Added fold-results lua filter, shortcodes section, updated site SEO i…

…mage for opengraph

_quarto.yml

@@ -3,7 +3,7 @@ project:
   output-dir: docs
 
 website:
-  image: "assets/images/featured.webp"
+  image: "assets/images/seo.webp"
   favicon: "assets/favicon.png"
   navbar:
     logo: "assets/logos/nbis-scilifelab.webp"
@@ -100,6 +100,8 @@ execute:
 
 filters:
   - assets/custom.lua
+  - assets/fold-results.lua
   - reveal-logo
   - fontawesome
 
+custom-metadata: "This is custom metdata"

assets/fold-results.lua

@@ -0,0 +1,20 @@
+-- Fold output from code chunks
+-- In code chunk, add #| attr.output: '.details summary="Output"'
+-- Only works for knitr chunks
+-- https://gist.github.com/atusy/f2b5b992e45c68ab6823499f2339c6e6
+
+function CodeBlock(elem)
+  if elem.classes and elem.classes:find("details") then
+    local summary = "Code"
+    if elem.attributes.summary then
+      summary = elem.attributes.summary
+    end
+    return{
+      pandoc.RawBlock(
+        "html", "<details><summary>" .. summary .. "</summary>"
+      ),
+      elem,
+      pandoc.RawBlock("html", "</details>")
+    }
+  end
+end

reports/demo-with-r/index.qmd

@@ -90,6 +90,34 @@ Sys.Date()
 ```
 ````
 
+Source code blocks can be folded.
+
+````         
+```{{r}}
+#| code-fold: true
+Sys.Date()
+```
+````
+
+```{r}
+#| code-fold: true
+Sys.Date()
+```
+
+There is not proper implementation to fold code output. Here is a hacky solution that uses a custom lua filter.
+
+````         
+```{{r}}
+#| attr.output: '.details summary="Output"'
+Sys.Date()
+```
+````
+
+```{r}
+#| attr.output: '.details summary="Output"'
+Sys.Date()
+```
+
 A code chunk can be given a code filename using the chunk attribute `filename`.
 
 ````
@@ -122,15 +150,15 @@ Sys.Date()
 sessionInfo()
 ```
 
-An advanced example showing bash code generated from R.
+An example showing bash code generated from R.
 
 ````
 ```{{r}}
 #| attr-output: "filename='bash'"
 #| class-output: bash
 #| echo: false
 d <- "custom"
-cat(paste("mkdir​", d))
+cat(paste("mkdir", d))
 ```
 ````
 
@@ -139,7 +167,7 @@ cat(paste("mkdir​", d))
 #| class-output: bash
 #| echo: false
 d <- "custom"
-cat(paste("mkdir​", d))
+cat(paste("mkdir", d))
 ```
 
 Code chunk attributes are documented [here](https://quarto.org/docs/output-formats/html-code.html).

reports/demo/index.qmd

@@ -561,6 +561,8 @@ This content is behind an accordion.
 
 ## Alerts
 
+This is not a quarto feature, but rather from bootstrap.
+
 ```         
 ::: {.alert .alert-primary}
 **Note:** This is an alert!
@@ -905,6 +907,45 @@ This is some material for topic 2.
 
 More layout settings are described [here](https://quarto.org/docs/authoring/article-layout.html) and [here](https://quarto.org/docs/output-formats/page-layout.html).
 
+## Shortcodes
+
+Shortcodes are sort of like quarto functions. 
+
+Two important shortcodes are `meta` and `var`. `meta` allows to read metadata from the yaml block in the current page or from `_quarto.yml`. Here are a few examples:
+
+`{{{< meta title >}}}` {{< meta title >}}
+
+`![]({{{< meta image >}}}){width="200px"}` 
+
+![]({{< meta image >}}){width="200px"}
+
+`{{{< meta custom-metadata >}}}` {{< meta custom-metadata >}}
+
+:::{.callout-note}
+Mostly only user-specified metadata in `_quarto.yml` can be accessed using `meta` shortcode.
+:::
+
+Similarly, `var` allows to read variables from `_variables.yml` if it has been defined. The `include` shortcode allows to add a child qmd document into a specific position in a qmd file. The `kbd` shortcode allows keyboard notations:
+
+`Press {{{< kbd Shift-Ctrl-P >}}}` Press {{< kbd Shift-Ctrl-P >}}
+
+The `video` shortcode allows to embed a video.
+
+`{{{< video https://www.youtube.com/watch?v=_f3latmOhew >}}}`
+
+{{< video https://www.youtube.com/watch?v=_f3latmOhew >}}
+
+Some of the custom shortcodes added with Specky template are:
+
+`{{{ < meta quarto_version > }}}` {{ < meta quarto_version > }}  
+
+`{{{ < meta current_date > }}}` {{ < meta current_date > }}
+
+`{{{ < meta current year > }}}` {{ < meta current year > }}
+
+`{{{ < meta current time > }}}` {{ < meta current time > }}
+
+Shortcodes are documented [here](https://quarto.org/docs/authoring/shortcodes.html).
 
 ## General tips