Add lab

R/format-md-bitly-link.R

@@ -0,0 +1,3 @@
+format_md_bitly_link <- function(link) {
+  glue::glue('[{link |> stringr::str_remove("https://")}]({link})')
+}

_freeze/labs/02_create-website/execute-results/html.json

@@ -0,0 +1,17 @@
+{
+  "hash": "12bb190c4a569fe91e8542f60c600ef1",
+  "result": {
+    "engine": "knitr",
+    "markdown": "---\ntitle: \"{{< fa laptop-code >}} Lab: Create your own website!\"\nfilters:\n  - ../filters/new-page-links.lua\n---\n\n::: {.cell}\n\n:::\n\n\n## Basic structure of Quarto document\n\nWe are going to create a website using a Quarto.\nQuarto documents are a mix of natural language and executed code and this pattern is called **literate programming**.\nA Quarto document usually contains:\n\n-   Text formatted in Markdown.\n-   Code is fenced as code chunk between ```` ```{r} ```` and ```` ``` ````.\n-   Metadata as YAML with the format `key: value`. You can find metadata in the header of the document fenced by `---`, or in code chunks starting with `#|`.\n\n````{.markdown}\n---\ntitle: \"Untitled\"\nformat: html\n---\n\n## Quarto\n\nQuarto enables you to weave together content and executable code into\na finished document. To learn more about Quarto see <https://quarto.org>.\n\n```{{r}}\n#| label: calculation\n\n1 + 1\n```\n````\n\n## Steps\n\n-   Open your workspace: [bit.ly/td-workspace](https://bit.ly/td-workspace).\n-   Create `index.qmd`.\n-   Click the \"Render\" button on top.\n-   Download the output directory `_site`.\n-   Open Netlify Drop: [app.netlify.com/drop](https://app.netlify.com/drop).\n-   Drag and drop the downloaded `_site` onto Netlify Drop.\n-   Post the link to your website in the comments below or on our Padlet: [bit.ly/td-padlet](https://bit.ly/td-padlet)\n\n## Resources\n\n-   [Daring Fireball: Markdown](https://daringfireball.net/projects/markdown/)\n-   [Interactive Commonmark Markdown tutorial](https://commonmark.org/help/tutorial/)\n-   [Quarto documentation](https://quarto.org/)\n-   [Get started with Quarto Workshop](https://rstudio-conf-2022.github.io/get-started-quarto/) inncluding the [material](https://github.com/jthomasmock/quarto-workshop) and this video:\n\n\n{{< video https://www.youtube.com/embed/yvi5uXQMvu4?si=kpSWaw19CudBB_uu >}}\n",
+    "supporting": [
+      "02_create-website_files"
+    ],
+    "filters": [
+      "rmarkdown/pagebreak.lua"
+    ],
+    "includes": {},
+    "engineDependencies": {},
+    "preserve": {},
+    "postProcess": true
+  }
+}

data/schedule.csv

@@ -1,4 +1,4 @@
 module,date,id,topic,workspace,social
 Diversity metrics,,,,,
-Reproducibility,2023-11-30,01,Reproducible reporting of computational analyses,https://bit.ly/td-workspace,https://padlet.com/stephankoenig/teaching_demo
-Reproducibility,2023-12-05,02,Collaborating on code,,
+Reproducibility,2023-11-30,01,Reproducible reporting of computational analyses,,
+Reproducibility,2023-12-01,02,Lab: Create your own website!,https://bit.ly/td-workspace,https://bit.ly/td-padlet

index.qmd

@@ -25,7 +25,8 @@ resources_paths <-
   c(
     path("pre-readings"),
     path("slides"),
-    path("worksheets")
+    path("worksheets"),
+    path("labs")
   )
 
 resources <- 
@@ -45,31 +46,27 @@ schedule <-
   left_join(resources, by = join_by(id), na_matches = "never")
 ```
 
-:::: {.columns}
-
+::: columns
 ::: {.column width="75%"}
 Welcome to the webpage for the seminar **"First steps into reproducible bioinformatics"**!
 
-For context, this talk assumes that students in MICB 2XX: Data science have gained experience in R and RStudio, completed a "Diversity metrics" module, and now start one on "Reproducibility."
-This page contains the pre-readings, slides and other resources for this talk if you want to work along.
+For context, this talk assumes that students in MICB 2XX: Data science have gained experience in R and RStudio, completed a "Diversity metrics" module, and now start one on "Reproducibility." This page contains the slides and worksheets for this talk if you want to work along.
 :::
 
 ::: {.column width="5%"}
 :::
 
 ::: {.column width="20%"}
-
 {{< qrcode https://bit.ly/td-website >}}
-
 :::
-::::
+:::
 
 ```{r}
 #| label: schedule
 #| echo: false
 
 schedule |>
-  relocate(pre_readings, slides, worksheets, workspace, .after = topic) |>
+  relocate(pre_readings, slides, worksheets, workspace, labs, .after = topic) |>
   gt() |> 
   fmt_date(
     date, 
@@ -95,11 +92,11 @@ schedule |>
     missing_text = fa("window-maximize", fill_opacity = 0.1)
   ) |>
   fmt_url(
-    columns = workspace,
+    columns = labs,
     label = fa("laptop-code")
   ) |>
   sub_missing(
-    columns = workspace,
+    columns = labs,
     missing_text = fa("laptop-code", fill_opacity = 0.1)
   ) |>
   fmt_url(
@@ -119,7 +116,7 @@ schedule |>
     missing_text = fa("padlet", fill_opacity = 0.1)
   ) |>
   cols_hide(
-    id
+    columns = c(id, workspace)
   ) |>
   cols_label(
     module = "Module",
@@ -128,7 +125,7 @@ schedule |>
     topic = "Topic",
     pre_readings = "Pre",
     slides = "Slides",
-    workspace = "Workspace",
+    labs = "Lab",
     worksheets = "Worksheet",
     social = "Social"
   ) |> 

labs/02_create-website.qmd

@@ -0,0 +1,77 @@
+---
+title: "{{< fa laptop-code >}} Lab: Create your own website!"
+filters:
+  - ../filters/new-page-links.lua
+---
+
+```{r}
+#| label: setup
+#| echo: false
+#| message: false
+
+library(conflicted)
+library(dplyr)
+conflicts_prefer(dplyr::filter)
+library(here)
+library(readr)
+
+source(here("R", "format-md-bitly-link.R"))
+       
+links <- read_csv(here("data", "schedule.csv"), show_col_types = FALSE) |> 
+  filter(id == "02")
+
+workspace <- links |> 
+  pull(workspace) |> 
+  format_md_bitly_link()
+
+padlet <- links |> 
+  pull(social) |> 
+  format_md_bitly_link()
+```
+
+## Basic structure of Quarto document
+
+We are going to create a website using a Quarto.
+Quarto documents are a mix of natural language and executed code and this pattern is called **literate programming**.
+A Quarto document usually contains:
+
+-   Text formatted in Markdown.
+-   Code is fenced as code chunk between ```` ```{r} ```` and ```` ``` ````.
+-   Metadata as YAML with the format `key: value`. You can find metadata in the header of the document fenced by `---`, or in code chunks starting with `#|`.
+
+````{.markdown}
+---
+title: "Untitled"
+format: html
+---
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into
+a finished document. To learn more about Quarto see <https://quarto.org>.
+
+```{{r}}
+#| label: calculation
+
+1 + 1
+```
+````
+
+## Steps
+
+-   Open your workspace: `r workspace`.
+-   Create `index.qmd`.
+-   Click the "Render" button on top.
+-   Download the output directory `_site`.
+-   Open Netlify Drop: [app.netlify.com/drop](https://app.netlify.com/drop).
+-   Drag and drop the downloaded `_site` onto Netlify Drop.
+-   Post the link to your website in the comments below or on our Padlet: `r padlet`
+
+## Resources
+
+-   [Daring Fireball: Markdown](https://daringfireball.net/projects/markdown/)
+-   [Interactive Commonmark Markdown tutorial](https://commonmark.org/help/tutorial/)
+-   [Quarto documentation](https://quarto.org/)
+-   [Get started with Quarto Workshop](https://rstudio-conf-2022.github.io/get-started-quarto/) including the [material](https://github.com/jthomasmock/quarto-workshop) and this video:
+
+{{< video https://www.youtube.com/embed/yvi5uXQMvu4?si=kpSWaw19CudBB_uu >}}