chore(sync): 🔨 synced file(s) with rostools/r3-theme

.air.toml

@@ -0,0 +1,8 @@
+[format]
+line-width = 80
+indent-width = 2
+indent-style = "space"
+line-ending = "auto"
+persistent-line-breaks = true
+exclude = []
+default-exclude = true

.github/workflows/build-website.yml

@@ -1,4 +1,4 @@
-name: Build website for R-based educational material 
+name: Build website for R-based educational material
 
 on:
   push:

.gitignore

@@ -30,4 +30,5 @@ public
 site
 slides/*.html
 _freeze
-
+*.html
+*_files

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+ci:
+  autofix_commit_msg: "chore(pre-commit): :pencil2: automatic fixes"
+  autoupdate_commit_msg: "ci(pre-commit): :construction_worker: update pre-commit CI version"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v4.7.0
+    hooks:
+      - id: commitizen
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.32.0
+    hooks:
+      - id: typos

.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+  "recommendations": [
+    "Posit.air-vscode",
+    "tekumara.typos-vscode",
+    "pshaddel.conventional-branch",
+    "vivaxy.vscode-conventional-commits",
+    "EditorConfig.EditorConfig",
+    "donjayamanne.githistory",
+    "felipecaputo.git-project-manager",
+    "GitHub.vscode-pull-request-github",
+    "pshaddel.conventional-branch",
+    "quarto.quarto",
+    "github.vscode-github-actions",
+    "redhat.vscode-yaml",
+    "eamodio.gitlens"
+  ],
+  "unwantedRecommendations": []
+}

.vscode/json.code-snippets

@@ -69,16 +69,16 @@
     ],
     "description": "Insert reading task section."
   },
-  "Insert instructor note": {
+  "Insert teacher note": {
     "scope": "quarto,markdown",
-    "prefix": "instructor_note",
+    "prefix": "teacher_note",
     "body": [
       "::: {.callout-note collapse=\"true\"}",
-      "## :teacher: Instructor note",
+      "## :teacher: Teacher note",
       "",
       "${0:Text body}",
       ":::",
     ],
-    "description": "Insert instructor note that is a Quarto callout note block."
+    "description": "Insert teacher note that is a Quarto callout note block."
   }
 }

.vscode/settings.json

@@ -21,23 +21,15 @@
   ],
   "conventional-branch.format": "{Type}/{Branch}",
   "files.insertFinalNewline": true,
-  "cSpell.enabledFileTypes": {
-    "quarto": true
-  },
-  "cSpell.language": "en,en-GB",
   "conventionalCommits.scopes": [
     "preamble",
     "sessions",
     "appendix"
   ],
-  "cSpell.customDictionaries": {
-    "project-words": {
-      "name": "repo-words",
-      "path": "${workspaceRoot}/includes/dictionary.txt",
-      "description": "Words used in this repository.",
-      "addWords": true
-    },
-    "custom": true, // Enable the `custom` dictionary
-    "internal-terms": false // Disable the `internal-terms` dictionary
-  }
+  "[r]": {
+    "editor.formatOnSave": true
+  },
+  "[quarto]": {
+    "editor.formatOnSave": true
+  },
 }

CONTRIBUTING.md

@@ -78,7 +78,7 @@ Making videos (on Linux) is done using
 1280x720), [OpenShot](https://www.openshot.org/) (to edit the video if
 necessary), and the below command to reduce the video file size:
 
-```         
+```
 ffmpeg -i input.mp4 -crf 28 output.mp4
 ```
 

DESCRIPTION

@@ -3,7 +3,7 @@ Version: 1.0
 Package: guides
 URL: https://github.com/rostools/guides/, https://guides.rostools.org
 Encoding: UTF-8
-Imports: 
+Imports:
     downlit,
     dplyr,
     ggplot2,
@@ -15,5 +15,5 @@ Imports:
     tidyr,
     usethis,
     xml2
-Remotes:  
+Remotes:
     rostools/r3admin

_extensions/rostools/r3-theme/_brand.yml

@@ -0,0 +1,35 @@
+meta:
+  name:
+    full: rostools
+  link:
+    github: https://github.com/rostools
+
+typography:
+  fonts:
+    - family: quattrocento sans
+      source: "bunny"
+    - family: outfit
+      source: "bunny"
+    - family: source code pro
+      source: "bunny"
+  base:
+    family: quattrocento sans
+    size: 18px
+  headings:
+    family: outfit
+    weight: 400
+  monospace: source code pro
+
+defaults:
+  bootstrap:
+    defaults:
+      mermaid-edge-color: "gray"
+    rules: |
+        .slide-deck {
+          border: 3px solid #203C6E;
+          width: 100%;
+          height: 425px;
+        }
+        kbd {
+          padding: .15rem .15rem;
+        }

_extensions/rostools/r3-theme/_extension.yml

@@ -18,8 +18,8 @@ contributes:
       code-overflow: scroll
       from: markdown+emoji
       theme:
+        - brand
         - yeti
-        - custom-site.scss
 
     revealjs:
       embed-resources: true
@@ -40,8 +40,10 @@ contributes:
       navbar:
         logo: "favicon-white.ico"
         logo-alt: "Graphic of a capital R with a 3 as a superscript."
-        search: true
         pinned: true
+      search:
+        location: navbar
+        type: textbox
       favicon: "favicon.ico"
       repo-branch: main
       repo-actions: [edit, issue, source]
@@ -57,3 +59,5 @@ contributes:
       opts_chunk:
         R.options:
           width: 72
+
+    brand: _brand.yml

_extensions/rostools/r3-theme/_extensions/quarto-ext/fontawesome/assets/css/all.css

@@ -6700,7 +6700,7 @@ readers do not read off random characters that represent icons */
 .fa-centos:before {
   content: "\f789"; }
 
-.fa-adn:before {
+.fa-and:before {
   content: "\f170"; }
 
 .fa-cloudsmith:before {
@@ -7291,7 +7291,7 @@ readers do not read off random characters that represent icons */
 .fa-spotify:before {
   content: "\f1bc"; }
 
-.fa-optin-monster:before {
+.fa-option-monster:before {
   content: "\f23c"; }
 
 .fa-fly:before {

_extensions/rostools/r3-theme/_extensions/quarto-ext/fontawesome/fontawesome.lua

@@ -44,7 +44,7 @@ return {
       group = icon
       icon = pandoc.utils.stringify(args[2])
     end
-    
+
     local title = pandoc.utils.stringify(kwargs["title"])
     if not isEmpty(title) then
       title = " title=\"" .. title  .. "\""
@@ -58,7 +58,7 @@ return {
     end
 
     local size = pandoc.utils.stringify(kwargs["size"])
-    
+
     -- detect html (excluding epub which won't handle fa)
     if quarto.doc.is_format("html:js") then
       ensureHtmlDeps()

_extensions/rostools/r3-theme/includes/code-appendix-r.qmd

@@ -1,5 +1,4 @@
-::: {.callout-tip appearance="minimal" icon="false" collapse="true"}
-## Code used in section
+## Code used in session
 
 This lists *some*, but not all, of the code used in the section. Some
 code is incorporated into Markdown content, so is harder to
@@ -13,4 +12,3 @@ the code from the exercises.
 #| eval: false
 #| ref-label: !expr stringr::str_subset(knitr::all_labels(), "^(unnamed-chunk-.*|purl-only-.*|setup|admin-.*|fig-.*)", negate = TRUE)
 ```
-:::

_extensions/rostools/r3-theme/includes/code-of-conduct.qmd

@@ -0,0 +1,94 @@
+
+Science thrives on diversity of thought and origin and we value the
+participation of every member of the scientific community and want all
+participants to have an enjoyable and fulfilling experience.
+Accordingly, all participants are expected to show respect and courtesy
+to other members throughout the workshop, in group work, and any
+activity associated with this workshop.
+
+To make clear what is expected, everyone taking part in this workshop,
+including teachers, helpers, organizers, and participants, is
+required to conform to the following Code of Conduct. Organizers will
+enforce this Code throughout events, but you may also contact us
+privately; all communication will be treated as confidential.
+
+We are dedicated to providing a welcoming and supportive environment for
+all people, regardless of background or identity. As such, we do not
+tolerate behaviour that is disrespectful to our teachers or learners or
+that excludes, intimidates, or causes discomfort to others. We do not
+tolerate discrimination or harassment based on characteristics that
+include, but are not limited to, gender identity and expression, sexual
+orientation, disability, physical appearance, body size, citizenship,
+nationality, ethnic or social origin, pregnancy, familial status,
+veteran status, genetic information, religion or belief (or lack
+thereof), membership of a national minority, property, age, education,
+socio-economic status, technical choices, and experience level.
+
+Everyone who participates in this workshop's activities is required to
+conform to this Code of Conduct. It applies to all spaces associated
+with this workshop including, but not limited to, group work, emails,
+and any online forums such as GitHub and Twitter. By participating,
+participants indicate their acceptance of the procedures by which the
+teachers and organizers resolves any Code of Conduct incidents.
+
+## Expected behavior
+
+All workshop participants are expected to show respect and courtesy to
+others. All interactions should be professional regardless of platform:
+either online or in-person. In order to foster a positive and
+professional learning environment we encourage the following kinds of
+behaviours in all interactions during this workshop:
+
+-   Be kind and aware of your words
+-   Use welcoming and inclusive language
+-   Be respectful of different viewpoints and experiences
+-   Gracefully accept constructive criticism
+-   Focus on what is best for the workshop members and the community
+    overall
+-   Show courtesy and respect towards other workshop members
+
+See the [four social
+rules](https://www.recurse.com/manual#sub-sec-social-rules) for further
+recommendations and details on proper behaviour.
+
+## Unacceptable behavior
+
+Examples of unacceptable behavior by participants include:
+
+-   Written or verbal comments which have the effect of excluding people
+    on the basis of membership of any specific group
+-   Causing someone to fear for their safety, such as through stalking,
+    following, or intimidation
+-   Violent threats or language directed against another person
+-   The display of sexual or violent images
+-   Unwelcome sexual attention
+-   Non-consensual or unwelcome physical contact
+-   Sustained disruption of talks, events or communications
+-   Insults or put downs
+-   Sexist, racist, homophobic, transphobic, ableist, or exclusionary
+    jokes
+-   Excessive swearing
+-   Incitement to violence, suicide, or self-harm
+-   Continuing to initiate interaction (including photography or
+    recording) with someone after being asked to stop
+-   Publication of private communication without consent
+
+## Consequences of unacceptable behavior
+
+Participants who are asked, either in person or online, to stop any
+inappropriate behavior are expected to comply immediately. If a
+participant engages in behaviour that violates this Code of Conduct, the
+organizers, teachers, or helpers may take any action they deem
+appropriate, including warning the offender or expulsion from the
+workshop.
+
+Thank you for helping make this a welcoming, friendly workshop for all
+:smile:
+
+::: {.callout-note appearance="default"}
+*Acknowledgements*: Large portions of this Code of Conduct were taken
+and modified from other Codes of Conduct, specifically [Software
+Carpentry](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html)
+and
+[UofTCoders](https://github.com/UofTCoders/studyGroup/blob/gh-pages/codeOfConduct.md).
+:::

_extensions/rostools/r3-theme/includes/installing-r-packages.qmd

@@ -1,5 +1,5 @@
 ```{=html}
-<!-- 
+<!--
 Need to set a project or document level "workshop_level" variable:
 
 So far, can only be: