Merge branch 'main' into feature/deno-2

Author: cscheid

.air.toml

@@ -5,4 +5,4 @@ indent-style = "space"
 line-ending = "auto"
 persistent-line-breaks = true
 exclude = []
-default-exclude = true
+default-exclude = true

.ruff.toml

@@ -0,0 +1,14 @@
+extend-exclude = [
+  "**/renv",
+  "**/.venv",
+  ".github",
+  ".vscode",
+  "**/node_modules",
+  "**/__pycache__",
+  "**/build",
+  # file with cell magic not parsed by ruff
+  "src/resources/jupyter/lang/python/cleanup.py",
+  "src/resources/jupyter/lang/python/setup.py",
+]
+# don't format .ipynb files as quarto cell comment 
+include = ["**/*.py"]

.vscode/extensions.json

@@ -4,6 +4,8 @@
     "esbenp.prettier-vscode",
     "sumneko.lua",
     "nvarner.typst-lsp",
-    "Posit.air-vscode"
+    "Posit.air-vscode",
+    "charliermarsh.ruff",
+    "tamasfe.even-better-toml"
   ]
 }

.vscode/settings.json

@@ -2,6 +2,18 @@
   "[typescript]": {
     "editor.defaultFormatter": "denoland.vscode-deno"
   },
+  "notebook.formatOnSave.enabled": false,
+  "notebook.codeActionsOnSave": {
+    "notebook.source.organizeImports": "explicit"
+  },
+  "pylint.enabled": false,
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "charliermarsh.ruff",
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": "explicit"
+    }
+  },
   "[r]": {
     "editor.formatOnSave": true,
     "editor.defaultFormatter": "Posit.air-vscode"
@@ -13,6 +25,10 @@
   "[html]": {
     "editor.formatOnSave": false
   },
+  "[toml]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "tamasfe.even-better-toml"
+  },
   "editor.defaultFormatter": "esbenp.prettier-vscode",
   "editor.formatOnSave": true,
   "editor.tabSize": 2,

dev-docs/checklist-make-a-new-quarto-release.md

@@ -17,6 +17,7 @@
   - this means flipping the profile group configuration in `_quarto.yml` from `[rc,prelease]` to `[prerelease,rc]`
     - [ ] push the changes to the `main` branch
 - [ ] quarto-dev/quarto-web changes
+
   - wait for the downloads file to be automatically updated by the GitHub Action on https://github.com/quarto-dev/quarto-web
     - [ ] wait for https://github.com/quarto-dev/quarto-web/actions/workflows/update-downloads.yml to run (it runs every 15 minutes, or you can manually trigger it)
       - This workflow run rendered the website: https://github.com/quarto-dev/quarto-web/actions/runs/12016407762
@@ -29,7 +30,7 @@
       - [ ] create `docs/prerelease/1.5/{_highlights, index, _pre-release-feature}.qmd` files based on the ones from the previous release
       - [ ] change `docs/prerelease/_highlights.qmd` so its include points to the new version-specific `_highlights.qmd` file (here, 1.5)
       - [ ] change `docs/prerelease/_highlights-release.qmd` so its include points to the new version-specific `_highlights.qmd` file (here, 1.4)
-    - [ ] add the stable version to the older downloads list by editing /docs/download/_download-older.yml
+    - [ ] add the stable version to the older downloads list by editing /docs/download/\_download-older.yml
     - [ ] run `quarto run tools/release-notes.R` to generate the release notes
   - [ ] push the changes to `prerelease` branch, ensure they build correctly
   - [ ] Merge the `prerelease` branch into `main`, push to `main`
@@ -43,16 +44,14 @@
     - [ ] edit `_quarto-prerelease-docs.yml` to point to the new version
   - [ ] publish the release blog post that should exist in https://github.com/quarto-dev/quarto-web/tree/main/docs/blog/posts
     - [ ] Create a branch off of `main` (to trigger our PR automation to make the corresponding change to `prerelease`).
-    - [ ] Removing the `draft: true` line in the metadata 
-    - [ ] Change the date to match the release date. 
+    - [ ] Removing the `draft: true` line in the metadata
+    - [ ] Change the date to match the release date.
 
 - [ ] Update https://github.com/quarto-dev/quarto-cli/blob/main/CITATION.cff
 - [ ] Packaging and package managers, etc
-  - TBD winget, etc?
-  - [ ] chocolatey
-    - https://github.com/quarto-dev/quarto-release-bundles/
-    - Go to "Select 'Publish Quarto PyPi'"
-    - [ ] Click "Run Workflow"
+  - [ ] chocolatey (Only once quarto.org download page is updated with the new release)
+    - https://github.com/quarto-dev/quarto-release-bundles/actions/workflows/build-and-publish-choco.yaml
+    - [ ] In "Build Choco package & Publish" workflow page, click "Run Workflow"
       - Check the "Whether to publish or not the package on chocolatey" checkbox
     - Wait for @cderv to receive email confirmation, no action needed
   - [ ] pypi
@@ -71,3 +70,11 @@
         - **Publishing Production**: You may elect to publish to production pypyi by checking the `Production Release` option
           - Published to: <https://pypi.org/project/quarto-cli/>
       - Take a sip of tea ☕, bask in the glory of automation.
+  - Others installers
+    - conda-forge: An automated PR will be created to update the package version in the feedstock <github.com/conda-forge/quarto-feedstock>
+      - This is community maintained, so no action is needed from us - except maybe helping if there are issues with the PR. We are assigned as reviewers to the PR.
+      - Winget: An automated PR will be created by a winget bot in <github.com/microsoft/winget-pkgs/>.
+        - This is community maintained, so no action is needed from us.
+      - Scoop: This will be updated automatically in the manifests repo. No action is needed from us. Maintained as personal project by @cderv.
+      - Homebrew: This is automated through an homebrew bot to update the cask <https://github.com/Homebrew/homebrew-cask>
+        - Manisfest: <https://github.com/Homebrew/homebrew-cask/blob/master/Casks/q/quarto.rb>

dev-docs/checklist-make-a-new-stable-quarto-release.md

@@ -8,6 +8,12 @@
     - Uncheck "Pre-release" (or ensure it's unchecked)
     - Check "Publish release" (or ensure it's checked)
     - [ ] Click "Run Workflow"
+    - Take a sip of tea ☕, bask in the glory of automation.
+- [ ] Trigger update for quarto.org website once new stable release is available
+  - Go to quarto-dev/quarto-web repo in [Update Downloads](https://github.com/quarto-dev/quarto-web/actions/workflows/update-downloads.yml) workflow
+  - Run the workflow with 'Run Workflow' button on `main` branch.
+    This will check the new release, and update the files in quarto-web to update the Download page.
+  - While this automation is running, update the release on pypi below.
 - [ ] update release on pypi repo
   - Goto the [quarto-cli-pypi repo](https://github.com/quarto-dev/quarto-cli-pypi)
   - Update `version.txt` to be the version you'd like to publish and commit
@@ -24,4 +30,17 @@
       - **Publishing Production**: You may elect to publish to production pypyi by checking the `Production Release` option
         - Published to: <https://pypi.org/project/quarto-cli/>
     - Take a sip of tea ☕, bask in the glory of automation.
+- [ ] push release to chocolatey (Only once quarto.org download page is updated with the new release)
+  - Got to <https://github.com/quarto-dev/quarto-release-bundles/actions/workflows/build-and-publish-choco.yaml>
+  - In the "Build Choco package & Publish" workflow, click "Run Workflow" and be sure to check the "Whether to publish or not the package on chocolatey" checkbox
+  - Wait for @cderv to receive email confirmation, no action needed.
 - [ ] Update the stable changelog by moving entries to the "in previous release". Use "[release checklist]" in the commit message to make it easier to spot if a new release is needed next month.
+
+- Others installers
+  - conda-forge: An automated PR will be created to update the package version in the feedstock <github.com/conda-forge/quarto-feedstock>
+    - This is community maintained, so no action is needed from us - except maybe helping if there are issues with the PR. We are assigned as reviewers to the PR.
+    - Winget: An automated PR will be created by a winget bot in <github.com/microsoft/winget-pkgs/>.
+      - This is community maintained, so no action is needed from us.
+    - Scoop: This will be updated automatically in the manifests repo. No action is needed from us. Maintained as personal project by @cderv.
+    - Homebrew: This is automated through an homebrew bot to update the cask <https://github.com/Homebrew/homebrew-cask>
+      - Manisfest: <https://github.com/Homebrew/homebrew-cask/blob/master/Casks/q/quarto.rb>

dev-docs/feature-format-matrix/create_table.py

@@ -2,8 +2,8 @@
 import json
 import pathlib
 
-class Trie:
 
+class Trie:
     def __init__(self):
         self.children = {}
         self.values = []
@@ -37,13 +37,12 @@ def tabulator(self):
             children = v.tabulator()
             feature = k
             if v.entry != "":
-                link = "<a href='%s' target='_blank'><i class='fa-solid fa-link' aria-label='link'></i></a>" % v.entry
+                link = (
+                    "<a href='%s' target='_blank'><i class='fa-solid fa-link' aria-label='link'></i></a>"
+                    % v.entry
+                )
                 feature = "%s %s" % (link, k)
-            d = {
-                "sort_key": k,
-                "feature": feature,
-                **v.tabulator_leaf()
-            }
+            d = {"sort_key": k, "feature": feature, **v.tabulator_leaf()}
             if children:
                 d["_children"] = children
             result.append(d)
@@ -60,13 +59,14 @@ def size(self):
             return 1
         return sum([v.size() for v in self.children.values()])
 
-    def walk(self, visitor, path = None):
+    def walk(self, visitor, path=None):
         if path is None:
             path = []
         visitor(self, path)
         for k, v in self.children.items():
             v.walk(visitor, path + [k])
 
+
 def extract_metadata_from_file(file):
     with open(file, "r") as f:
         lines = f.readlines()
@@ -78,10 +78,13 @@ def extract_metadata_from_file(file):
                 start = i
             else:
                 end = i
-                metadata = yaml.load("".join(lines[start+1:end]), Loader=yaml.SafeLoader)
+                metadata = yaml.load(
+                    "".join(lines[start + 1 : end]), Loader=yaml.SafeLoader
+                )
                 return metadata
     raise ValueError("No metadata found in file %s" % file)
 
+
 def table_cell(entry, _feature, _format_name, format_config):
     if type(format_config) == str:
         format_config = {}
@@ -90,8 +93,22 @@ def table_cell(entry, _feature, _format_name, format_config):
     if quality is not None:
         if type(quality) == str:
             quality = quality.lower()
-        qualities = {-1: "&#x1F6AB;", 0: "&#x26A0;", 1: "&#x2713;", 2: "&#x2713;&#x2713;", "unknown": "&#x2753;", "na": "NA"}
-        colors = {-1: "bad", 0: "ok", 1: "good", 2: "good", "unknown": "unknown", "na": "na"}
+        qualities = {
+            -1: "&#x1F6AB;",
+            0: "&#x26A0;",
+            1: "&#x2713;",
+            2: "&#x2713;&#x2713;",
+            "unknown": "&#x2753;",
+            "na": "NA",
+        }
+        colors = {
+            -1: "bad",
+            0: "ok",
+            1: "good",
+            2: "good",
+            "unknown": "unknown",
+            "na": "na",
+        }
         color = colors[quality]
         quality_icon = qualities.get(quality, "&#x2753;")
         result.append(f"<span class='{color}'>{quality_icon}</span>")
@@ -101,7 +118,8 @@ def table_cell(entry, _feature, _format_name, format_config):
         result.append(f"<span title='{comment}'>&#x1F4AC;</span>")
     return "".join(result)
 
-def compute_trie(detailed = False):
+
+def compute_trie(detailed=False):
     trie = Trie()
     pattern = "qmd-files/**/*.qmd" if detailed else "qmd-files/**/document.qmd"
     for entry in pathlib.Path(".").glob(pattern):
@@ -115,26 +133,37 @@ def compute_trie(detailed = False):
         except KeyError:
             raise Exception("No format found in %s" % entry)
         for format_name, format_config in format.items():
-            trie.insert(feature, {
-                "feature": "/".join(feature),
-                "format": format_name,
-                "entry": entry,
-                "format_config": format_config,
-                "table_cell": table_cell(entry, feature, format_name, format_config)
-            })
+            trie.insert(
+                feature,
+                {
+                    "feature": "/".join(feature),
+                    "format": format_name,
+                    "entry": entry,
+                    "format_config": format_config,
+                    "table_cell": table_cell(
+                        entry, feature, format_name, format_config
+                    ),
+                },
+            )
     return trie
 
-def render_features_formats_data(trie = None):
+
+def render_features_formats_data(trie=None):
     if trie is None:
         trie = compute_trie()
     entries = trie.tabulator()
-    return "```{=html}\n<script type='text/javascript'>\nvar tableData = %s;\n</script>\n```\n" % json.dumps(entries, indent=2)
+    return (
+        "```{=html}\n<script type='text/javascript'>\nvar tableData = %s;\n</script>\n```\n"
+        % json.dumps(entries, indent=2)
+    )
+
 
-def compute_quality_summary(trie = None):
+def compute_quality_summary(trie=None):
     if trie is None:
         trie = compute_trie()
     quality_summary = {"unknown": 0, -1: 0, 0: 0, 1: 0, 2: 0, "na": 0}
     n_rows = 0
+
     def visit(node, _path):
         nonlocal n_rows
         if not node.children or len(node.values):
@@ -149,5 +178,6 @@ def visit(node, _path):
             if quality_summary.get(quality) is None:
                 raise ValueError("Invalid quality value %s" % quality)
             quality_summary[quality] += 1
+
     trie.walk(visit)
-    return {"n_rows": n_rows, "quality": quality_summary}
+    return {"n_rows": n_rows, "quality": quality_summary}

news/changelog-1.8.md

@@ -1,21 +1,32 @@
 All changes included in 1.8:
 
+## Regression fixes
+
+- ([#6607](https://github.com/quarto-dev/quarto-cli/issues/6607)): Add missing beamer template update for beamer theme options: `colorthemeoptions`, `fontthemeoptions`, `innerthemeoptions` and `outerthemeoptions`.
+- ([#12625](https://github.com/quarto-dev/quarto-cli/pull/12625)): Fire resize event on window when light/dark toggle is clicked, to tell widgets to resize.
+- ([#12657](https://github.com/quarto-dev/quarto-cli/pull/12657)): Load Giscus in generated script tag, to avoid wrong-theming in Chrome.
+
 ## Formats
 
+### `html`
+
+- ([#12259](https://github.com/quarto-dev/quarto-cli/issues/12259)): Fix conflict between `html-math-method: katex` and crossref popups (author: @benkeks).
+
 ### `revealjs`
 
 - ([#12598](https://github.com/quarto-dev/quarto-cli/pull/12598)): Ensure `.fragment` on an image with caption applies to whole figure.
 
 ### `docx`
 
-- ([#8392](https://github.com/quarto-dev/quarto-cli/issues/8392)): Fix `docx` generation issues in tables 
+- ([#8392](https://github.com/quarto-dev/quarto-cli/issues/8392)): Fix `docx` generation issues in tables
 
 ## Projects
 
 ### `website`
 
 - ([#12551](https://github.com/quarto-dev/quarto-cli/pull/12551)): Improve warning issued when `aliases` would overwrite an existing document.
 - ([#12616](https://github.com/quarto-dev/quarto-cli/issues/12616)): find SVG images in image discovery for listings.
+- ([#12693](https://github.com/quarto-dev/quarto-cli/issues/12693)): Prevent resource exhaustion on large websites by serializing `NotebookContext` information to file instead of the environment.
 
 ## Crossrefs
 

quarto-cli.code-workspace

@@ -37,5 +37,6 @@
     "deno.inlayHints.variableTypes.enabled": false,
     "deno.inlayHints.variableTypes.suppressWhenTypeMatchesName": false
   },
-  "typst-lsp.exportPdf": "never"
+  "typst-lsp.exportPdf": "never",
+  "notebook.formatOnSave.enabled": false
 }

quarto_cli/__init__.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 import sys
 
+
 def find_version():
     g = str((Path(__file__).parent / "quarto-*").resolve())
     g = str((Path(glob.glob(g)[0]) / "bin" / "quarto").resolve())
@@ -12,8 +13,10 @@ def find_version():
         g += ".exe"
     return g
 
+
 def call_quarto(*args, **kwargs):
     return subprocess.run([find_version(), *sys.argv[1:], *args], **kwargs)
 
+
 def run_quarto(*args, **kwargs):
-    call_quarto(*args, **kwargs)
+    call_quarto(*args, **kwargs)