Merge branch 'main' into feature/finegrained-luacov

Author: cscheid

.github/workflows/actions/quarto-dev/action.yml

@@ -39,6 +39,7 @@ runs:
         If ( "$(git status --porcelain)" -ne "" ) { Exit 1 }
 
     - name: Quarto Check
+      if:  runner.debug == '1'
       working-directory: tests
       shell: pwsh
       run: quarto check

.github/workflows/test-smokes.yml

@@ -124,9 +124,9 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
+          python-version: "3.11"
           cache: "pipenv"
           cache-dependency-path: "./tests/Pipfile.lock"
-          python-version-file: "./tests/.python-version"
 
       - name: Restore Python Dependencies
         working-directory: tests
@@ -148,16 +148,24 @@ jobs:
       - name: Setup Julia
         uses: julia-actions/setup-julia@v1
         with:
-          version: 1.8.5
+          version: 1.9.3
 
       - name: Cache Julia Packages
         uses: julia-actions/cache@v1
+        with:
+          cache-name: version-1
+          cache-registries: true
 
       - name: Restore Julia Packages
         working-directory: tests
         shell: bash
         run: |
-          julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.build(\"IJulia\"); Pkg.precompile()"
+          # Setup IJulia with the jupyter from the Python environment
+          # https://julialang.github.io/IJulia.jl/stable/manual/installation/
+          export JUPYTER=$(find $(dirname $(pipenv run which jupyter))/ -type f -name "jupyter.exe" -o -name "jupyter")        
+          pipenv run julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.build(\"IJulia\"); Pkg.precompile()"
+          echo "Julia Jupyter:"
+          julia --project=. -e "import IJulia;println(IJulia.JUPYTER);println(IJulia.find_jupyter_subcommand(\"notebook\"))"
 
       - name: Setup timing file for timed test
         if: ${{ matrix.time-test == true }}

configuration

@@ -18,7 +18,7 @@ export TYPST=0.8.0
 # Bootstrap dependencies from bslib
 # (use commit hash from bslib repo)
 export BOOTSTRAP=ad946cafdbf1c91cfd714cb39948bb203ae66e66 # 0.5.1 + consolidated components
-export HTMLTOOLS=0.5.6
+export HTMLTOOLS=0.5.7
 export BOOTSTRAP_FONT=1.11.1
 export BOOTSWATCH=5.3.1
 

news/changelog-1.4.md

@@ -11,7 +11,7 @@
 
 ## Dependencies
 
-- Update to Pandoc 3.1.6.1
+- Update to Pandoc 3.1.8
 - Update to Typst 0.7.0
 
 ## HTML Format
@@ -38,6 +38,7 @@
 - ([#6833](https://github.com/quarto-dev/quarto-cli/issues/6833)): Handle partially-specified aspect ratio, width, and height attributes in `video` shortcode.
 - ([#7137](https://github.com/quarto-dev/quarto-cli/discussions/7137)): Automatically set `rel="noopener"` when setting a target on external links
 - ([#7187](https://github.com/quarto-dev/quarto-cli/issues/7187)): Add `html-table-processing: none` to document- and project-level metadata to disable HTML table processing. Add `{html-table-processing="none"}` to a fenced div to disable HTML table processing for the elements in that div. Add `html-table-processing: none` on knitr or jupyter cell to disable HTML table processing for the cell output content.
+- ([#7441](https://github.com/quarto-dev/quarto-cli/issues/7441)): Links in hover box (e.g. links to DOI when hover for citations is opt-in) are now correctly process for external and new window processing (when `link-external-icon: true` and `link-external-newwindow: true`).
 
 ## Appendix
 
@@ -119,6 +120,7 @@
 - ([#5932](https://github.com/quarto-dev/quarto-cli/issues/5932)): Correct Open Graph metadata key name for `og:site_name`
 - ([#6432](https://github.com/quarto-dev/quarto-cli/issues/6432)): Don't decorate navigation tools with external link icon (we generally don't decorate navigation chrome in this way)
 - ([#6708](https://github.com/quarto-dev/quarto-cli/issues/6708)): Prevent duplication of footnotes within the abstract or description within websites and books.
+- ([#7447](https://github.com/quarto-dev/quarto-cli/issues/7447)): Changing the `$primary` color in a SCSS theme will now properly change the navigation bar background color.
 
 ## Website Search
 
@@ -222,6 +224,7 @@
 ## Other Fixes and Improvements
 
 - Exit if project pre or post render script fails
+- Support `--output-dir` for rendering individual files.
 - Use InternalError in typescript code, and offer a more helpful error message when an internal error happens.
 - ([#1392](https://github.com/quarto-dev/quarto-cli/issues/1392)): Add tools and LaTeX information to `quarto check` output.
 - ([#2214](https://github.com/quarto-dev/quarto-cli/issues/2214), reopened): don't report a non-existing version of Google Chrome in macOS.
@@ -251,3 +254,4 @@
 - ([#7032](https://github.com/quarto-dev/quarto-cli/issues/7032)): `quarto` is now correctly working when installed in a folder with spaces in path.
 - ([#7131](https://github.com/quarto-dev/quarto-cli/issues/7131)): Fix typo in ISBN entry for JATS subarticle template (author: @jasonaris).
 - ([#3599](https://github.com/quarto-dev/quarto-cli/issues/3599), [#5870](https://github.com/quarto-dev/quarto-cli/issues/5870)): Fix hash issue causing unexpected render when `freeze` is activated on Windows but re-rendered on Linux (e.g. in Github Action).
+- ([#7252](https://github.com/quarto-dev/quarto-cli/issues/7252)): Improve handling with `tlmgr` of some mismatched LaTeX support files, associated with `expl3.sty` loading.

src/command/render/cmd.ts

@@ -36,7 +36,7 @@ export const renderCommand = new Command()
   )
   .option(
     "--output-dir",
-    "Write project output to DIR (path is project relative)",
+    "Write output to DIR (path is input/project relative)",
   )
   .option(
     "-M, --metadata",

src/command/render/latexmk/parse-error.ts

@@ -230,7 +230,7 @@ const packageMatchers = [
       return "lua-uni-algos.lua";
     },
   },
-
+  { regex: /.* Loading '([^']+)' aborted!.*/g },
   { regex: /.*! LaTeX Error: File `([^']+)' not found.*/g },
   { regex: /.* file ['`]?([^' ]+)'? not found.*/g },
   { regex: /.*the language definition file ([^ ]+) .*/g },

src/command/render/latexmk/pdf.ts

@@ -156,7 +156,6 @@ async function initialCompileLatex(
   quiet?: boolean,
 ) {
   let packagesUpdated = false;
-  let tlmgrUpdated = false;
   while (true) {
     // Run the pdf engine
     const response = await runPdfEngine(
@@ -197,7 +196,6 @@ async function initialCompileLatex(
           logProgress("updating tlmgr");
         }
         await pkgMgr.updatePackages(false, true);
-        tlmgrUpdated = true;
         info("");
 
         if (!quiet) {
@@ -208,23 +206,6 @@ async function initialCompileLatex(
       }
 
       const logText = Deno.readTextFileSync(response.log);
-      // See if tlmgr just needs to be updated
-      // https://github.com/rstudio/tinytex/commit/5946a2a1bf3c6ecefbd1213178a4e473ff4c26dc
-      // https://github.com/quarto-dev/quarto-cli/issues/7087
-      if (logText.match(/.* Loading '([^']+)' aborted!/)) {
-        if (!tlmgrUpdated) {
-          continue;
-        } else {
-          // We've already tried updating, just need to throw and die
-          // We failed to install packages (but there are missing packages), give up
-          displayError(
-            "tlmgr needs to be updated, but the update failed",
-            response.log,
-            response.result,
-          );
-          return Promise.reject();
-        }
-      }
 
       // Try to find and install packages
       const packagesInstalled = await findAndInstallPackages(

src/command/render/latexmk/texlive.ts

@@ -225,6 +225,28 @@ async function installPackage(
   opts?: string[],
   quiet?: boolean,
 ) {
+  // if any packages have been installed already, update packages first
+  let isInstalled = await verifyPackageInstalled(pkg, context);
+  if (isInstalled) {
+    // update tlmgr itself
+    const updateResult = await updatePackages(
+      true,
+      true,
+      context,
+      opts,
+      quiet,
+    );
+    if (updateResult.code !== 0) {
+      return Promise.reject();
+    }
+
+    // Rebuild format tree
+    const fmtutilResult = await fmtutilCommand(context);
+    if (fmtutilResult.code !== 0) {
+      return Promise.reject();
+    }
+  }
+
   // Run the install command
   let installResult = await tlmgrCommand(
     "install",
@@ -240,8 +262,8 @@ async function installPackage(
     );
   }
 
-  // Check whether we should update and retry the install
-  const isInstalled = await verifyPackageInstalled(pkg, context);
+  // Check whether we should update again and retry the install
+  isInstalled = await verifyPackageInstalled(pkg, context);
   if (!isInstalled) {
     // update tlmgr itself
     const updateResult = await updatePackages(
@@ -255,6 +277,12 @@ async function installPackage(
       return Promise.reject();
     }
 
+    // Rebuild format tree
+    const fmtutilResult = await fmtutilCommand(context);
+    if (fmtutilResult.code !== 0) {
+      return Promise.reject();
+    }
+
     // Rerun the install command
     installResult = await tlmgrCommand(
       "install",
@@ -417,3 +445,16 @@ function tlmgrCommand(
     return execTlmgr([tlmgr.fullPath, tlmgrCmd, ...args]);
   }
 }
+
+// Execute fmtutil
+// https://tug.org/texlive/doc/fmtutil.html
+function fmtutilCommand(context: TexLiveContext) {
+  const fmtutil = texLiveCmd("fmtutil-sys", context);
+  return execProcess(
+    {
+      cmd: [fmtutil.fullPath, "--all"],
+      stdout: "piped",
+      stderr: "piped",
+    },
+  );
+}

src/command/render/pandoc.ts

@@ -960,7 +960,7 @@ export async function runPandoc(
     );
   });
 
-  // Ensure that citationMetadat is expanded into
+  // Ensure that citationMetadata is expanded into
   // and object for downstream use
   if (
     typeof (pandocMetadata[kCitation]) === "boolean" &&

src/command/render/project.ts

@@ -173,7 +173,8 @@ export async function renderProject(
   // if there is an output dir then remove it if clean is specified
   if (
     renderAll && hasProjectOutputDir(context) &&
-    (options.flags?.clean == true) && (projType.cleanOutputDir === true)
+    (options.forceClean ||
+      (options.flags?.clean == true) && (projType.cleanOutputDir === true))
   ) {
     // ouptut dir
     const realProjectDir = normalizePath(context.dir);