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quarto-issues

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## Main - [ ] Update main dependency - [ ] Update plugins - [ ] Check and document new features - [ ] Update tests ## New features - [ ] [Custom fragments](https://revealjs.com/fragments/#custom-fragments) (https://github.com/quarto-dev/quarto-cli/discussions/4794) - [ ] [New go to slide shortcut](https://revealjs.com/jump-to-slide/)

### Bug description Just create a book project and render it. References should be rendered in the page references as stipulated by the yaml. However in quarto 1.3.260 references are also included in each chapter where they are referenced. `quarto create-project abook --type book ` render from RStudio quarto version 1.3.260, RStudio version 2022.12.1 Build 362, windows 11 OS and macOS as well. (note deno is up to date) ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Rendering a project results in 404 error: <img width="1386" alt="image" src="https://user-images.githubusercontent.com/8541095/224642709-9f98dcde-0d3c-467b-aa92-342671604c0b.png"> Quarto-VS v1.73.0

When I render a qmd in a directory with a notebook, it overwrites and deletes the notebook. This happens both when rendering on the CLI and when using "Quarto: Render Project". I believe this is happening during execution. Can Quarto please rely on a temporary notebook for rendering qmd files rather than potentially clobbering the existing one? Quarto-VS v1.73.0

### Bug description Ubuntu 20.04, running the below file from vscode's render causes the text at the bottom of this file to run off the bottom of the page. A new page is not created, If I put, say, a plot on the next page to force a new page, the text still does not appear. Removing the second table seems to fix things. ```` --- title: "Tables trouble" author: "Daniel Claborne" format: pdf engine: knitr execute: echo: false message: false warning: false editor: visual --- ## A HEADER! ### such header Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur, from a Lorem Ipsum passage, and going through the cites of the word in classical literature, discovered the undoubtable source. Lorem Ipsum comes from sections 1.10.32 and 1.10.33 of "de Finibus Bonorum et Malorum" (The Extremes of Good and Evil) by Cicero, written in 45 BC. This book is a treatise on the theory of ethics, very popular during the Renaissance. The first line of Lorem Ipsum, "Lorem ipsum dolor sit amet..", comes from a line in section 1.10.32. ```{r} #| label: fig-ggplot #| fig-cap: "a plot that is very good" library(ggplot2) library(knitr) ggplot(aes(x = 1:1000, y = 1:1000), data = NULL) + geom_point() ``` ### header3[^asdf] **boldtext** Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur. @tbl-tab1 [^asdf]: footnote ```{r} #| label: tbl-tab1 #| tbl-cap: "a table using kable" kable(table(c(1,2,3), c(1,2,3)), row.names = TRUE) ``` **b)** Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur. @tbl-tab2 <!-- ```{r} #| label: tbl-tab2 #| tbl-cap: "A pipe table" cmatrix = data.frame( "1" = c(7, 0, 5, 2), "2" = c(0, 20, 0, 1), "3" = c(0, 0, 62, 27), "4" = c(0, 0, 2, 9), check.names = FALSE ) rownames(cmatrix) = c("1", "2", "3", "4") kable(cmatrix, row.names = TRUE) ``` --> | | 1 | 2 | 3 | 4 | |---|---|----|----|---| | 1 | 7 | 0 | 5 | 0 | | 2 | 0 | 20 | 1 | 0 | | 3 | 0 | 0 | 62 | 2 | | 4 | 2 | 1 | 27 | 9 | : A pipe table {#tbl-tab2} ## Wow, now thats a header **part 1** Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur, from a Lorem Ipsum passage, and going through the cites of the word in classical literature, discovered the undoubtable source. Lorem Ipsum comes from sections 1.10.32 and 1.10.33 of "de Finibus Bonorum et Malorum" (The Extremes of Good and Evil) by Cicero, written in 45 BC. This book is a treatise on the theory of ethics, very popular during the Renaissance. The first line of Lorem Ipsum, "Lorem ipsum dolor sit amet..", comes from a line in section 1.10.32. Contrary to popular belief, Lorem Ipsum is not simply random text. It has roots in a piece of classical Latin literature from 45 BC, making it over 2000 years old. Richard McClintock, a Latin professor at Hampden-Sydney College in Virginia, looked up one of the more obscure Latin words, consectetur, from a Lorem Ipsum passage, and going through the cites of the word in classical literature, discovered the undoubtable source. Lorem Ipsum comes from sections [TEXT IS CUT OFF APPROXIMATELY HERE aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaAAaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaAAaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaAAaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaAAaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaAAaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaAA ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

`validate-yaml: false` only works if it exists in the YAML itself. That's annoying.

Looking for "short caption" in quarto docs yields the code cell options, but nothing on LaTeX authoring. See #4776 for the confusion this generates.

TIL via @tarleb that `PANDOC_STATE.log` has a list of warning strings emitted by Pandoc. We could forward those to the front-end in `quarto preview` so they'd be more visible.

### Bug description _No response_ ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Quarto renders the nbdev2 `#|export` directives in Jupyter notebooks as `::: {.cell 0=‘e’ 1=‘x’ 2=‘p’ 3=‘o’ 4=‘r’ 5=‘t’}` ... `:::`. This is preventing me using nbdev2 together with my Quarto blog. I'm running Quarto dev version from git, on Debian GNU/Linux 12 testing (bookworm). I also tried the latest Quarto release, a previous release, and an old version from git on July 2022; and I found the same behaviour in each case. Screenshot of notebook:  Screenshot of wrong rendered HTML web page:  Minimal example file, quarto_export.ipynb: ```json { "cells": [ { "cell_type": "raw", "id": "f360288e-bb2e-4bd7-9120-a313b9b0f6b5", "metadata": {}, "source": [ "---\n", "title: \"quarto renders #|export wrongly\"\n", "---" ] }, { "cell_type": "code", "execution_count": null, "id": "b38565d2-0b01-4e99-9b3f-4c97250d12c3", "metadata": {}, "outputs": [], "source": [ "#|export\n", "print(\"Hello, world\")" ] } ], "metadata": { "kernelspec": { "display_name": "python3", "language": "python", "name": "python3" } }, "nbformat": 4, "nbformat_minor": 5 } ``` Then when I run: ``` $ quarto render quarto_export.ipynb pandoc to: html output-file: quarto_export.html standalone: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png metadata document-css: false link-citations: true date-format: long lang: en title: 'quarto renders #|export wrongly' ``` I get this HTML output, text dump of the HTML: ``` $ lynx -dump quarto_export.html quarto renders #|export wrongly ::: {.cell 0=‘e’ 1=‘x’ 2=‘p’ 3=‘o’ 4=‘r’ 5=‘t’} print("Hello, world")(BUTTON) ::: References Visible links: Hidden links: 2. file://localhost/home/sam/ai/bugs/quarto_export.html#cb1-1 ``` The wrong part of the HTML: ```html <p>::: {.cell 0=‘e’ 1=‘x’ 2=‘p’ 3=‘o’ 4=‘r’ 5=‘t’}</p> <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="st">"Hello, world"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div> <p>:::</p> ``` Full HTML: ```html <!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head> <meta charset="utf-8"> <meta name="generator" content="quarto-99.9.9"> <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes"> <title>quarto renders #|export wrongly</title> <style> code{white-space: pre-wrap;} span.smallcaps{font-variant: small-caps;} div.columns{display: flex; gap: min(4vw, 1.5em);} div.column{flex: auto; overflow-x: auto;} div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} ul.task-list{list-style: none;} ul.task-list li input[type="checkbox"] { width: 0.8em; margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ vertical-align: middle; } /* CSS for syntax highlighting */ pre > code.sourceCode { white-space: pre; position: relative; } pre > code.sourceCode > span { display: inline-block; line-height: 1.25; } pre > code.sourceCode > span:empty { height: 1.2em; } .sourceCode { overflow: visible; } code.sourceCode > span { color: inherit; text-decoration: inherit; } div.sourceCode { margin: 1em 0; } pre.sourceCode { margin: 0; } @media screen { div.sourceCode { overflow: auto; } } @media print { pre > code.sourceCode { white-space: pre-wrap; } pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; } } pre.numberSource code { counter-reset: source-line 0; } pre.numberSource code > span { position: relative; left: -4em; counter-increment: source-line; } pre.numberSource code > span > a:first-child::before { content: counter(source-line); position: relative; left: -1em; text-align: right; vertical-align: baseline; border: none; display: inline-block; -webkit-touch-callout: none; -webkit-user-select: none; -khtml-user-select: none; -moz-user-select: none; -ms-user-select: none; user-select: none; padding: 0 4px; width: 4em; } pre.numberSource { margin-left: 3em; padding-left: 4px; } div.sourceCode { } @media screen { pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } } </style> <script src="quarto_export_files/libs/clipboard/clipboard.min.js"></script> <script src="quarto_export_files/libs/quarto-html/quarto.js"></script> <script src="quarto_export_files/libs/quarto-html/popper.min.js"></script> <script src="quarto_export_files/libs/quarto-html/tippy.umd.min.js"></script> <script src="quarto_export_files/libs/quarto-html/anchor.min.js"></script> <link href="quarto_export_files/libs/quarto-html/tippy.css" rel="stylesheet"> <link href="quarto_export_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"> <script src="quarto_export_files/libs/bootstrap/bootstrap.min.js"></script> <link href="quarto_export_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet"> <link href="quarto_export_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light"> </head> <body class="fullcontent"> <div id="quarto-content" class="page-columns page-rows-contents page-layout-article"> <main class="content" id="quarto-document-content"> <header id="title-block-header" class="quarto-title-block default"> <div class="quarto-title"> <h1 class="title">quarto renders #|export wrongly</h1> </div> <div class="quarto-title-meta"> </div> </header> <p>::: {.cell 0=‘e’ 1=‘x’ 2=‘p’ 3=‘o’ 4=‘r’ 5=‘t’}</p> <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="st">"Hello, world"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div> <p>:::</p> </main> <!-- /main column --> <script id="quarto-html-after-body" type="application/javascript"> window.document.addEventListener("DOMContentLoaded", function (event) { const toggleBodyColorMode = (bsSheetEl) => { const mode = bsSheetEl.getAttribute("data-mode"); const bodyEl = window.document.querySelector("body"); if (mode === "dark") { bodyEl.classList.add("quarto-dark"); bodyEl.classList.remove("quarto-light"); } else { bodyEl.classList.add("quarto-light"); bodyEl.classList.remove("quarto-dark"); } } const toggleBodyColorPrimary = () => { const bsSheetEl = window.document.querySelector("link#quarto-bootstrap"); if (bsSheetEl) { toggleBodyColorMode(bsSheetEl); } } toggleBodyColorPrimary(); const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { placement: 'right', icon: icon }; anchorJS.add('.anchored'); const isCodeAnnotation = (el) => { for (const clz of el.classList) { if (clz.startsWith('code-annotation-')) { return true; } } return false; } const clipboard = new window.ClipboardJS('.code-copy-button', { text: function(trigger) { const codeEl = trigger.previousElementSibling.cloneNode(true); for (const childEl of codeEl.children) { if (isCodeAnnotation(childEl)) { childEl.remove(); } } return codeEl.innerText; } }); clipboard.on('success', function(e) { // button target const button = e.trigger; // don't keep focus button.blur(); // flash "checked" button.classList.add('code-copy-button-checked'); var currentTitle = button.getAttribute("title"); button.setAttribute("title", "Copied!"); let tooltip; if (window.bootstrap) { button.setAttribute("data-bs-toggle", "tooltip"); button.setAttribute("data-bs-placement", "left"); button.setAttribute("data-bs-title", "Copied!"); tooltip = new bootstrap.Tooltip(button, { trigger: "manual", customClass: "code-copy-button-tooltip", offset: [0, -8]}); tooltip.show(); } setTimeout(function() { if (tooltip) { tooltip.hide(); button.removeAttribute("data-bs-title"); button.removeAttribute("data-bs-toggle"); button.removeAttribute("data-bs-placement"); } button.setAttribute("title", currentTitle); button.classList.remove('code-copy-button-checked'); }, 1000); // clear code selection e.clearSelection(); }); function tippyHover(el, contentFn) { const config = { allowHTML: true, content: contentFn, maxWidth: 500, delay: 100, arrow: false, appendTo: function(el) { return el.parentElement; }, interactive: true, interactiveBorder: 10, theme: 'quarto', placement: 'bottom-start' }; window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); for (var i=0; i<noterefs.length; i++) { const ref = noterefs[i]; tippyHover(ref, function() { // use id or data attribute instead here let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href'); try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); return note.innerHTML; }); } let selectedAnnoteEl; const selectorForAnnotation = ( cell, annotation) => { let cellAttr = 'data-code-cell="' + cell + '"'; let lineAttr = 'data-code-annotation="' + annotation + '"'; const selector = 'span[' + cellAttr + '][' + lineAttr + ']'; return selector; } const selectCodeLines = (annoteEl) => { const doc = window.document; const targetCell = annoteEl.getAttribute("data-target-cell"); const targetAnnotation = annoteEl.getAttribute("data-target-annotation"); const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation)); const lines = annoteSpan.getAttribute("data-code-lines").split(","); const lineIds = lines.map((line) => { return targetCell + "-" + line; }) let top = null; let height = null; let parent = null; if (lineIds.length > 0) { //compute the position of the single el (top and bottom and make a div) const el = window.document.getElementById(lineIds[0]); top = el.offsetTop; height = el.offsetHeight; parent = el.parentElement.parentElement; if (lineIds.length > 1) { const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]); const bottom = lastEl.offsetTop + lastEl.offsetHeight; height = bottom - top; } if (top !== null && height !== null && parent !== null) { // cook up a div (if necessary) and position it let div = window.document.getElementById("code-annotation-line-highlight"); if (div === null) { div = window.document.createElement("div"); div.setAttribute("id", "code-annotation-line-highlight"); div.style.position = 'absolute'; parent.appendChild(div); } div.style.top = top - 2 + "px"; div.style.height = height + 4 + "px"; let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter"); if (gutterDiv === null) { gutterDiv = window.document.createElement("div"); gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter"); gutterDiv.style.position = 'absolute'; const codeCell = window.document.getElementById(targetCell); const gutter = codeCell.querySelector('.code-annotation-gutter'); gutter.appendChild(gutterDiv); } gutterDiv.style.top = top - 2 + "px"; gutterDiv.style.height = height + 4 + "px"; } selectedAnnoteEl = annoteEl; } }; const unselectCodeLines = () => { const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"]; elementsIds.forEach((elId) => { const div = window.document.getElementById(elId); if (div) { div.remove(); } }); selectedAnnoteEl = undefined; }; // Attach click handler to the DT const annoteDls = window.document.querySelectorAll('dt[data-target-cell]'); for (const annoteDlNode of annoteDls) { annoteDlNode.addEventListener('click', (event) => { const clickedEl = event.target; if (clickedEl !== selectedAnnoteEl) { unselectCodeLines(); const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active'); if (activeEl) { activeEl.classList.remove('code-annotation-active'); } selectCodeLines(clickedEl); clickedEl.classList.add('code-annotation-active'); } else { // Unselect the line unselectCodeLines(); clickedEl.classList.remove('code-annotation-active'); } }); } const findCites = (el) => { const parentEl = el.parentElement; if (parentEl) { const cites = parentEl.dataset.cites; if (cites) { return { el, cites: cites.split(' ') }; } else { return findCites(el.parentElement) } } else { return undefined; } }; var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); for (var i=0; i<bibliorefs.length; i++) { const ref = bibliorefs[i]; const citeInfo = findCites(ref); if (citeInfo) { tippyHover(citeInfo.el, function() { var popup = window.document.createElement('div'); citeInfo.cites.forEach(function(cite) { var citeDiv = window.document.createElement('div'); citeDiv.classList.add('hanging-indent'); citeDiv.classList.add('csl-entry'); var biblioDiv = window.document.getElementById('ref-' + cite); if (biblioDiv) { citeDiv.innerHTML = biblioDiv.innerHTML; } popup.appendChild(citeDiv); }); return popup.innerHTML; }); } } }); </script> </div> <!-- /content --> </body></html> ``` A similar slightly larger example: https://github.com/sswam/ai/blob/main/blog/posts/nbdev_vs_quarto/nbdev_vs_quarto.ipynb The rendered HTML: https://sam.ucm.dev/blog/posts/nbdev_vs_quarto/nbdev_vs_quarto.html ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Hello, Per this [issue](https://github.com/pandoc/lua-filters/issues/265), I am reporting a bug when trying to crossreference a figure: Using quarto, I am unable to crossref using regular citation syntax, with short-captions.lua pandoc filter. Figures without the short caption filter can be crossreferenced but not with that filter. I am forced to use the latex alternative which is less practical for another reason. I am not sure if the problem comes from quarto or this filter. `![**Bold caption** [@Armas.2004]](figure.jpeg){#fig-cap short-caption="**short-cap**"}` `@fig-cap` returns **?@fig-cap** Anything that is not `@fig- `breaks as quarto expects a bibliography citation instead. `@fig:test` returns (fig:test<empty citation>). `\ref{fig-cap}` works. [Here is a minimal reproductible example.](https://github.com/pandoc/lua-filters/files/10949365/short-captions-test.zip) Instead, I have to use \ref{fig-cap} to reference my figure. The issue is that going to visual mode would remove the bold modifications I make, which is why I would have liked to use the quarto syntax. For example, `(**Figure \ref{fig-cap}**)` is returned as `(**Figure** \ref{fig-cap})` in visual mode which is not what I want. I am using the latest version of quarto (1.2.335) and RStudio (4.2.2) on Windows 11, 22H2 lastest version. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Currently, when running `quarto preview` for a while and editing multiple pages, there's lots of output on `stdout`. If I accidentally close the tab with the preview (and if I'm not able to reopen it because it's been a while), I'm not able to go back to the terminal and see the URL where the preview server is hosting the code. I have to either try to scroll all the way up (sometimes this has exceeded my scrollback buffer) or I have to restart `quarto preview` (which before using `freeze` and `cache` took a long time to execute). One of these options would solve it for me - Either show the URL after updates, or allow the user to press a key that prints out the URL. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description To simplify my large project, I rely on subdirectories, each of which contains a "listing" file. For example: ``` ├── grid │   ├── famous_deaths.qmd │   └── gridpost.qmd - index.qmd ``` where `gridpost.qmd` just has a `listing` item in its metadata yml. the output correctly shows the grid listing, but the thumbnails are missing. Hint: from inspecting the html code that was generated, it appears that the pathnames are screwed up. Instead of `<src = "image.jpg" /> ` it generates `<src = "grid/image.jpg" /> I placed a simple example of this in [my github repo](https://github.com/richardsprague/quartosample/tree/extrapage). The thumbnails display correctly on v1.2, but not on v1.3.257. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description I have a number of really short blog posts that are quick notes or just references for myself. <img width="226" alt="image" src="https://user-images.githubusercontent.com/1813121/224511459-43309a98-dec5-487e-918c-5c8e11246d40.png"> They all render as `0 min` in the reading time for the table view in the index page listings. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

As originally discussed in #2249, here is a separate issue to discuss exposing LUA variables. Currently, users do not have access to all LUA variables (from Quarto and Pandoc) which could be useful. With that in mind I wrote a LUA filter/shortcode (<https://github.com/mcanouil/quarto-lua-env>) to expose the following objects recursively, or at least the scalar variables. ``` lua-env: quarto: "quarto" pandoc: PANDOC_STATE: "PANDOC_STATE" FORMAT: "FORMAT" PANDOC_READER_OPTIONS: "PANDOC_READER_OPTIONS" PANDOC_WRITER_OPTIONS: "PANDOC_WRITER_OPTIONS" PANDOC_VERSION: "PANDOC_VERSION" PANDOC_API_VERSION: "PANDOC_API_VERSION" PANDOC_SCRIPT_FILE: "PANDOC_SCRIPT_FILE" ``` Variables can be accessed using: - `{{< lua-env pandoc.PANDOC_VERSION >}}` - `{{< meta lua-env.pandoc.PANDOC_VERSION >}}` - `{{< lua-env quarto.doc.input_file >}}` - `{{< meta lua-env.quarto.doc.input_file >}}` This could be integrated into Quarto if deemed useful to have such behaviour as exposing "all" LUA variables to shortcode for use in Quarto document and possibly in code cells in the future.

### Bug description I am currently working on a larger project utilising the strcture of multiple .qmd documents which I have to render to a pdf. While doing this I have encountered some formatting issues that I can't seem to find solutions to. 1. TOC/LOF/LOT I would like to include a table of content, list of figures and list of tables in my document and have specified these in my _quarto.yml document as follows: format: pdf: documentclass: scrreprt links-as-notes: true reference-location: section toc: true toc-depth: 2 lof: true lot: true number-sections: true fig-width: 8 fig-height: 6 However in the final document I have pages devoted to these parts of the document, but these are empty and don't show the chapters, tables and figures of my document. 2. Footnotes I would like to include footnotes at the end of each chapter (or even preferably at the end of the book in an own section) which does not seem to work in pdf, even though I have included reference-location: section in my .yml document. 3. Cross referencing Cross referencing does not work across as well as within the different parts of the documents for chapters/sections, figures and tables.

Make a draft and set the image property for the twitter card.

### Bug description `code-tools: true` functionality is broken by the combination of `link-external-icon` + `link-external-filter` as presented in the example of YAML: ```yaml --- title: Project format: html: code-tools: true code-fold: show link-external-icon: true link-external-filter: "^https://" jupyter: python3 --- ``` By "broken", I mean that the _Show All Code_/_Hold All Code_ buttons do not respond. The broken output:  I expect `code-tools: true` to work perfectly in all situations. I use Windows 10, VS Code and  Example to test: [code-fold-tools-issue-4.zip](https://github.com/quarto-dev/quarto-cli/files/10948249/code-fold-tools-issue-4.zip) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description `subtitle: ...` is ignored if the title is not present. YAML: ```yaml subtitle: Subtitle jupyter: python3 ``` Output  The issue is not present with the following YAML: ```yaml --- title: Project subtitle: Subtitle jupyter: python3 --- ``` Then output:  I use Windows 10, VS Code and  # Expected behavior 1) Either fix the issue (show the toolbar) in both situations 2) Or produce a **clear** warning that some setup options are ignored and provide an example of how to get the desired outcome. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Code tools `code-tools: true` do not respond (are not present in HYML) if "title: " is not present. I use Jupyter notebook in VS Code on Windows 10 and Quarto 1.3.242. YAML when no code tools are present: ```yaml --- format: html: code-fold: show code-tools: true jupyter: python3 --- ``` Here is a print screen of the code:  HTML output (broken):  YAML that does not produce the issue: ```yaml --- title: Project format: html: code-fold: show code-tools: true jupyter: python3 --- ``` Output (as expected):  Some examples: [code-fold-tools-issue-1.zip](https://github.com/quarto-dev/quarto-cli/files/10948173/code-fold-tools-issue-1.zip) # Expected behavior 1) Either fix the issue (show the toolbar) in both situations 2) Or produce a **clear** warning that some setup options are ignored and provide an example of how to get the desired outcome. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Hi,  I get this error when I try to execute: conda install r-quarto. Can you please help me? I tried to update conda, anaconda, but nothing works for me and I would like to use quarto in jupyter lab in Anaconda Navigator. Thanks an regards from Poland! Michal ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Hi - I set up a `_variables.yml` file for a Quarto book project here: https://github.com/dspatterns/dspatterns-book/blob/main/_variables.yml I followed the example from the [docs](https://quarto.org/docs/authoring/variables.html) to format my markdown links: ``` version: 1.2 email: info: [email protected] support: [email protected] engine: jupyter: "[Jupyter](https://jupyter.org)" knitr: "[Knitr](<https://yihui.name/knitr>)" ``` This works-ish: the self-contained markdown formatted links always render perfectly on the first use of the variable in a given `.qmd`. The problem is using that variable again in the same `.qmd`: it looks like it doesn't parse correctly. I tried this by switching out several different variables and this was always true: the first works, any other uses of the same variable in the same `.qmd` are gobbledy-gook. Here is a good example using `{{< var gha.docs >}}` and `{{< var web.host >}}` 2x each: ``` The combination of Link ("",[],[]) [Str "GitHub",Space,Str "Actions",Space,Str "(GHA)"] ("https://github.com/features/actions","") and Link ("",[],[]) [Str "Netlify"] ("https://www.netlify.com","") means that the book is automatically updated after every commit to the main branch on GitHub. ``` Source: https://github.com/dspatterns/dspatterns-book/blob/main/onboarding/book.qmd You can see what happens here: https://dspatterns.netlify.app/onboarding/book.html

This yaml should give us a warning: ``` format: html: layout: some-other-entry ``` YAML allows an empty object to be the value of `layout`, but that's clearly wrong. We should emit a warning when we have a linter. And maybe we should change our schemas to disallow empty values.

### Bug description Quarto version: pull from today, code executed by jupyter example.qmd: # header 1 - item1 - item2 - item3a ```{python} 1 + 1 ``` `quarto render example.qmd --to html` generates: ``` .... <ul> <li><p>item1</p></li> <li><p>item2</p></li> <li><p>item3a</p></li> </ul> .... ``` This didn't happen with my last pull from a week ago. It only happens when a code cell is present. I tried to bisect it and it seems that https://github.com/quarto-dev/quarto-cli/commit/d03158946ddeef6fef7c1b9b1a702bc8d051df92 is related. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Hi, and thanks for a highly usable tool; quarto. I have a couple of related issues with a table made by `kableExtra::kbl()` and `kableExtra::kable_styling()` which spans multiple pages in the resulting pdf. ### First issue When I render the pdf in quarto with a label `#| label: tbl-longTable` the table are cut on the first page. If I instead remove the label the whole table is rendered spanning multiple pages but of course the cross reference in the text does not work. ### Second issue If I use a `#| tbl-cap: ` for the same table I get following error while rendering the report. `````` Package array Error: Illegal pream-token (\caption): `c' used. `````` However, if I do not have the label the table is generated but without caption. Also with the lable the R-code is not showing in the pdf. I have traced the issues to when you add the `column_spec()`, without them the table renders fine with both *label:* and *tbl-cap:*. Everything does work with the `row_spec()` however. Any Ideas of how to proceed? -------------- **R-studio** ``` RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Ubuntu Jammy Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36 ``` **Linux** `Linux Mint 21.1, kernel 5.15.0-67-generic` **Quarto** `quarto 1.2.335` ------------------------ ### A .qmd with example code Below is a reprex with the YAML and R-code which reproduce my error on my system. ```` --- title: "reprex_kable" format: pdf documentclass: scrreprt execute: warning: false error: false message: false --- The table @tbl-cars should be a table spaning more than one page, with a caption. ```{r} #| label: tbl-cars #| echo: false #| cache: true #| tbl-cap: "A table with many models repeating itself" library(tidyverse) library(kableExtra) mtcars %>% bind_rows(mtcars, mtcars) %>% kableExtra::kbl(booktabs = T, longtable = T) %>% kableExtra::kable_styling(latex_options = c("hold_position", "striped"), full_width = F, repeat_header_continued = T, repeat_header_text = "Continuation table:") %>% column_spec(column = 1:2, width = "4cm") %>% column_spec(column = 1, bold = T) %>% row_spec(row = 0, bold = T, background = "#3e77c1", font_size = 12, color = "white", hline_after = F) %>% row_spec(1:107, hline_after = T, font_size = 10) ``` ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Quarto outputs proper HTML for an image file like this one: ```  ```  But v1.3.253 will not embed that into a PDF. Instead, I get this error: ``` compilation failed- error Missing endcsname inserted. <to be read again> & l.200 ...width=256\&height=192\&cropmode=none.pdf} ``` I assume that's an [issue with how TeX handles filename characters](https://tex.stackexchange.com/questions/448314/not-able-to-use-images-if-i-call-gb4e-sty) ? P.S. Full working example is [in this repo.](https://github.com/richardsprague/quartosample) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4736 <div type='discussions-op-text'> ^{Originally posted by **harrelfe** March 9, 2023} I can't get monobackgroundcolor to take effect as described in https://quarto.org/docs/output-formats/html-themes.html#sass-variables. Here is a reproducible example. ```` --- title: "Test" format: html: monobackgroundcolor: red backgroundcolor: cornsilk self-contained: true toc: true toc-location: left toc-title: Contents --- Here is some code: `xvariable <- pi`. Regular text follows. ```` </div>

### Bug description A listing grid view should, by default, display the first image found in the post. That's what I get in v1.2  But in v1.3.253, the image is greyed out.  gridpost.qmd ``` --- title: "Typical grid" listing: categories: true type: grid sort: date desc --- ``` index.qmd ``` --- title: "Intro" --- # Sample Page This is a simple page with the following image:  ``` Note: the error happens whether it's a remote URL image or local. See a working example [here](https://github.com/richardsprague/quartosample) FWIW I'm using VS Code on OSX 13.2.1 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

This might need to go through quarto's api and messages so that we know where to get things from. Because we're talking specifically about tables, and our new "table input syntax" is "just HTML", we should probably also read from the table classes themselves and insert the right prefixes, like we do for markdown tables in 1.3.

### Bug description If exporting to PDF or previewing the markdown document, the following snippet works great and as expected ``` The maximum entropy method is equivalent to least-squares fitting the available time series data to an autoregressive model: \begin{equation} X_t=\sum_{k=1}^M \alpha_k X_{t-k}+\epsilon_k \end{equation} ``` However, if I export this to `.docx`, it does not seem to export the block style equation above. In order to do so, one must enclose the `equation` environment with the `$$` delimiters, i.e. ``` The maximum entropy method is equivalent to least-squares fitting the available time series data to an autoregressive model: $$ \begin{equation} X_t=\sum_{k=1}^M \alpha_k X_{t-k}+\epsilon_k \end{equation} $$ ``` While this works great for exporting to .docx, it now breaks exporting to pdf since `xelatex` complains about the `$$` delimiters being used in a block env. Is there a simple fix to this? My version: ``` quarto --version 1.2.280 ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description To reproduce, create a minimal book project: ```shell quarto create-project book --type book ``` and then modify `_quarto.yml` to add `reader-mode: true`. After rendering and displaying the project, switch to a mobile view with reduced width and a collapsed sidebar. If you then start reader mode, the sidebar is empty but the reader-mode collapsed sidebar can't be open., making navigation impossible. This is a minor inconvenience but I thought it was worth mentioning. I'm working on VSCode under Linux (KDE Neon). ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

See, specifically, the comment on relative paths. There are two conflicting goals: - for the file to render correctly, the -speaker.html file needs to live in the same directory as the audience file (because of relative paths). - if we put the file in the same directory, then there's a large risk that users will accidentally publish the speaker file, and that's really not good (anyone with access to the content of -speaker.html can control the presentation). I don't know exactly how we could solve this, but the current situation doesn't seem that great. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4718 <div type='discussions-op-text'> ^{Originally posted by **jkub6** March 8, 2023} All of the *-speaker.html files generated by revealjs multiplex don't end up in the output-dir directory specified in _quarto.yml. Ideally (for me) they would end up right beside the client *.html presentation files. Instead, they remain beside the .qmd files. Is this expected behavior? If so, is there a way to configure the output directory for these files?</div>

This is a topic that comes up often and I think our current guide is not enough and needs to be updated. Also some improvment needs to be made first. Context below ## To solve - [ ] https://github.com/quarto-dev/quarto-cli/issues/1463 ## Related * https://github.com/quarto-dev/quarto-cli/issues/4716 ## Resources - [Windows python setup FAQ](https://learn.microsoft.com/en-us/windows/python/faqs)

### Bug description Hej! In a larger project, I would like to use my own `latexmk` pipeline because manually running `latexmk` with the LaTeX file generated by Quarto works successfully whereas compilation is unsuccessful when I try to generate the PDF with quarto and `pdf-engine: latexmk`. Based on the docs, I assumed I could opt out of Quarto's machinery by setting `latex-auto-mk: false`. However, changing this setting does seem to make a difference (as someone else had noticed before apparently: https://github.com/quarto-dev/quarto-cli/discussions/819#discussioncomment-2704475). In contrast to other configurations, these options also don't show up in the pandoc/metadata output in the terminal. So I tried to set some of the other `latex-...` options and they also did not seem to affect compilation. For instance, I played around with the following somewhat minimal example: ```md --- title: MWE format: pdf: pdf-engine: latexmk pdf-engine-opt: '-verbose' latex-auto-mk: false latex-output-dir: "/home/david/quarto-mwe/" --- A MWE for debugging the `latex-` options. ``` I rendered it by running ```shell quarto render mwe.qmd --log-level=debug ``` in the terminal. Both with Quarto 1.2.335 and 1.3.34 (Fedora 37), the `latex-...` options do not change the output in the terminal and, e.g., regardless of the option `latex-output-dir` always a directory `/tmp/...` is used by latexmk. Am I doing something wrong or do these options not work currently? ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

(This appears to work in document front matter, but not extensions for some reason: ``` --- title: Untitled format: html+bar: toc: false author: Charles Teague date: last-modified --- ``` works as I'd expect, but not: ``` formats: html: toc: true theme: [yeti, custom.scss] html+bar: toc: false theme: [sketchy, custom.scss] ``` ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4700 <div type='discussions-op-text'> ^{Originally posted by **juba** March 8, 2023} Hi, I'm currently developing a custom HTML format which provides both a light and dark theme. I have something like the following in my `_extension.yml` : ```yaml theme: light: [bookup.scss] dark: [bookup.scss, bookup_dark.scss] ``` This is working fine, but maybe the custom format users will want to only use the light theme, or only the dark theme, or even provide both but with the dark one by default. Is there a way to provide such a feature in a custom format ? I took a look at the documentation but didn't find a way to do this. Thanks in advance ! </div>

### Bug description I'm trying to generate parameterized reports in parallel on Ubuntu 22.04 LTS using `quarto=1.2.335`. For this, I'm using the following `test.qmd` file: ```r --- title: paralell report generation fails params: counter: 1 format: html: embed-resources: true --- \```{r} Sys.sleep(5) \``` This is report number `r params$counter` ``` Generating both report `out1.html` and `out2.html` works fine when running sequentially: ```sh quarto render test.qmd -P counter:1 --output out1.html quarto render test.qmd -P counter:2 --output out2.html ``` However, when I try to run them in parallel I get: ``` quarto render test.qmd -P counter:1 --output out1.html &; quarto render test.qmd -P counter:2 --output out2.html # Error in readLines(con, warn = FALSE) : cannot open the connection # Calls: .main ... partition_yaml_front_matter -> grep -> is.factor -> read_utf8 -> readLines ``` I suspect this is because both reports store their temporary files in `test_files/`. Wouldn't it make more sense to use the output file base as directory, because this should not conflict? ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

STR Description: Index flattening isn't working for root page. Steps to Reproduce: - Create a simple site with `index.qmd` as the only file in the root. Expected Result: - The title and contents of the `index.qmd` are used to populate the site parent - the root page. The index page is filtered out as a stand-alone page. Actual Result: - The title and contents of the `index.qmd` are not used to populate the site parent - the root page. The index page remains as a stand-alone page.

STR Description: Error publishing to site URL with param Steps to Reproduce: - Publish a doc to the following personal site URL `https://allenmanning.atlassian.net/wiki/spaces/~557058634d59d0949841909bb13093ab41d0c5/overview?homepageId=65617` Expected Result: It should work. Actual Result: It fails with ```` ERROR: Invalid Confluence parent URL: https://allenmanning.atlassian.net/wiki/spaces/~557058634d59d0949841909bb13093ab41d0c5/overview?homepageId=65617 Error: Invalid Confluence parent URL: https://allenmanning.atlassian.net/wiki/spaces/~557058634d59d0949841909bb13093ab41d0c5/overview?homepageId=65617 at verifyConfluenceParent (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/confluence/confluence-verify.ts:57:11) at Object.publish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/confluence/confluence.ts:256:9) at async publishDocument (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/publish.ts:293:36) at async publish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:282:9) at async doPublish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:195:7) at async publishAction (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:258:7) at async Command.fn (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:153:11) at async Command.execute (file:///Users/amanning/projects/github/quarto/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///Users/amanning/projects/github/quarto/quarto-cli/src/quarto.ts:119:3) at async file:///Users/amanning/projects/github/quarto/quarto-cli/src/quarto.ts:151:5 ````

### Bug description With this .quarto.yml file: ```yaml project: type: website website: title: "blog" sidebar: style: docked format: html: theme: - default ``` This index.qmd file: ````md --- title: test quarto docked sidebar with margin notes date: 2023-02-25T21:14:15-0500 --- ## title for toc [Here's a aside note.]{.aside} ```` renders this: <img width="1512" alt="Screenshot 2023-03-08 at 23 28 53" src="https://user-images.githubusercontent.com/1813121/223917463-3e01b261-9e9f-4196-8b9e-830c8b6ce505.png"> But this index.qmd file: ````md --- title: test quarto docked sidebar with margin notes date: 2023-02-25T21:14:15-0500 --- ## title for toc <!-- [Here's a aside note.]{.aside} --> ```` renders this: <img width="1512" alt="Screenshot 2023-03-08 at 23 29 10" src="https://user-images.githubusercontent.com/1813121/223917508-5edb516c-8dad-4cac-9b6e-8fd8f53a53a7.png"> In this particular theme, seemingly the only difference here is the horizontal rule below the header, but basically, when there is a margin note _with_ `sidebar: style: docked`, there's lots of excess space on the right, and the center body seems to be shrunk. When you remove the margin note, the layout appears to change. With `sidebar: style: float`, adding or removing a margin note does not affect the layout. I like the behavior of the docked sidebar, but when I write blog posts with margin notes the body shrinks. 1) It doesn't match the layout of other blog posts without margin notes 2) it makes the body smaller and makes the page longer than it would be otherwise 3) Since this doesn't happen with `sidebar: style: float`, I'm assuming this is a bug. ``` shell> quarto --version 1.3.242 ``` ``` Platform Info: OS: macOS (arm64-apple-darwin21.5.0) CPU: 10 × Apple M1 Pro WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1) Threads: 1 on 8 virtual cores ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Table header rule much heavy than before in HTML output, is it intentional? ## a minimal example ```` --- title: "My document" format: html: theme: cosmo --- # Table ```{r} knitr::kable(head(iris,3)) ``` ```` ## HTML output from Quarto 1.2.335 <img width="843" alt="截屏2023-03-09 08 38 58" src="https://user-images.githubusercontent.com/12031874/223885184-4ffb4a62-7f89-435b-894f-d4523b65d450.png"> ## HTML output from Quarto 1.3.250 <img width="835" alt="截屏2023-03-09 08 43 39" src="https://user-images.githubusercontent.com/12031874/223885747-89a5cf88-c074-4138-b078-87d2500f59f1.png"> ## RStudio Info RStudio 2023.03.0+382 "Cherry Blossom" Release (3a8b92eb66f0754a31f03c010b41496abc65fb70, 2023-03-01) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+382 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description **This is the code -- full qmd below** ```{python} #| echo: true from sympy.solvers.diophantine.diophantine import diop_solve from sympy import symbols ``` **This is the error message:** ModuleNotFoundError: No module named 'sympy' Sympy is installed in my virtual environment. When I start Python from my virtual environment and I run the code snippet, it runs. I have tried doing !pip install sympy and !pip3 install sympy from within the code snipped and it runs but does not change the error message. Whether I try to render as a docx, PDF, or word document does not change the outcome. **This is the full QMD that gets me the error message**. I have also tried adding pip install sympy and pip3 install sympy from the code snippet and it runs but does not affect the error message --- title: "Solving A Linear Equation Two Ways In Python" author: "Abigail Haddad" date: "March 08, 2023" --- ```{python} #| echo: true from sympy.solvers.diophantine.diophantine import diop_solve from sympy import symbols ``` I am running this on Windows from a virtual environment. I am not using RStudio. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description The `transition: transfom` is overridden with the `transition: position` while resp. the first one is a css3 property and the latter is a css2 property. Thus no transition will be performed. I would reorder the 2 lines. You can also change this to `all` instead of `transform`  ```css .headroom-target, header.headroom { will-change: transform; transition: transform 200ms linear; transition: position 200ms linear; } ``` suggestion ```css .headroom-target, header.headroom { will-change: transform; transition: position 200ms linear; transition: transform 200ms linear; } ``` suggestion nr. 2 ```css .headroom-target, header.headroom { will-change: transform; transition: position 200ms linear; transition: all 200ms linear; } ``` ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Using Quarto 1.2.335 (which is included in recent RStudio dailies, including 2023.03.0+385). This problem can be recreated without using the RStudio IDE when rendering using Quarto from the command-line. Given a `code.R` file: ```r cat("this is code.R\n") ``` The following revealjs document does not show the embedded code: ````markdown --- title: embedding with reveal format: revealjs engine: knitr --- ## Embed! ```{embed, file = "code.R"} ``` ```` <img width="850" alt="image" src="https://user-images.githubusercontent.com/362187/223846591-cbcdd571-c6c3-484e-b323-54ec5e7c6ee6.png"> The generated HTML contains a block, but no code: ```html <section id="embed" class="slide level2"> <h2>Embed!</h2> <div class="cell" data-file="code.R"> </div> <div class="footer footer-default"> </div> </section> ``` In contrast, when we do not output to HTML, the embedded code is shown. ````markdown --- title: embedding without reveal engine: knitr --- ## Embed! ```{embed, file = "code.R"} ``` ```` <img width="544" alt="image" src="https://user-images.githubusercontent.com/362187/223846616-9f633a3c-7c00-4bb2-9562-47f3740c15b0.png"> Using the most recent version of knitr from CRAN and R 3.6.3 on macOS 12.6.3. ```bash R -s -e "packageVersion('knitr')" #> [1] ‘1.42’ ``` Discovered while trying to apply the workaround from https://github.com/quarto-dev/quarto-cli/issues/1237 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Repro: ```` --- title: fig-in-lists --- - Stuff ```{r} #| label: fig-join-left #| echo: false #| fig-cap: A caption plot(mtcars) ``` ````

It would be nice if we could add the same `code-fold` options to a markdown code block that is not a computation block just by adding appropriate classes. I would like something like `{.julia code-fold=true}` to make that specific code block collapsed by default with an option to expand it.

Our current conda package reports a wrong quarto version, which is problematic: ``` The following NEW packages will be INSTALLED: dart-sass conda-forge/osx-arm64::dart-sass-1.58.3-hce30654_0 deno conda-forge/osx-arm64::deno-1.25.2-hce30654_0 deno-dom conda-forge/osx-arm64::deno-dom-0.1.23-hb9e0d3b_0 esbuild conda-forge/osx-arm64::esbuild-0.15.5-hce30654_1 pandoc conda-forge/osx-arm64::pandoc-2.19.2-hce30654_2 quarto conda-forge/osx-arm64::quarto-1.2.335-hce30654_1 The following packages will be UPDATED: conda 22.11.1-py310hbe9552e_1 --> 23.1.0-py310hbe9552e_0 Proceed ([y]/n)? y Downloading and Extracting Packages Preparing transaction: done Verifying transaction: done Executing transaction: done $ which quarto /Users/cscheid/conda/bin/quarto $ quarto --version 1.2.1 ``` Our build script is here https://github.com/conda-forge/quarto-feedstock/blob/main/recipe/build.sh And @msarahan tells me that the conda version information is taken from https://github.com/quarto-dev/quarto-cli/blob/v1.2/configuration#L46. Instead, `build.sh` should be setting QUARTO_VERSION to whatever the right information is. In the installers, I believe this info comes ultimately from the git tag (@dragonstyle can confirm). So we need to figure out where this mismatch happens and fix.

### Bug description Currently if I publish an individual docs it is still editable (this on Confluence Public Cloud). I also noted that duplicates receive a uuid-based suffix rather than an index (not sure if its straightforward to remedy this though).  ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Using Plotly tables in separate tabsets seems to create issues rendering, especially cells with spaces. The first tab renders correctly but the others do not, and the figure dimensions have to be set manually as the article layout for the column size doesn't apply the same way to the following tabs. However, if the table is large enough and requires scrolling, scrolling down and back up may render the data. This was rendered as a ".ipynb" file on Windows 11 Enterprise with Python 3.9.13, Plotly 5.13.1, and Quarto 1.2.335. ````md --- title: "MOVES Benchmark Comparisons" author: "Max Collins" date: "2/28/2023" execute: echo: false format: html: code-fold: true embed-resources: true theme: materia --- ```py import plotly.graph_objects as go import dash_bootstrap_components as dbc import plotly.express as px import pandas as pd import numpy as np from plotly.colors import n_colors import plotly.io as pio import matplotlib as plt pio.renderers.default = "plotly_mimetype+notebook_connected" ``` ::: {.column-screen} ## Run Definitions ::: :::: {.column-screen-inset} ::: {.panel-tabset} ## Nonroad and Rates ```py perf_tableNR_Rates = readExcel(r'C:\Users\mcolli03\OneDrive - Environmental Protection Agency (EPA)\Documents\Python Scripts\Performance\data\compiled\performance_testing_NR_Rates.xlsx', 'RunDef') df = perf_tableNR_Rates col_widths = [400]*14 + [850] table2 = go.Figure(data=[go.Table( columnwidth=col_widths, header=dict(values=list(df.columns), line_color=grey, fill_color=grey, align='center', font=dict(size=14), height=40), cells=dict(values=[df.Run, df.Model, df.Scale, df.Type, df['Year(s)'], df['Month(s)'], df['Day(s)'], df['Hour(s)'], df.Location, df.Vehicle, df['Fuel/Type'], df.Road, df['Output Agg'], df.PreAgg, df['Pollutants/Processes']], align='left', height=50)) ]) table2.update_layout(width=1700, height=500) table2.show() ``` ## PreAgg ```py perf_tablePreAgg = readExcel(r'C:\Users\mcolli03\OneDrive - Environmental Protection Agency (EPA)\Documents\Python Scripts\Performance\data\compiled\performance_testing_PreAgg.xlsx', 'RunDef') df = perf_tablePreAgg col_widths = [400]*14 + [850] table3 = go.Figure(data=[go.Table( columnwidth=col_widths, header=dict(values=list(df.columns), line_color=grey, fill_color=grey, align='center', font=dict(size=14), height=40), cells=dict(values=[df.Run, df.Model, df.Scale, df.Type, df['Year(s)'], df['Month(s)'], df['Day(s)'], df['Hour(s)'], df.Location, df.Vehicle, df['Fuel/Type'], df.Road, df['Output Agg'], df.PreAgg, df['Pollutants/Processes']], align='left', height=50)) ]) table3.update_layout(width=1700, height=500) table3.show() ``` ## By Size ```py perf_tableScales = readExcel(r'C:\Users\mcolli03\OneDrive - Environmental Protection Agency (EPA)\Documents\Python Scripts\Performance\data\compiled\performance_testing_Scales.xlsx', 'RunDef') df = perf_tableScales col1 = ['rgb(255, 244, 134)'] col1_light = ['rgb(255, 250, 192)'] col2 = ['rgb(255, 172, 228)'] col2_light = ['rgb(255, 225, 246)'] col3 = ['rgb(112, 183, 126)'] col3_light = ['rgb(170, 209, 177)'] col4 = ['rgb(161, 205, 241)'] col4_light = ['rgb(213, 230, 243)'] col5 = ['rgb(235, 190, 155)'] col5_light = ['rgb(242, 222, 207)'] col6 = ['rgb(217,153,185)'] col6_light = ['rgb(225, 197, 211)'] grey = ['rgb(202, 197, 200)'] l_grey = ['rgb(235,231,233)'] lgrey_line = l_grey*15 lcol1_line = col1+(col1_light*14) lcol2_line = col2+(col2_light*14) lcol3_line = col3+(col3_light*14) lcol4_line = col4+(col4_light*14) lcol5_line = col5+(col5_light*14) colors = np.array([lgrey_line, lgrey_line, lgrey_line, lcol1_line, lgrey_line, lgrey_line, lgrey_line, lcol2_line, lcol3_line, lcol4_line, lcol5_line]).T col_widths = [400]*14 + [850] table1 = go.Figure(data=[go.Table( columnwidth=col_widths, header=dict(values=list(df.columns), line_color=grey, fill_color=grey, align='center', font=dict(size=14), height=40), cells=dict(values=[df.Run, df.Model, df.Scale, df.Type, df['Year(s)'], df['Month(s)'], df['Day(s)'], df['Hour(s)'], df.Location, df.Vehicle, df['Fuel/Type'], df.Road, df['Output Agg'], df.PreAgg, df['Pollutants/Processes']], fill_color=colors, align='left', height=50)) ]) table1.update_layout(width=1700, height=450) table1.show() ``` ::: ::::    ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

See #4696. Chrome.js is an external dependency. We ported it to deno, but we now made fixes to. We should track the upstream somewhere so we can add fixes and potentially take their changes as well.

### Bug description STR Description: Publish to Confluence is failing. Steps to Reproduce: - Attempt to render to `confluence-publish` format Expected Result: - Render without a failure Actual Result: ```` Error running Lua: ...i/src/resources/extensions/quarto/confluence/publish.lua:112: attempt to index a nil value (field '_quarto') stack traceback: ERROR: Error at renderFiles (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/render/render-files.ts:532:23) at async renderProject (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/render/project.ts:263:23) at async renderForPublish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/publish.ts:69:24) at async renderSite (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/confluence/confluence.ts:222:38) at async publishSite (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/confluence/confluence.ts:627:40) at async Object.publish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/confluence/confluence.ts:835:12) at async publishSite (file:///Users/amanning/projects/github/quarto/quarto-cli/src/publish/publish.ts:114:36) at async publish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:275:9) at async doPublish (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:195:7) at async publishAction (file:///Users/amanning/projects/github/quarto/quarto-cli/src/command/publish/cmd.ts:258:7) ```` ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4558 <div type='discussions-op-text'> ^{Originally posted by **rleyvasal** February 28, 2023} It would help presenters to have the ability to highlight code and also do `code-fold` when the code is only for demonstration in a language non executable such as `scss`. At the moment code in R, Python, can use `code-fold` but if other languages are in a code block which is only highlighted, then the code is not fold-able. ## Python code is foldable with `code-fold` but scss highlighted is not foldable as seen below:  ## Reproducible Code ````markdown --- title: "My document" format: html: code-fold: true code-summary: "Show code" --- ```{python} #| eval: false // Content.scss @use 'colors' as colors; body > content { padding: 40px; margin: auto; max-width: 100% } ``` Show code below folded ```scss // Content.scss @use 'colors' as colors; body > content { padding: 40px; margin: auto; max-width: 100% } ``` ```` </div>

### Bug description ## A minimal example ```` --- title: "My document" format: pdf: documentclass: article html: theme: cosmo --- # Callout All callout's border color are different in HTML and PDF output since Quarto 1.3.x, I prefer HTML output than PDF. ::: {.callout-tip} hello ::: ::: {.callout-note} hello ::: ::: {.callout-warning} hello ::: ::: {.callout-caution} hello ::: ```` ## The output ### HTML <img width="840" alt="截屏2023-03-08 08 35 10" src="https://user-images.githubusercontent.com/12031874/223588508-30366588-6856-4c71-bb46-46a268e40096.png"> ### PDF <img width="665" alt="截屏2023-03-08 08 34 28" src="https://user-images.githubusercontent.com/12031874/223588343-692cd930-ca03-4679-b1be-8f15c5f53e6d.png"> ## Quarto and RStudio version I use Quarto 1.3.242 RStudio 2023.03.0+382 "Cherry Blossom" Release (3a8b92eb66f0754a31f03c010b41496abc65fb70, 2023-03-01) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+382 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Reprex of qmd file: ````` --- title: "reprex" format: html --- ```{r} myfun <- function() print("helloworld") ``` This doesn't work: ```{r} #| fig-cap: !expr 'myfun()' hist(rnorm(1000)) ``` ````` Following error on Windows 10 rendering from Rstudio & the quarto vscode extension: ``` processing file: quarto_reprex.qmd Error in myfun() : could not find function "myfun" Error in yaml::yaml.load(yaml, eval.expr = TRUE) : Could not evaluate expression: myfun() Calls: .main ... parse_block -> partition_yaml_options -> <Anonymous> Execution halted ``` Quarto version: 1.2.335 Rstudio version: 2022.07.2 Build 576 R version: 4.0.4 (2021-02-15) -- "Lost Library Book"

See #4678 - we should investigate if we can behave better when the compute engine configuration changes from under us.

### Bug description With Quarto 1.3.242, shortcode variables are rendered with deubgging information when they're included in page footers, which then also makes them render incorrectly everywhere. Here's a MWE, based on a brand new vanilla Quarto site (RStudio > New Project > Quarto website). **_variables.yml** ```yaml version: 1.2 email: info: [email protected] support: [email protected] engine: jupyter: "[Jupyter](https://jupyter.org)" knitr: "[Knitr](<https://yihui.name/knitr>)" ``` **index.qmd** ``` --- title: "Example site" --- Version {{< var version >}} is a minor upgrade. Here's an e-mail address: {{< var email.info >}} ``` Ordinarily, this renders just fine: <kbd><img width="486" alt="image" src="https://user-images.githubusercontent.com/73663/223497238-d979d503-2453-4366-97b1-37f5f8e0b4fc.png"></kbd> If I include the shortcodes in a footer, though, like this: **_quarto.yml**: ```yaml website: title: "Example site" page-footer: left: | {{< var version >}} {{< var email.info >}} ``` …the shortcodes that are part of a nested YAML list (i.e. `email.info` and not `version`) do not render correctly, both in the main body and in the footer <kbd><img width="533" alt="image" src="https://user-images.githubusercontent.com/73663/223497462-53a26478-5a56-44cc-a55d-c013e1a72d56.png"></kbd> --- This wasn't happening in earlier versions of Quarto 1.3 (like down in the 1.3.50s). This is with Quarto 1.3.242, R 4.2.2, on macOS Ventura 13.2.1 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description I updated from Ubuntu 20 to 22.04 and my system-wide python version changed from 3.8 to 3.10.6. I have checked that python is recognized by quarto. ``` quarto check all [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3, ssam, si_env [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.1.2 Path: /usr/lib/R LibPaths: - /home/matias/R/x86_64-pc-linux-gnu-library/4.1 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` During running chunk by chunk (inside Rstudio), the code works with no problem. When I try to render in either Rstudio or the command line, I get errors that boil down to "no module named ...". Because quarto is looking for modules in the old `.local/lib/python3.8` directory instead of the proper `python3.10` directory. It's not just one package, I could reproduce this by moving the python3.8 folder one directory up and quarto will find no module (which means it's looking in that path for modules). I am not using any virtual environment for this project, and Rstudio also finds python correctly  I uninstalled and reinstalled quarto but still face this issue. Just in case this is needed, I put my session info ``` sessioninfo::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.1.2 (2021-11-01) os Ubuntu 22.04.2 LTS system x86_64, linux-gnu ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2023-03-07 rstudio 2022.12.0+353 Elsbeth Geranium (desktop) pandoc 2.9.2.1 @ /usr/bin/pandoc ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.2) bit 4.0.5 2022-11-15 [1] CRAN (R 4.1.2) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.2) cli 3.6.0 2023-01-09 [1] CRAN (R 4.1.2) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.1.2) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.1.2) data.table 1.14.8 2023-02-17 [1] CRAN (R 4.1.2) dplyr * 1.1.0 2023-01-29 [1] CRAN (R 4.1.2) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2) fansi 1.0.4 2023-01-22 [1] CRAN (R 4.1.2) farver 2.1.1 2022-07-06 [1] CRAN (R 4.1.2) forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.1.2) fs 1.6.1 2023-02-06 [1] CRAN (R 4.1.2) generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.2) GGally 2.1.2 2021-06-21 [1] CRAN (R 4.1.2) ggplot2 * 3.4.1 2023-02-10 [1] CRAN (R 4.1.2) ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.1.2) ggthemes 4.2.4 2021-01-20 [1] CRAN (R 4.1.2) glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2) gtable 0.3.1 2022-09-01 [1] CRAN (R 4.1.2) here 1.0.1 2020-12-13 [1] CRAN (R 4.1.2) hms 1.1.2 2022-08-19 [1] CRAN (R 4.1.2) jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.1.2) knitr 1.42 2023-01-25 [1] CRAN (R 4.1.2) labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.2) lattice 0.20-45 2021-09-22 [4] CRAN (R 4.1.1) lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.1.2) lubridate * 1.9.2 2023-02-10 [1] CRAN (R 4.1.2) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.2) Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.1.2) mgcv 1.8-41 2022-10-21 [1] CRAN (R 4.1.2) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2) nlme 3.1-162 2023-01-31 [1] CRAN (R 4.1.2) pak 0.4.0 2023-01-15 [1] CRAN (R 4.1.2) paletteer 1.5.0 2022-10-19 [1] CRAN (R 4.1.2) patchwork * 1.1.2 2022-08-19 [1] CRAN (R 4.1.2) pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.2) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2) plyr 1.8.8 2022-11-11 [1] CRAN (R 4.1.2) png 0.1-8 2022-11-29 [1] CRAN (R 4.1.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.2) progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.2) purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.1.2) R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2) RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.1.2) Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.1.2) readr * 2.1.4 2023-02-10 [1] CRAN (R 4.1.2) rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.1.2) reshape 0.8.9 2022-04-12 [1] CRAN (R 4.1.2) reticulate * 1.28 2023-01-27 [1] CRAN (R 4.1.2) rlang 1.0.6 2022-09-24 [1] CRAN (R 4.1.2) rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.1.2) rsconnect 0.8.29 2023-01-09 [1] CRAN (R 4.1.2) rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.1.2) scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.2) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2) stringi 1.7.12 2023-01-11 [1] CRAN (R 4.1.2) stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.1.2) tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.1.2) tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.1.2) tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.1.2) tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.1.2) timechange 0.2.0 2023-01-11 [1] CRAN (R 4.1.2) tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.1.2) usethis 2.1.6 2022-05-25 [1] CRAN (R 4.1.2) utf8 1.2.3 2023-01-31 [1] CRAN (R 4.1.2) vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.1.2) vroom 1.6.1 2023-01-22 [1] CRAN (R 4.1.2) withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2) xfun 0.37 2023-01-31 [1] CRAN (R 4.1.2) yaml 2.3.7 2023-01-23 [1] CRAN (R 4.1.2) [1] /home/matias/R/x86_64-pc-linux-gnu-library/4.1 [2] /usr/local/lib/R/site-library [3] /usr/lib/R/site-library [4] /usr/lib/R/library ─ Python configuration ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────── python: /usr/bin/python3.10 libpython: /usr/lib/python3.10/config-3.10-x86_64-linux-gnu/libpython3.10.so pythonhome: //usr://usr version: 3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0] numpy: /usr/lib/python3/dist-packages/numpy numpy_version: 1.21.5 NOTE: Python version was forced by use_python function ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Current PDF export mode rom revealjs doesn't work reliable on most browsers. For example on Firefox you will still get garbage resp. wrong page breaks in the printed results after activating this mode. Well, you'll find a warning note about this flaw in the documentation, but it's IMHO still a very disappointing behavior. I would therefore prefer a more reliable solution, which provides reproducible correct results in arbitrary browsers. This can be realized in practice by integrating [decktape](https://github.com/astefanutti/decktape) resp. [puppeteer](https://github.com/puppeteer/puppeteer), [playwright](https://github.com/microsoft/playwright) or another similar mechanism into the CLI-tool for the document processing to generate a PDF-document beside the HTML-output and just add a download button in the HTML-menu or -toolbar instead of the present print style-switch entry. That's the way, how for example [slidev](https://github.com/slidevjs/slidev) handles this task in a much more reliable manner (see: <https://sli.dev/guide/exporting#pdf>). _Originally posted by @mash-graz in https://github.com/quarto-dev/quarto-cli/issues/2988#issuecomment-1455245996_

DecoratedCodeBlock exists in 1.3 to solve a fairly narrow problem. Concurrently, there's now a feature request for code folding in custom formats (confluence specifically). Our filter chain makes it hard for code folding to be detected in custom formats because they're done in a specific post- filter. If we added code folding to the set of things that DecoratedCodeBlock is responsible for, then custom writers could handle it as well.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2432 <div type='discussions-op-text'> ^{Originally posted by **andrewcstewart** September 13, 2022} It would be great if Quarto could allow you to generate a link in the navbar (or wherever) to download a copy of the notebook you are viewing. Other frameworks like Jupyterbook implement examples of this feature. Or, a picture is worth a thousand words, as they say... <img width="1087" alt="image" src="https://user-images.githubusercontent.com/1420654/190014713-e2639b2b-5555-4e90-9677-29c3b2c28583.png"> </div>

In my testing, we appear to require markdown 2.3 or later. We should consider either documenting / checking this minimum in `quarto check`, or adding support for older versions, whatever makes the most sense.

### Bug description In a book project with Quarto 1.3.247 (and 1.3 versions before) there is an issue with cross references when the document contains a list (numbered or bulleted), and later in the document a callout with a figure in it. Rendering gives then a warning: unable to resolve crossref. Commenting out the list clears the error. And when the list is after the callout then also no problem. Furthermore there are no problems when rendering with Quarto version 1.2.335 OS: Windows 10, Repro: [crossreftest](https://github.com/bwelman/crossreftest) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4659 <div type='discussions-op-text'> ^{Originally posted by **jimjam-slam** March 7, 2023} Quarto's CSS grid system has 13 grid column tracks:  The main elements in those tracks—the sidebar, article body (or header block) and margin, all have elements in the document, so they can be targeted by CSS.  The gutter elements, though (column tracks 1, 2, 6, 8, 12 and 13), are empty. As far as I can tell, [the only way to target empty grid cells](https://stackoverflow.com/questions/46308048/how-to-target-a-specific-column-or-row-in-css-grid-layout) is with CSS Grid-Structural Selectors, which are still in development and don't yet have any browser support. Using `:nth-child` doesn't work, as that targets the nth HTML child, not the nth grid cell. In other words, it only works if every grid cell is occupied. This isn't a big issue, but if the empty gutters had empty HTML elements in them, you could do things like have a sidebar or margin with a background colour that goes out to the page edge (say, if I wanted tracks 1–5 to all be blue).</div>

### Bug description My project is in a Dropbox folder. When I have more than one .qmd file and use the quarto book (though I suspect the issue would persist for any quarto project), the rendering process is incredibly unstable. The intermediate files that appear (e.g. `..\site_libs\bootstrap\`) seem to induce conflicts of the type: "The process cannot access the file because it is being used by another process.". They cite `os error 32` and `os error 145` as the issue. The issue has subsided now that I am using a local folder, not Dropbox. I would imagine any web syncable folder (e.g. OneDrive, GoogleDrive, etc) would present this issue. Hopefully someone is able to fix this, as I am sure this poses an issue to a lot of teams' workflow. Background Info: R 4.2.2 Windows 11 Pro 22H2 RStudio Info: 2022.12.0 Build 353 © 2009-2022 Posit Software, PBC "Elsbeth Geranium" Release (7d165dcf, 2022-12-03) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Hi, A useful feature for people with many articles/posts sharing multiple authors would be to declare a central list of authors and be able to reference them from individual pages, in a similar fashion to `affiliations`: `_authors.yml` ``` authors: - id: author1 name: ... affiliations: - ref: lab1 - id: author2 name: ... affiliations: - ref: lab1 affiliations: - id: lab1 name: ... ``` `my_pub.qmd` ``` title: ... metadata-files: [_authors.yml] author: - ref: author1 ``` Thanks ! ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4630 <div type='discussions-op-text'> ^{Originally posted by **ma-riviere** March 5, 2023} Hi, Is there a way to have a centralized list of authors as a standalone file that can then be imported in multiple .qmd files, but only have a selection of those authors listed in each .qmd ? **Example:** `_authors.yml` ``` authors: - id: author1 name: ... affiliations: - ref: lab1 - id: author2 name: ... affiliations: - ref: lab1 affliliations: - id: lab1 name: ... ``` `my_pub.qmd` ``` title: ... metadata-files: [_authors.yml] # This part gets completely ignored author: - ref: author1 ``` If I do the above, it will list **all** the authors referenced in `_authors.yml` in each .qmd file importing `_authors_yml`. Is there a way to specify which authors of that central author list I want to see displayed in a specific file ? (the same way we can reference affiliations) Useful info: - Website project (outputting to HTML) - Quarto v1.3.242 on Ubuntu 22.04 Thank you</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4664 <div type='discussions-op-text'> ^{Originally posted by **shinneuro** March 7, 2023} Hi, I am building an website with multiple submodules as mentioned in #1282. `*.qmd` files are located inside each submodules, and they are all rendered together inside `_site` folder of the main repository. One feature I would like to implement, but seems currently not working, is separate `repo-url` for `*.qmd` files inside separate submodules. I tried creating `_metadata.yml` inside the submodule, and added a new `repo-url` for the submodule but it seemed not working. So, `quarto.yml` inside the root directory would be like ``` website: title: "quarto" repo-url: https://github.com/quarto-dev/quarto-cli repo-actions: [edit] ``` and `_metadata.yml` inside the submodule would be something like ``` website: repo-url: https://github.com/quarto-dev/quarto-web ``` However, this approach did not work. Would there be any way to accomplish this type of work? Thank you in advance. Best regards, Minho</div>

We are using a lot `Deno.build.os === "windows"` though we have cleaner solution for our code. We have our own wrapper https://github.com/quarto-dev/quarto-cli/blob/20e627913e1f4ebd4df9ad8d8140c40b08752824/src/core/platform.ts#L12-L14 and there is one also in https://deno.land/[email protected]/_util/os.ts I believe this would be beneficial for our code to be simpler with less duplication

### Bug description As far as I can tell, code folding is not (yet) supported in confluence output? It would be amazing to have this and I think confluence provides [`expand` macros](https://support.atlassian.com/confluence-cloud/docs/insert-the-expand-macro/) that could be used for this purpose? quarto version 1.3.242 e.g. for file --- title: "Test code folding" format: confluence-html: code-fold: true --- ```{r} 2 + 2 ``` It looks like there's no code folding available. <img width="981" alt="Screenshot 2023-03-07 at 08 45 03" src="https://user-images.githubusercontent.com/118288090/223370759-e518bd73-348e-4bba-b1c8-d9e8eaf1a268.png"> ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description The [docs](https://quarto.org/docs/prerelease/1.3/embed.html#embedding-code) suggest this should show the **code** and output: ``` {{< embed plots.ipynb#plot-dot echo=true >}} ``` I'd expect to see the code: ``` import matplotlib.pyplot as plt x=[3,4,5,6,7,8,9,10,11,12] y= [9,16,25,36,49,64,81,100,121,144] plt.scatter(x,y) plt.show() ``` But, no code is shown. @dragonstyle Also checked in a minimal project locally and don't get an echo. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Attempted to "Download Notebook" at: https://quarto.org/docs/prerelease/1.3/plots.ipynb File that is downloaded has `.ipynb` extension, but the contents is actually HTML. This line in the page source is the culprit: ```html <a href="https://quarto.org/docs/prerelease/1.3/plots.html" class="btn btn-primary quarto-download-embed" download="plots.ipynb">Download Notebook</a> ``` However, I don't know where this gets generated. @dragonstyle this is part of the Jupyter Cell Embedding feature so perhaps your domain. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Hello, Í'm using: - Latest version of R (4.2.2) - Latest version of Rstudio (2022.12.0 Build 353) - Latest Quarto (version 1.2.335) - Windows 10 Enterprise 22H2 When rendering a PDF from a .QMD-file containing a Mermaid diagram [(https://quarto.org/docs/authoring/diagrams.html)](https://quarto.org/docs/authoring/diagrams.html), my Rstudio gives the error "ERROR: No inspectable targets" and crashes (I'm unable to press stop). In the past the same .QMD file rendered to PDF without any problem. Rendering to .HTML still works. The same error was recently reported by an Obsidian user: [https://forum.obsidian.md/t/about-quarto-no-inspectable-targets-error/54757](https://forum.obsidian.md/t/about-quarto-no-inspectable-targets-error/54757). The .QMD-file i'm using can be found in the attached .ZIP (Github doesn't allow uploading QMD's directly, therefore I zipped). Thanks for the good work! Best, Thomas [testdia.zip](https://github.com/quarto-dev/quarto-cli/files/10902790/testdia.zip) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description For example, with the [example site](https://github.com/rstudio/quarto-confluence-test/blob/main/sites/example), editing `reports-folder/index.qmd` to be: ```` --- title: "Reports" --- * [January](2022-01.qmd) * [March](2022-03.qmd) ```` Looks and works fine on local preview: <img width="353" alt="Screen Shot 2023-03-06 at 12 13 38 PM" src="https://user-images.githubusercontent.com/25964/223220302-fe7fa661-a50c-4c13-bacc-51bf6cd2e581.png"> But, no links appear on Confluence: <img width="539" alt="Screen Shot 2023-03-06 at 12 14 12 PM" src="https://user-images.githubusercontent.com/25964/223220420-4b090d3b-1867-43b7-ac5f-3fe0eb63f34b.png"> ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4635 <div type='discussions-op-text'> ^{Originally posted by **andrewpbray** March 5, 2023} Hello, I've just tried putting a document listing as conditional content and it didn't work. Here's a MWE. [conditional-listing.zip](https://github.com/quarto-dev/quarto-cli/files/10892937/conditional-listing.zip) The operative part is in this doc: ``` --- title: "Conditional-listing" listing: id: blog contents: - post-1.qmd - post-2.qmd --- This is a Quarto website. To learn more about Quarto websites visit <https://quarto.org/docs/websites>. :::{.content-hidden when-profile="noblog"} :::{#blog} ::: ::: ``` I had hoped that on `quarto render` I'd see the blog but on `quarto render --profile noblog` I would not, but alas, both versions have the blog. I'm guessing this has something to do with the order of operations on render? Thanks for any thoughts / suggestions.</div>

### Bug description I am trying to render a Quarto document that includes a Mermaid diagram. I get this error message: ``` ERROR: Chrome not found No Chrome or Chromium installation was detected. Please run 'quarto tools install chromium' to install Chromium. ``` However, I have [Chromium](https://archlinux.org/packages/extra/x86_64/chromium/) installed through the Archlinux package manager pacman. `chromium --version` gives me `Chromium 110.0.5481.177 Arch Linux`, and I can also open the browser. I suppose the problem is that the command is called `chromium` on my system, whereas Quarto [expects it to be named `chromium-browser`](https://github.com/quarto-dev/quarto-cli/blob/063c6a1422883a229f091bc949a9690c7b2318d1/src/core/puppeteer.ts#L209). I am running Quarto version 1.2.313. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

STR Description: [Confluence isn't listed as a destination](https://github.com/quarto-dev/quarto-cli/issues/4645) Steps to Reproduce: - Publish a document to Confluence using `quarto publish my-doc.qmd` - Select "Add a new destination..." Expected Result: - Confluence is listed Actual Result: - Confluence is not listed 

### Bug description Description: Quarto Web “locking up” on last file of render. Mac OS Steps to Reproduce: Render a big site like quarto web. Expected Result: After the last file is rendered, the total render job completes. Actual Result: It seems to hang after the last file render.  ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.

It's possible that some work Charles doing with title blocks needs to get reflected in our local confluence project preview. Note there that the title block is left aligned but the content is nudged to the center (which is I believe how it started out in your initial work on local confluence project preview). It may just be that we need to tweak our CSS to also target the title block? 

### Bug description I tried to have both `toc-location: left` and custom grid sizes for margin and sidebar in a HTML format. However, the custom grid format only works without `toc-location: left`, i.e. in default (right) position. It seems that when `toc-location: left` is provided, the margin width become the same as the sidebar width (600px in the example below). Reproducible example: ``` --- title: "quarto_grid-margin-width" format: html: toc: true toc-location: left grid: body-width: 800px sidebar-width: 600px margin-width: 50px --- # Title ## Title 2 Body content ::: {.column-margin} Margin content of length greater than 50px ::: ``` RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for WindowsMozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36 Quarto version: 1.3.242 OS: Windows 10 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

From https://community.rstudio.com/t/images-from-cloud-storage-direct-download-links-are-not-shown-in-quarto-html-document/160750 by @lnnrtwttkhn ## Problem Quarto HTML document does not display images from external direct download links to a publicly accessible cloud share provider (in this case [Keeper](https://keeper.mpdl.mpg.de/), based on Seafile). The problem does not occur for e.g., the GitHub README.md file. ## Demonstration A demonstration of the problem can be found here: https://lennartwittkuhn.com/keeper-image/. ## Quarto version On my local machine: ``` $ quarto --version 1.2.313 ``` Any hints appreciated! Thank you!

### Bug description Hello quarto team, I have found this pull request https://github.com/conda-forge/quarto-feedstock/pull/1 to enable the build of conda packages for windows. However this PR is open since a bit more than half a year. What's the status of this PR? Will there be any windows conda packages available anytime soon? ## Context We'd like to use quarto to generate some internal reports. Unfortunately, we have to use Windows to run our report generation pipeline and having an extra manual installation/ maintenance step instead of using a package manager handling this causes additional effort and some trouble from time to time. ## System R Studio Version: - OS: Windows 10 Pro, 19044.2604 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description (I'm not sure if it is a bug, or if I'm doing something wrong) I'm trying to get a summary stats table in Quarto with CrossRef. For LaTeX it works perfectly. However in HTML it cannot recognice it and stays @tbl-stats. (See first example). If I add a div with id containing tbl- at the beginning (also tried tbl-stats, there is not difference) the CrossRef works, however below the table it writes "?(caption)" and in the HTML-Code it adds a new div around my div with the set id. (if I use tbl-stats in my div, it's repeated) The set caption itself is above the table. Markdown-Text: @tbl-stat zeigt die daraus entstandene Tabelle. ````md ```{r} #| results: asis #| echo: false #| tbl-cap: "Statistiktabelle" #| label: tbl-stat stargazer::stargazer(glm.predict::selects2015, header = FALSE, type = ifelse(knitr::is_latex_output(),"latex", "html")) ``` ```` ````md ```{r} #| results: asis #| echo: false #| tbl-cap: "Statistiktabelle" #| label: tbl-stat if(knitr::is_html_output()){ cat("<div id='tbl-'>") } stargazer::stargazer(glm.predict::selects2015, header = FALSE, type = ifelse(knitr::is_latex_output(),"latex", "html")) if(knitr::is_html_output()){ cat("</div>") } ``` ```` R Studio Version: RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36 OS: Windows 11 Pro, 22621.1265 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Quarto CLI seems to be very useful for creating basic Linux and Bash shell documentation. It would be nice if Quarto supported syntax highlighting and execution of shell code without the need for the full Knitr or Jupyter stacks. What would it take to create a standalone execution engine just for the shell?

I find myself sometimes running multiple copies of `quarto preview` over the same directory (a shell and VS code is the most common way I make this mistake). It would be nice if we had a lockfile that described which files are currently being previewed by some quarto process, so that we wouldn't step on our own toes.

`body` is ambiguous in contexts where users might assume we mean the <body> element, and not the content inserted by Pandoc templates in many different formats. We should clarify this in our schema docs. See #4628 for how this causes confusion.

### Bug description ## Here is a minimal example. ```` --- title: "Untitled" format: html: include-in-header: - header.html --- ## Math $$ \bm{x} + x + \cancel{\text{///}} $$ ```` ## The content of `header.html` as follow ```js <script type="text/x-mathjax-config"> MathJax.Hub.Config({ TeX: { Macros: { bm: ["{\\boldsymbol #1}",1], }, extensions: ["cancel.js"] } }); </script> ``` ## The output is  That means user-defined TeX macros doesn't work. ## Quarto and RStudio IDE I use Quarto 1.3.242 RStudio 2023.03.0+382 "Cherry Blossom" Release (3a8b92eb66f0754a31f03c010b41496abc65fb70, 2023-03-01) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+382 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description I have a quarto website and here is a minimal example. **_quarto.yml** ``` project: type: website website: title: "Website" navbar: background: transparent left: - text: Home href: "index.html" page-footer: left: Left content right: Right content format: html ``` **index.html** ``` --- format: html: include-after-body: "include.html" --- # Hello This is the index page. ``` **include.html** ``` <script type="text/javascript"> console.log("hello"); </script> ```  As seen in the screenshot, the **include.html** content (highlighted red) is placed inside the `quarto-content` div rather than the `body` div. I think it should be below the footer div and at the bottom along with the other scripts highlighted in green. I have tried moving ` include-after-body: "include.html"` from **index.html** to **_quarto.yml**, but that doesn't change this. I am also unsure what the difference between ` include-after-body` and `include-after` is. `include-after` seems to place it in the right place but literally adds the text rather the content in the path. ``` 🢒 quarto --version 1.2.1 🢒 lsb_release -a No LSB modules are available. Distributor ID: Zorin Description: Zorin OS 16.2 Release: 16 Codename: focal ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description - **Setup:** I use `.ipynb` documents in VS Code and quarto cli (v. 1.3.242) on Windows 10 to render the report to HTML. - **Issue:** I want to render Pandas tables with table captions. The column alignment is different when the index is included and excluded. - **Expected behaviour:** the same defaults despite the fact that the index is included or excluded. - **Details.** HTML output:  The result in VS code – column alignment is the same in each case.  Code: ```python import pandas as pd df = pd.DataFrame({ 'Country': {0: 'Belgium', 1: 'England'}, 'League': {0: 'Belgium Jupiler League', 1: 'England Premier League'} }) #| label: tbl-1 #| tbl-cap: This column name alignment is expected. df.style.hide(axis="index") #| label: tbl-2 #| tbl-cap: Why are column labels aligned differently in this table compared # to in the previous example? df ``` File: `ipynb` file and rendered HTML output are attached [quarto_col_alignmet_bug.zip](https://github.com/quarto-dev/quarto-cli/files/10891707/quarto_col_alignmet_bug.zip) **Update** This might be related to `.style` accessor/attribute. ``` #| label: tbl-3 #| tbl-cap: It seams that `.style` changes the output. df.style ``` - If this issue is not related to Quarto, can more examples of Quarto with Pandas and ipynb files be added? ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Variables in my _variable.yml file that are arbitrary markdown content are not interpreted as markdown when my .qmd file is rendered. The variable behaves as a simple string. My .qmd file is shown below. ```md --- title: Test --- :::{.content-hidden when-format="revealjs"} My content for HTML {{< var slide.open >}} My content for revealjs {{< var slide.close >}} My other content for HTML ::: ``` My _variable.yml has the following keys ```yaml slide: open: | ::: :::{.content-visible when-format="revealjs"} close: | ::: :::{.content-hidden when-format="revealjs"} ``` The rendered output looks like ```HTML Test MODIFIED Fr 2023-03-03 22:01 My content for HTML ::: :::{.content-visible when-format=“revealjs”} My content for revealjs ::: :::{.content-hidden when-format=“revealjs”} My other content for HTML ``` Is this the intended behavior? I've tried some other arbitrary markdown (e.g., **) and have yet to be successful. The [documentation](https://quarto.org/docs/authoring/variables.html#var) leads me to believe that any arbitrary markdown may be used, but that doesn't seem to be the case. Using links as provided in the example in the documentation seems to work, though. I'm using Windows 10 with the 2022.12.0 Build 353 of RStudio, and the 1.3.208 version of quarto. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Hello, Crossrefs are not resolving when figure is created inside a div. The crossref doesn't work either inside the div or outside. ```` --- title: "Crossref bug" --- :::{.callout-note} ```{r} #| label: fig-div-plot #| fig-cap: my plot! plot(1:10, 1:10) ``` Check out @fig-div-plot ::: Check out @fig-div-plot ```` (If the figure is created outside of a div, the crossref *does* resolve inside a div). Example at <https://ellakaye.github.io/quarto-bug/> from repo <https://github.com/EllaKaye/quarto-bug> This is a bug that has appeared in the pre-release (v1.3.242). It works fine in the current stable release (v.1.2.335). I'm on macOS Ventura 13.2.1 working in RStudio 2023.03.0-daily+30. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description I just tried out the [external links](https://quarto.org/docs/output-formats/html-basics.html#external-links) feature of Quarto's HTML format and noticed that the icon after external links gets line-wrapped like regular whitespace-separated text which is clearly undesirable. Example screenshot:  I see that technically no whitespace is used between the link and the icon. Instead it is inserted via the CSS pseudo-element [`::after`](https://developer.mozilla.org/en-US/docs/Web/CSS/::after). I'm no CSS expert, so I can't judge what the best solution looks like. A possible solution would be to [move `display:inline-block;` from `a.external::after` to `a.external`](https://stackoverflow.com/questions/14851320/how-to-avoid-line-breaks-after-before-in-css). But maybe you got an even better solution. Thanks for looking into this! ^{I'm using the latest stable Quarto CLI v1.2.335} ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Dear Quarto team I’m struggling to solve an issue with epub generated using Quarto. Here is a repo with a simple book: https://github.com/b-rodrigues/epubcheck_quarto_test that causes the issue. using `quarto render` creates an epub version of the book in the _book folder. But using epubcheck on it (https://www.w3.org/publishing/epubcheck/) I get the following error message: ``` ERROR(RSC-005): example_book.epub/EPUB/content.opf(6,39): Error while parsing file: character content of element "dc:date" invalid; be a string with length at least 1 (actual length was 0) WARNING(OPF-053): example_book.epub/EPUB/content.opf(6,39): Date value "" does not follow recommended syntax as per http://www.w3.orNOTE-datetime:zero-length string. ``` and indeed, if I take a look at the ` example_book.epub/EPUB/content.opf` file, I see that the `dc:date` tag is empty. However, in the `_quarto.yml` file, you’ll see that I’ve added the following: ``` format: html: theme: cosmo epub: toc: true date: "2023-03-01" ``` I have the same issue on Linux (see Github actions, and the generated ebook in the gh-pages branch) and on Windows 10 with the latest version of Quarto installed (1.2.335). ### EDIT The error message disappears if I add the language as well: ``` format: html: theme: cosmo epub: toc: true lang: en-GB date: "2023-03-01" ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

Found while investigating #4593 Take this simple example ````markdown --- title: "test" format: html --- Test ```` I put that on another drives than when Quarto is installed and called example `K:` It will error ````powershell quarto render test.qmd pandoc to: html output-file: test.html standalone: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png metadata document-css: false link-citations: true date-format: long lang: en title: test ERROR: NotFound: Le fichier spécifié est introuvable. (os error 2), readdir 'test_files\mediabag' NotFound: Le fichier spécifié est introuvable. (os error 2), readdir 'test_files\mediabag' at Object.readDirSync (deno:runtime/js/30_fs.js:120:16) at removeIfEmptyDir (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/core/path.ts:49:31) at renderCleanup (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cleanup.ts:103:3) at file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render.ts:293:9 at withTiming (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/core/timing.ts:37:20) at Object.complete (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render.ts:292:7) at async Object.onPostProcess (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:565:28) at async renderFiles (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:521:7) at async render (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:101:18) at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cmd.ts:210:26) ```` First investigation shows that `Deno.readDirSync` has an issue on Windows reading this mediabag dir * Folder is there on disk, with no content ````powershell > tree Structure du dossier pour le volume KBFS Le numéro de série du volume est 0000-0000 K:. └───test_files ├───mediabag └───libs ├───bootstrap ├───clipboard └───quarto-html > ls test_files/mediabag ```` but from Deno REPL ```node // folder is seen > Deno.lstatSync("test_files/mediabag") { isFile: false, isDirectory: true, isSymlink: false, size: 4, mtime: 2023-03-03T09:38:54.289Z, atime: 2023-03-03T09:38:54.289Z, birthtime: 2023-03-03T09:38:54.289Z, dev: null, ino: null, mode: null, nlink: null, uid: null, gid: null, rdev: null, blksize: null, blocks: null } // folders are listed > for (const _entry of Deno.readDirSync("test_files")) { console.log(_entry) } { name: "libs", isFile: false, isDirectory: true, isSymlink: false } { name: "mediabag", isFile: false, isDirectory: true, isSymlink: false } undefined // but Deno will error on reading mediabag > for (const _entry of Deno.readDirSync("test_files/mediabag")) { console.log(_entry) } Uncaught NotFound: Le fichier spécifié est introuvable. (os error 2), readdir 'test_files/mediabag' at Object.readDirSync (internal:runtime/js/30_fs.js:119:14) at <anonymous>:2:27 ``` We currently rely on this to remove empty dir (`existsSync` return TRUE for `mediabag`) https://github.com/quarto-dev/quarto-cli/blob/86b22ca080cefca5efe8746972515bcd8f0d29df/src/core/path.ts#L47-L52 Looking at the code for `Deno.emptyDir` which is supposed also to check for emptyness, it seems the TryCatch on `NotFound` error (that we have here) is important https://github.com/denoland/deno_std/blob/635da0f56c8c7b2294b0448763bda1d055dcfe44/fs/empty_dir.ts#L11 This is also the function we use to create the mediabag dir , so it seems the right way https://github.com/quarto-dev/quarto-cli/blob/dee0d817154a0bdec1a502da715b9e61cff570b0/src/command/render/render.ts#L97-L98 So something is not ok here. **IMPORTANT** This does not happen when I am in the same drive on Windows as quarto - `mediabag` is correctly remove for the same qmd file.

### Bug description When running action Render and Publish in my blog, since version 1.3.242 (last week with v1.3.231 it was OK) I have the following error `ERROR: File name too long (os error 36), stat '/home/runner/work/blog/blog/posts/home/runner/work/blog/blog/data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAbAAAAEeCAYAAADrWEC0AAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAALEgAACxIB0t1+/AAAADh0RVh0U29mdHdhcmUAbWF0cGxvdGxpYiB2ZXJzaW9uMy4xLjMsIGh0dHA6Ly9tYXRwbG90b` (this is a 70KB base64 png file. I don't know exactly what happens. My action file is ``` on: workflow_dispatch: push: branches: main name: Quarto Publish jobs: build-deploy: runs-on: ubuntu-latest permissions: contents: write steps: - name: Check out repository uses: actions/checkout@v2 - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 with: version: 'pre-release' - name: Render and Publish uses: quarto-dev/quarto-actions/publish@v2 with: target: gh-pages env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} ``` I switched to pre-release version to get 1.3 and use code annotation. Will switch back to stable version for now. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description As mentioned in #2417, ````` --- title: "Untitled" format: latex keep-md: true --- ```{r} #| label: main-plot #| out-width: 50% plot(mtcars) ``` ````` generates the following in LaTeX (as of version 1.2.335, RStudio 2022.12.0 on Windows 11): ``` \includegraphics[width=0.5\textwidth,height=\textheight]{test_files/figure-latex/main-plot-1.pdf} ``` In a 2-column document, the figure is not formated as expected: it is wider than its column. In R Markdown, the same options generated ``` \includegraphics[width=0.5\textwidth]{test_files/figure-latex/main-plot-1.pdf} ``` which worked perfectly. A temporary workaround is to divide the desired width by 2. So I think `height=\textheight` should not be added if `#| out-height:` is not specified in the Quarto file: LaTeX does not need it and it does not allow correct format in 2-column documents. Thanks!

Drafts: * [x] Multi-format Publishing * [x] Code Annotation * [x] Confluence * [x] Jupyter Cell Embedding * [ ] Other features and point to highlights

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4609 <div type='discussions-op-text'> ^{Originally posted by **jameshowison** March 2, 2023} I'm loving using mermaid inside quarto (run from Rstudio on a Mac). I'm teaching git stuff and making some collaboration diagrams, you can see them at: https://howisonlab.github.io/open_source_software_course/skills/git_cherrypick_split_pr.html#split-before-submit I'm seeing a small rounded corner square box in the bottom left of my images. Same thing with sequence diagrams, e.g.,: https://howisonlab.github.io/open_source_software_course/skills/github_collaboration.html Screen Shot 2023-03-02 at 11 13 17 AM I cross-posted this at Mermaid: https://github.com/mermaid-js/mermaid/discussions/4176 The little squares don't show up using mermaid.live so it's possible/likely it's something in the rendering pipeline that quarto is using (maybe Chrome as render?). I don't see the squares in other quarto mermaid output: e.g.,: https://quarto.org/docs/authoring/diagrams.html. So probably it's something to do with my install (obtained quarto via homebrew)? </div>

### Bug description The `jupyter-cache` package is currently maintained in the `conda-forge` channel (see [this search on `anaconda.org`](https://anaconda.org/search?q=jupyter-cache)) which is not included in the list of default channels used by `Conda.jl` on a fresh install on Windows 10. Thus, to install `jupyter-cache`, the correct command is ```julia Conda.add("jupyter-cache"; channel="conda-forge") ``` On a fresh install, attempting to use `Conda.add("jupyter-cache")` as instructed by the [Using Julia](https://quarto.org/docs/computations/julia.html#jupyter-cache) documentation page results in the following error: ``` julia> Conda.add("jupyter-cache") [ Info: Running `conda install -y jupyter-cache` in root environment Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - jupyter-cache Current channels: - https://repo.anaconda.com/pkgs/main/win-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/win-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/msys2/win-64 - https://repo.anaconda.com/pkgs/msys2/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description # Reproducing To set up for reproduction quickly, clone this repo and follow the instructions in "Repro steps" below: https://github.com/MattF-NSIDC/sscce-quarto-listing-issue ## Setup steps 1. Create the project ``` quarto create-project demo-filter-issue --type=website ``` 1. Change the `index.qmd` to a "table"-type listing ``` --- title: "demo-filter-issue" listing: "table" --- ``` 1. Create an `items/` dir and populate with 4 markdown files with numbered titles, e.g. `# Item #1: Foo`, `# Item #2: Bar`, etc. 1. Remove `about.qmd` ## Repro steps 1. `quarto preview` 1. In your browser on the index page, try filtering the listing for `1`, `2`, `3`, and `4` separately. 1. At least one of these filter attempts will not actually cause any filtering. If this doesn't happen, delete `.quarto` and `_site` directories and start over. Each time, the behavior should be different. E.g. the first time filtering for `1` may be ineffective, and next time filtering for `4` may be ineffective, and the next time both `1` and `2` will not be filterable. ## Repro screenshot sample Because this issue is non-deterministic, each run of `quarto preview` will behave differently. Therefore, the issue won't reproduce exactly the same as these screenshots. * Filtering for `2` is effective  * Filtering for `3` is ineffective  # Versions tested * Quarto 1.3.241, 1.3.217, 1.2.335 * Ubuntu 20 * No IDE ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.