update index.qmd

RP/index.qmd

@@ -1,18 +1,11 @@
 ---
-subtitle: "研究报告"
+subtitle: "Report"
-lang: "zh"
 format: dwhm-html
 ---
 
-```{r}
-#| include: false
-
-require(drwateR)
-require(rmdify)
-rmdify::rmd_init()
-```
 
 ```{r}
+#| echo: false
 #| output: asis
 data.frame(fd = dir(".", pattern = "\\d{4}[-_]")) |>
   dplyr::mutate(

SD/index.qmd

@@ -1,43 +1,40 @@
 ---
-subtitle: "演示材料"
+subtitle: "Slides"
 ---
 
 
 ```{r}
-#| echo: false
 #| output: asis
+#| echo: false
+
 data.frame(fd = dir(".", pattern = "\\d{4}[-_]")) |>
   dplyr::mutate(
     fn = purrr::map_chr(
       fd,
-      ~ file.path(
+      ~ file.path(.x, dir(.x, pattern = "index.qmd|index.html|index.ppt*"))[1]
-        .x,
-        dir(.x, pattern = "index.qmd|index.doc|index.pdf|index.ppt")
-      )
     )
   ) |>
   dplyr::transmute(
-    htmlstr = purrr::map_chr(
+    htmlstr = purrr::map2_chr(fn, fd, \(x, y) {
-      fn,
+      paste0(
-      ~ paste0(
         "## [",
-        .x,
+        y,
         "](",
-        .x,
+        x,
         ")\n\n",
         ifelse(
-          !grepl("qmd$", .x),
+          !grepl("qmd$", x),
           "",
           paste0(
             "<iframe title='",
-            gsub("^.*[_-]([^\\/]*)\\/.*$", "\\1", .x),
+            gsub("^.*[_-]([^\\/]*)\\/.*$", "\\1", x),
             "' width=800 height=600 src = '",
-            gsub("qmd$", "html", .x),
+            gsub("qmd$", "html", x),
             "'></iframe>\n\n"
           )
         )
       )
-    )
+    })
   ) |>
   dplyr::pull(htmlstr) |>
   paste(collapse = "") |>

_metadata_pub.yml

@@ -0,0 +1,161 @@
+project:
+  type: website
+  output-dir: www/
+  render:
+    - index.qmd
+    - version.qmd
+    - MS/HL.qmd
+    - MS/SM.qmd
+    - MS/MS.qmd
+    - MS/index.qmd
+    # - TC/index.qmd
+    - SD/
+    - MS/AC.qmd
+    # - RP/
+    # - AC/
+    - about.qmd
+
+lang: en
+date: last-modified
+# bibliography: [BB/Ref.bib, BB/localRef.bib]
+prefer-html: true
+crossref:
+  fig-title: Fig. # (default is "Figure")
+  tbl-title: Table # (default is "Table")
+  eq-title: Eq. # (default is "Equation")
+  title-delim: ":" # (default is ":")
+  fig-prefix: Fig. # (default is "Figure")
+  tbl-prefix: Table # (default is "Table")
+  eq-prefix: Eq.
+  ref-hyperlink: true # (default is true)
+  custom:
+    - kind: float
+      key: sfg
+      reference-prefix: "Supplementary Fig."
+      space-before-numbering: true
+      caption-prefix: "Supplementary Fig."
+      latex-env: sfg
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Supplementary Figure
+    - kind: float
+      key: stb
+      reference-prefix: "Supplementary Table"
+      space-before-numbering: true
+      caption-prefix: "Supplementary Table"
+      latex-env: stb
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Supplementary Table
+    - kind: float
+      key: seq
+      reference-prefix: "Supplementary Eq."
+      space-before-numbering: true
+      caption-prefix: "Supplementary Eq."
+      latex-env: seq
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Supplementary Equation
+    - kind: float
+      key: rfg
+      reference-prefix: "Fig. R"
+      space-before-numbering: false
+      caption-prefix: "Fig. R"
+      latex-env: rfg
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Revision Figure
+    - kind: float
+      key: rtb
+      reference-prefix: "Table R"
+      space-before-numbering: false
+      caption-prefix: "Table R"
+      latex-env: rtb
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Revision Table
+    - kind: float
+      key: req
+      reference-prefix: "Eq R"
+      space-before-numbering: false
+      caption-prefix: "Eq R"
+      latex-env: req
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Revision Equation
+    - kind: float
+      key: efg
+      reference-prefix: "Extended Data Fig."
+      space-before-numbering: true
+      caption-prefix: "Extended Data Fig."
+      latex-env: efg
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Extended Data Figure
+    - kind: float
+      key: etb
+      reference-prefix: "Extended Data Table"
+      space-before-numbering: true
+      caption-prefix: "Extended Data Table"
+      latex-env: etb
+      latex-list-of-file-extension: lost
+      latex-list-of-description: Extended Data Table
+website:
+  title: "{{< var reponame >}}: {{< var branch >}}"
+  reader-mode: true
+  site-url: https://drc.drwater.net/{{< var projtype >}}/{{< var reponame >}}/{{< var branch >}}
+  repo-url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}
+  repo-actions: [edit, source, issue]
+  page-navigation: true
+  page-footer: "Copyright 2025, [Dr. Water](https://drwater.net)"
+  navbar:
+    logo: "./_extensions/drwater/dwinst/drwater-white0.svg"
+    background: "#3D6E3B"
+    search: true
+    right:
+      - icon: house
+        text: "Home"
+        file: index.qmd
+      - text: "Main files"
+        menu:
+          - text: "Manuscript"
+            file: MS/MS.qmd
+          - text: "Supplementary Materials"
+            file: MS/SM.qmd
+          - text: "Highlights"
+            file: MS/HL.qmd
+      - text: "Slides"
+        file: SD/index.qmd
+      - text: "Links"
+        menu:
+          - text: "Version"
+            href: version.qmd
+          - text: "DRC"
+            href: "https://drc.drwater.net/"
+          - text: "Dr. Water"
+            href: "https://drwater.net/"
+      - text: "Others"
+        menu:
+          # - text: "Reports"
+          #   file: RP/index.qmd
+          # - text: "Author Credits"
+          #   file: MS/AC.qmd
+          - text: "Accomplishment"
+            file: AC/index.qmd
+          # - text: "Trackchanges"
+          # file: TC/index.qmd
+          # - text: "MS with raw bibkey"
+          #   file: MS/MS_nobib.docx
+      - text: "About"
+        file: about.qmd
+      - icon: git
+        menu:
+          - text: Codes
+            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/src/branch/{{< var branch >}}
+          - text: Issue
+            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues
+
+  comments:
+    hypothesis:
+      theme: clean
+      openSidebar: false
+
+execute:
+  freeze: true # re-render only when source changes
+  cache: true
+
+format:
+  dwhm-html: default

version.qmd

@@ -19,7 +19,9 @@ tibble::tibble(branch = system("git branch -a", intern = TRUE)) |>
     htmlstr = paste0(
       "## [**Version**: ",
       branch,
-      "](https://drc.drwater.net/{{< var projtype >}}/{{< var pubtype >}}/{{< var reponame >}}/",
+      "](https://drc.drwater.net/{{< var projtype >}}/",
+      ifelse(grepl("pub", branch, ignore.case = TRUE), "public", "protected"),
+      "/{{< var reponame >}}/",
       branch,
       "/)"
     )