refactor report deployment

R/deploy_reports.R

@@ -9,22 +9,10 @@
 #' 
 
 deploy_report <- function(report_links) {
-  report_links <- stringr::str_detect(report_links, "Rmd|qmd", negate = TRUE) |>
-    (\(x) report_links[x])()
-
-  directory_name <- dirname(report_links) |> basename() |> unique()
-
-  file_name <- basename(report_links)
-
-  to <- file.path("docs", directory_name)
-
-  dir.create(path = to, showWarnings = FALSE)
+  to <- dirname(report_links) |> basename() |> unique()
 
   file.copy(from = report_links, to = to, recursive = TRUE)
 
 
-  file.path(
-    "https://oxford-ihtm.io/fair-equitable-research", 
-    directory_name, file_name
-  )
+  file.path("https://oxford-ihtm.io/fair-equitable-research", file_name)
 }

R/render_quarto.R

@@ -0,0 +1,18 @@
+#'
+#' Render quarto reports
+#' 
+#' @param input The input file or project directory to be rendered.
+#' 
+#' @returns File path to rendered report
+#' 
+
+render_quarto_report <- function(input) {
+  quarto::quarto_render(input = input)
+
+  file_names <- paste(
+    tools::file_path_sans_ext(basename(input)), 
+    c("html", "pdf"), sep = "."
+  )
+
+  file.path(dirname(input), "docs", file_names)
+} 

_targets.R

@@ -68,9 +68,16 @@ output_targets <- tar_plan(
 
 ### Reporting targets
 report_targets <- tar_plan(
-  tar_quarto(
+  # tar_quarto(
+  #   name = ferc_scoping_review_report,
+  #   path = "reports/scoping-review/ferc_scoping_review.qmd"
+  # )
+  tar_target(
     name = ferc_scoping_review_report,
-    path = "reports/scoping-review/ferc_scoping_review.qmd"
+    command = render_quarto_report(
+      input = "reports/scoping-review/ferc_scoping_review.qmd"
+    ),
+    format = "file"
   )
 )
 

reports/scoping-review/.gitignore

@@ -0,0 +1 @@
+/.quarto/

reports/scoping-review/_quarto.yml

@@ -0,0 +1,26 @@
+project:
+  output-dir: docs
+
+bibliography: ../references.bib
+
+format: 
+  html:
+    toc: true
+    toc-location: left
+    embed-resources: true
+    grid:
+      body-width: 900px
+      margin-width: 300px
+    code-tools:
+      source: https://github.com/OxfordIHTM/fair-equitable-research/blob/main/reports/ferc_scoping_review.qmd
+  pdf:
+    documentclass: scrartcl
+    papersize: a4
+    toc: true
+    toc-title: Contents
+    lof: true
+    lot: true
+    number-sections: true
+    number-depth: 3
+    highlight-style: breeze
+

docs/scoping-review/ferc_scoping_review.html → reports/scoping-review/docs/ferc_scoping_review.html

@@ -3102,7 +3102,7 @@ <h2 id="toc-title">Table of contents</h2>
   </ul></li>
   <li><a href="#bibliography" id="toc-bibliography" class="nav-link" data-scroll-target="#bibliography">Bibliography</a></li>
   </ul>
-<div class="quarto-alternate-formats"><h2>Other Formats</h2><ul><li><a href="../../ferc_scoping_review.pdf"><i class="bi bi-file-pdf"></i>PDF</a></li></ul></div></nav>
+<div class="quarto-alternate-formats"><h2>Other Formats</h2><ul><li><a href="ferc_scoping_review.pdf"><i class="bi bi-file-pdf"></i>PDF</a></li></ul></div></nav>
 </div>
 <div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">
 </div>

reports/scoping-review/ferc_scoping_review.qmd

@@ -9,35 +9,6 @@ subtitle: A Scoping Review
 #       - name: Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford
 #         city: Oxford
 date: "`r format(Sys.Date(), '%d %B %Y')`"
-bibliography: ../references.bib
-format: 
-  html:
-    toc: true
-    toc-location: left
-    embed-resources: true
-    grid:
-      body-width: 900px
-      margin-width: 300px
-    code-tools:
-      source: https://github.com/OxfordIHTM/fair-equitable-research/blob/main/reports/ferc_scoping_review.qmd
-  # docx:
-  #   toc: true
-  #   toc-depth: 3
-  #   toc-title: Table of Contents
-  #   number-sections: true
-  #   number-depth: 3
-  #   reference-doc: ../reference_doc.docx
-  #   highlight-style: breeze
-  pdf:
-    documentclass: scrartcl
-    papersize: a4
-    toc: true
-    toc-title: Contents
-    lof: true
-    lot: true
-    number-sections: true
-    number-depth: 3
-    highlight-style: breeze
 ---
 
 ```{r setup}