false,
+    "deno.inlayHints.variableTypes.suppressWhenTypeMatchesName": false
   }
 }

src/command/command.ts

@@ -28,6 +28,7 @@ import { useCommand } from "./use/cmd.ts";
 import { addCommand } from "./add/cmd.ts";
 import { uninstallCommand } from "./uninstall/cmd.ts";
 import { createCommand } from "./create/cmd.ts";
+import { editorSupportCommand } from "./editor-support/cmd.ts";
 
 // deno-lint-ignore no-explicit-any
 export function commands(): Command<any>[] {
@@ -54,5 +55,6 @@ export function commands(): Command<any>[] {
     toolsCommand,
     checkCommand,
     buildJsCommand,
+    editorSupportCommand,
   ];
 }

src/command/editor-support/cmd.ts

@@ -0,0 +1,17 @@
+/*
+* cmd.ts
+*
+* Copyright (C) 2020-2022 Posit Software, PBC
+*
+*/
+
+import { Command } from "cliffy/command/mod.ts";
+import { crossrefCommand } from "./crossref.ts";
+
+export const editorSupportCommand = new Command()
+  .name("editor-support")
+  .description(
+    "Miscellaneous tools to support Quarto editor modes",
+  )
+  .hidden()
+  .command("crossref", crossrefCommand);

src/command/editor-support/crossref.ts

@@ -0,0 +1,79 @@
+/*
+* command.ts
+*
+* Copyright (C) 2020-2022 Posit Software, PBC
+*
+*/
+
+import { join } from "path/posix.ts";
+import { readAll } from "streams/mod.ts";
+import { error } from "log/mod.ts";
+import { encode as base64Encode } from "encoding/base64.ts";
+
+import { Command } from "cliffy/command/mod.ts";
+
+import { execProcess } from "../../core/process.ts";
+import { pandocBinaryPath, resourcePath } from "../../core/resources.ts";
+import { globalTempContext } from "../../core/temp.ts";
+import { exitWithCleanup } from "../../core/cleanup.ts";
+
+export const crossrefCommand = new Command()
+  .description("Index cross references for content")
+  .action(async () => {
+    // read input
+    const stdinContent = await readAll(Deno.stdin);
+    const input = new TextDecoder().decode(stdinContent);
+
+    // create directory for indexing and write input into it
+    const indexingDir = globalTempContext().createDir();
+
+    // setup index file and input type
+    const indexFile = join(indexingDir, "index.json");
+    Deno.env.set("QUARTO_CROSSREF_INDEX_PATH", indexFile);
+    Deno.env.set("QUARTO_CROSSREF_INPUT_TYPE", "qmd");
+
+    // build command
+    const cmd = [pandocBinaryPath(), "+RTS", "-K512m", "-RTS"];
+    cmd.push(...[
+      "--from",
+      "markdown",
+      "--to",
+      "native",
+      "--data-dir",
+      resourcePath("pandoc/datadir"),
+      "--lua-filter",
+      resourcePath("filters/quarto-init/quarto-init.lua"),
+      "--lua-filter",
+      resourcePath("filters/crossref/crossref.lua"),
+    ]);
+
+    // create filter params
+    const filterParams = base64Encode(
+      JSON.stringify({
+        ["crossref-index-file"]: "index.json",
+        ["crossref-input-type"]: "qmd",
+      }),
+    );
+
+    // run pandoc
+    const result = await execProcess(
+      {
+        cmd,
+        cwd: indexingDir,
+        env: {
+          "QUARTO_FILTER_PARAMS": filterParams,
+          "QUARTO_SHARE_PATH": resourcePath(),
+        },
+      },
+      input,
+    );
+
+    // check for error
+    if (!result.success) {
+      error("Error running Pandoc: " + result.stderr);
+      exitWithCleanup(1);
+    }
+
+    // write back the index
+    Deno.stdout.writeSync(Deno.readFileSync(indexFile));
+  });

src/command/publish/account.ts

@@ -155,7 +155,7 @@ interface ProviderAccountToken extends AccountToken {
 export async function manageAccounts() {
   // build a list of all authorized accounts
   const accounts: ProviderAccountToken[] = [];
-  for (const provider of await publishProviders()) {
+  for (const provider of publishProviders()) {
     for (const account of await provider.accountTokens()) {
       if (account.type === AccountTokenType.Authorized) {
         accounts.push({ provider: provider.name, ...account });