update github action to newer

Author: blenback

.github/workflows/quarto_render.yml

@@ -1,40 +1,66 @@
+# on:
+#   push:
+#     branches:
+#       - main
+# 
+# name: Render quarto project
+# 
+# permissions:
+#   contents: write
+#   pages: write
+# 
+# jobs:
+#   build-deploy:
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: Check out repository
+#         uses: actions/checkout@v4
+#         
+#       - name: Set up Quarto
+#         uses: quarto-dev/quarto-actions/setup@v2
+#         env:
+#           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#         with:
+#           tinytex: true 
+#           
+#       - name: Setup R
+#         uses: r-lib/actions/setup-r@v2
+# 
+#       - name: Render Quarto Project
+#         uses: quarto-dev/quarto-actions/render@v2
+#         with:
+#           to: html # If set, it will be equivalent to `quarto render --to html`
+#       - name: Publish
+#         uses: quarto-dev/quarto-actions/publish@v2
+#         with:
+#           target: gh-pages
+#           render: false
+#         env:
+#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
 on:
+  workflow_dispatch:
   push:
-    branches:
-      - main
-
-name: Render quarto project
+    branches: main
 
-permissions:
-  contents: write
-  pages: write
+name: Quarto Publish
 
 jobs:
   build-deploy:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-        
+
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tinytex: true 
-          
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v2
 
-      - name: Render Quarto Project
-        uses: quarto-dev/quarto-actions/render@v2
-        with:
-          to: html # If set, it will be equivalent to `quarto render --to html`
-      - name: Publish
+      - name: Render and Publish
         uses: quarto-dev/quarto-actions/publish@v2
         with:
           target: gh-pages
-          render: false
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

quarto-eth-phd-thesis.qmd

@@ -149,7 +149,7 @@ Also in the `.Rprofile` are some functions to streamline uniform styling of figu
 
 For tables the `thesis_tbl()` function sets options for `knitr::kbl()` and `kableExtra::kable_styling()` to produce booktabs style tables, with center aligned content and bold column titles:
 
-```{r}
+```{r, eval=FALSE}
 thesis_tbl <- function(x, escape, ltable = FALSE) {
   x %>%
     kbl(digits = 3,
@@ -171,7 +171,7 @@ thesis_tbl <- function(x, escape, ltable = FALSE) {
 
 An example of applying this function is included in `chapters/paper-01-qmd`:
 
-```{r}
+```{r, eval=FALSE}
 #| tbl-pos: H
 
 #load csv of allocation parameter summary statistics
@@ -188,7 +188,7 @@ Calibration_summary %>%
 
 For figures the function `theme_publication()` sets a custom `ggplot2` theme:
 
-```{r}
+```{r, eval=FALSE}
 #' theme_publication
 #' 
 #' custom ggplot2 theme to apply to all plots
@@ -235,7 +235,7 @@ theme_thesis <- function(
 
 In addition the `.Rprofile` contains a series of functions for producing custom continuous and discrete color palettes with the base set of colors specified within the function `thesis_color()`:
 
-```{r}
+```{r, eval=FALSE}
 thesis_color <- function(...) {
   
   thesis_colors <- c(
@@ -270,7 +270,7 @@ thesis_color <- function(...) {
 
 These color palettes can be applied using defined `ggplot2::scale_color_*` and `ggplot2::scale_fill_*` methods. An example of applying the `theme_thesis()` and `scale_color_thesis()` functions is provided in `chapters/paper-01/paper-01-figs.R:`
 
-```{r}
+```{r, eval=FALSE}
 p <- ggplot(mtcars, aes(x = wt, y = mpg, color = factor(cyl))) +
   geom_point(size = 3) +
   labs(
@@ -393,7 +393,7 @@ The code for this is included in `chapters/paper-01/paper-01.qmd` and it uses th
 
 My preferred method of preparing figures for Quarto documents is to produce and save them via dedicated R scripts rather than directly within the `.qmd` files themselves. This R script is then sourced directly at the head of the respective `.qmd` file to ensure the most up to date figures are used and the images are then included for each figure as in `paper-01.qmd`:
 
-```{r}
+```{r, eval=FALSE}
 #source the script that prepares all the figures
 source("chapters/paper-01/paper-01-figs.R")