Merge branch 'main' into post-render/logging

Author: cderv

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -13,7 +13,7 @@ body:
 
         - If you're reporting an issue with the **Visual Editor** or with the **Visual Studio Code / Positron extension**, please visit https://github.com/quarto-dev/quarto
         - If you're reporting an issue inside **RStudio**, please visit https://github.com/rstudio/rstudio
-        - If you're reporting an issue inside **Positron**, please visit https://github.com/posit-dev/positron
+        - If you're reporting an issue inside **Positron**, please visit https://github.com/posit-dev/positron/discussions
         - If you want to ask for a feature, please use the [Feature Requests GitHub Discussions](https://github.com/quarto-dev/quarto-cli/discussions/categories/feature-requests).
         - If you want to ask for help, please use the [Q&A GitHub Discussions](https://github.com/quarto-dev/quarto-cli/discussions/categories/q-a).
 

.github/workflows/create-release.yml

@@ -194,6 +194,8 @@ jobs:
 
   make-tarball-rhel:
     runs-on: ubuntu-latest
+    # temporarily disable due to unavailability of latest deno in conda-forge
+    if: false
     needs: [configure]
     steps:
       - uses: actions/checkout@v4

configuration

@@ -11,12 +11,12 @@
 # in src/command/check/check.ts
 
 # Binary dependencies
-export DENO=v2.3.1
+export DENO=v2.4.5
 # TODO figure out where 0.1.41 apple silicon libs are available
 export DENO_DOM=v0.1.41-alpha-artifacts
 export PANDOC=3.6.3
 export DARTSASS=1.87.0
-export ESBUILD=0.25.3
+export ESBUILD=0.25.10
 export TYPST=0.13.0
 
 

news/changelog-1.9.md

@@ -1,3 +1,10 @@
 All changes included in 1.9:
 
+## Regression fixes
 
+- ([#13396](https://github.com/quarto-dev/quarto-cli/issues/13396)): Fix `quarto publish connect` regression.
+
+## Dependencies
+
+- Update `esbuild` to 0.25.10
+- Update `deno` to 2.4.5

src/command/render/latexmk/texlive.ts

@@ -238,7 +238,7 @@ async function installPackage(
       quiet,
     );
     if (updateResult.code !== 0) {
-      return Promise.reject("Problem running `tlgmr update`.");
+      return Promise.reject("Problem running `tlmgr update`.");
     }
 
     // Rebuild format tree
@@ -277,7 +277,7 @@ async function installPackage(
       quiet,
     );
     if (updateResult.code !== 0) {
-      return Promise.reject("Problem running `tlgmr update`.");
+      return Promise.reject("Problem running `tlmgr update`.");
     }
 
     // Rebuild format tree

src/deno_ral/tar.ts

@@ -6,36 +6,47 @@
  * Abstraction layer over Deno's `tar` utilities.
  */
 
-import { TarStream, type TarStreamInput } from "jsr:@std/tar/tar-stream";
+import { TarStream, type TarStreamInput } from "tar/tar-stream";
+import { join } from "../deno_ral/path.ts";
+import { pathWithForwardSlashes } from "../core/path.ts";
 
 /**
  * Creates a tar archive from the specified files and directories.
  * @param outputPath The path where the tar archive will be created.
- * @param filePaths An array of file and directory paths to include in the tar archive. Paths are relative to outputPath.
+ * @param filePaths An array of file and directory paths to include in the tar archive.
+ * @param options Optional configuration for tar creation.
+ * @param options.baseDir Base directory for resolving relative paths in the archive.
  * @returns A promise that resolves when the tar archive is created.
  */
 export async function createTarFromFiles(
   outputPath: string,
   filePaths: string[],
+  options?: { baseDir?: string },
 ) {
+  const baseDir = options?.baseDir;
+
   // Create array of TarStreamInput objects from file paths
   const inputs: TarStreamInput[] = await Promise.all(
     filePaths.map(async (path) => {
-      const stat = await Deno.stat(path);
+      const fullPath = baseDir ? join(baseDir, path) : path;
+      const stat = await Deno.stat(fullPath);
+
+      // Use original path for archive, full path for reading
+      const archivePath = pathWithForwardSlashes(path);
 
       if (stat.isDirectory) {
         // Handle directory
         return {
           type: "directory",
-          path: path + (path.endsWith("/") ? "" : "/"),
+          path: archivePath + (archivePath.endsWith("/") ? "" : "/"),
         };
       } else {
         // Handle file
         return {
           type: "file",
-          path: path,
+          path: archivePath,
           size: stat.size,
-          readable: (await Deno.open(path)).readable,
+          readable: (await Deno.open(fullPath)).readable,
         };
       }
     }),

src/execute/julia.ts

@@ -3,7 +3,11 @@ import { join } from "../deno_ral/path.ts";
 import { MappedString, mappedStringFromFile } from "../core/mapped-text.ts";
 import { partitionMarkdown } from "../core/pandoc/pandoc-partition.ts";
 import { readYamlFromMarkdown } from "../core/yaml.ts";
-import { asMappedString } from "../core/lib/mapped-text.ts";
+import {
+  asMappedString,
+  mappedIndexToLineCol,
+  mappedLines,
+} from "../core/lib/mapped-text.ts";
 import { ProjectContext } from "../project/types.ts";
 import {
   DependenciesOptions,
@@ -52,6 +56,13 @@ import {
   isJupyterPercentScript,
   markdownFromJupyterPercentScript,
 } from "./jupyter/percent.ts";
+import { resolve } from "path";
+
+export interface SourceRange {
+  lines: [number, number];
+  file?: string;
+  sourceLines?: [number, number];
+}
 
 export interface JuliaExecuteOptions extends ExecuteOptions {
   oneShot: boolean; // if true, the file's worker process is closed before and after running
@@ -578,6 +589,64 @@ function getConsoleColumns(): number | null {
   }
 }
 
+function buildSourceRanges(markdown: MappedString): Array<SourceRange> {
+  const lines = mappedLines(markdown);
+  const sourceRanges: Array<SourceRange> = [];
+  let currentRange: SourceRange | null = null;
+
+  lines.forEach((line, index) => {
+    // Get mapping info directly from the line's MappedString
+    const mapResult = line.map(0, true);
+    if (mapResult) {
+      const { originalString } = mapResult;
+      const lineColFunc = mappedIndexToLineCol(originalString);
+      const lineCol = lineColFunc(mapResult.index);
+      const fileName = originalString.fileName
+        ? resolve(originalString.fileName) // resolve to absolute path using cwd
+        : undefined;
+      const sourceLineNum = lineCol.line;
+
+      // Check if this line continues the current range
+      if (
+        currentRange &&
+        currentRange.file === fileName &&
+        fileName !== undefined &&
+        currentRange.sourceLines &&
+        currentRange.sourceLines[1] === sourceLineNum
+      ) {
+        // Extend current range
+        currentRange.lines[1] = index + 1; // +1 because lines are 1-indexed
+        currentRange.sourceLines[1] = sourceLineNum + 1;
+      } else {
+        // Start new range
+        if (currentRange) {
+          sourceRanges.push(currentRange);
+        }
+        currentRange = {
+          lines: [index + 1, index + 1], // +1 because lines are 1-indexed
+        };
+        if (fileName !== undefined) {
+          currentRange.file = fileName;
+          currentRange.sourceLines = [sourceLineNum + 1, sourceLineNum + 1];
+        }
+      }
+    } else {
+      // No mapping available - treat as separate range
+      if (currentRange) {
+        sourceRanges.push(currentRange);
+        currentRange = null;
+      }
+    }
+  });
+
+  // Don't forget the last range
+  if (currentRange) {
+    sourceRanges.push(currentRange);
+  }
+
+  return sourceRanges;
+}
+
 async function executeJulia(
   options: JuliaExecuteOptions,
 ): Promise<JupyterNotebook> {
@@ -600,9 +669,12 @@ async function executeJulia(
       );
     }
   }
+
+  const sourceRanges = buildSourceRanges(options.target.markdown);
+
   const response = await writeJuliaCommand(
     conn,
-    { type: "run", content: { file, options } },
+    { type: "run", content: { file, options, sourceRanges } },
     transportOptions.key,
     options,
     (update: ProgressUpdate) => {
@@ -643,7 +715,14 @@ interface ProgressUpdate {
 type empty = Record<string | number | symbol, never>;
 
 type ServerCommand =
-  | { type: "run"; content: { file: string; options: JuliaExecuteOptions } }
+  | {
+    type: "run";
+    content: {
+      file: string;
+      options: JuliaExecuteOptions;
+      sourceRanges: Array<SourceRange>;
+    };
+  }
   | { type: "close"; content: { file: string } }
   | { type: "forceclose"; content: { file: string } }
   | { type: "isopen"; content: { file: string } }
@@ -854,7 +933,9 @@ function populateJuliaEngineCommand(command: Command) {
       "Get status information on the currently running Julia server process.",
     ).action(logStatus)
     .command("kill", "Kill server")
-    .description("Kill the control server if it is currently running. This will also kill all notebook worker processes.")
+    .description(
+      "Kill the control server if it is currently running. This will also kill all notebook worker processes.",
+    )
     .action(killJuliaServer)
     .command("log", "Print julia server log")
     .description(

src/publish/common/bundle.ts

@@ -10,10 +10,7 @@ import { ensureDirSync } from "../../deno_ral/fs.ts";
 import { PublishFiles } from "../provider-types.ts";
 import { TempContext } from "../../core/temp-types.ts";
 import { md5HashBytes } from "../../core/hash.ts";
-import { pathWithForwardSlashes } from "../../core/path.ts";
 
-import { copy } from "io/copy";
-import { TarStream, type TarStreamInput } from "tar/tar-stream";
 import { createTarFromFiles } from "../../deno_ral/tar.ts";
 
 interface ManifestMetadata {
@@ -110,7 +107,7 @@ export async function createBundle(
   // await copy(tar.getReader(), writer);
   // writer.close();
 
-  await createTarFromFiles(tarFile, tarFiles);
+  await createTarFromFiles(tarFile, tarFiles, { baseDir: stageDir });
 
   // compress to tar.gz
   const targzFile = `${tarFile}.gz`;

src/resources/julia/Project.toml

@@ -1,5 +1,8 @@
 [deps]
 QuartoNotebookRunner = "4c0109c6-14e9-4c88-93f0-2b974d3468f4"
 
-[compat]
-QuartoNotebookRunner = "=0.17.3"
+# [compat]
+# QuartoNotebookRunner = "=0.17.3"
+
+[sources]
+QuartoNotebookRunner = {url = "https://github.com/PumasAI/QuartoNotebookRunner.jl", rev = "jk/source-ranges"}

tests/docs/smoke-all/julia/_included.qmd

@@ -0,0 +1,3 @@
+```{julia}
+"$(@__FILE__):$(@__LINE__)"
+```