update brand and metadata.yml

MS/AC.aux

@@ -1,17 +0,0 @@
-\relax 
-\providecommand\babel@aux[2]{}
-\@nameuse{bbl@beforestart}
-\providecommand\hyper@newdestlabel[2]{}
-\providecommand*\HyPL@Entry[1]{}
-\bibstyle{elsarticle-harv}
-\emailauthor{mingsu@rcees.ac.cn}{Ming Su}
-\emailauthor{yangmin@rcees.ac.cn}{Min Yang\corref {cor1}}
-\Newlabel{cor1}{1}
-\bibdata{../BB/Ref.bib,../BB/localRef.bib}
-\HyPL@Entry{0<</S/D>>}
-\babel@aux{english}{}
-\Newlabel{1}{a}
-\Newlabel{2}{b}
-\newlabel{credit-authorship-contribution-statement}{{b}{1}{CRediT authorship contribution statement}{section*.1}{}}
-\@writefile{toc}{\contentsline {section}{CRediT authorship contribution statement}{1}{section*.1}\protected@file@percent }
-\gdef \@abspage@last{1}

RP/index.qmd

@@ -14,9 +14,7 @@ rmdify::rmd_init()
 
 ```{r}
 #| output: asis
-data.frame(fd = dir(".", pattern = ".[-_]")) |>
+data.frame(fd = dir(".", pattern = "\\d{4}[-_]")) |>
-  dplyr::filter(!grepl("_files", fd)) |>
-  dplyr::filter(!grepl("quarto", fd)) |>
   dplyr::mutate(
     fn = purrr::map_chr(
       fd,

SD/index.qmd

@@ -2,16 +2,11 @@
 subtitle: "演示材料"
 ---
 
-```{r}
-#| include: false
-require(drwateR)
-require(rmdify)
-rmdify::rmd_init()
-```
 
 ```{r}
+#| echo: false
 #| output: asis
-data.frame(fd = dir(".", pattern = ".[-_]")) |>
+data.frame(fd = dir(".", pattern = "\\d{4}[-_]")) |>
   dplyr::mutate(
     fn = purrr::map_chr(
       fd,

TC/index.qmd

@@ -2,17 +2,10 @@
 subtitle: "Track Changes"
 ---
 
-
-```{r}
-#| include: false
-require(drwateR)
-rmdify::rmd_init()
-```
-
 ```{r}
+#| echo: false
 #| output: asis
 data.frame(fn = dir("./", pattern = ".*-.*.docx")) |>
-  # dplyr::mutate(oldfn = gsub("^MS([0-9]*)-([0-9]*)_([a-z0-9]*)-([a-z0-9]*).docx$", "MS\\1_\\3.docx", fn)) |>
   dplyr::mutate(
     newfn = gsub(
       "^MS([0-9]*)-([0-9]*)_([a-z0-9]*)-([a-z0-9]*).docx$",
@@ -20,7 +13,6 @@ data.frame(fn = dir("./", pattern = ".*-.*.docx")) |>
       fn
     )
   ) |>
-  # dplyr::mutate(time1 = lubridate::ymd_hm(gsub("MS([0-9]*)_([a-z0-9]*).docx$", "\\1", oldfn))) |>
   dplyr::mutate(
     time2 = lubridate::ymd_hm(gsub(
       "MS([0-9]*)_([a-z0-9]*).docx$",
@@ -28,9 +20,6 @@ data.frame(fn = dir("./", pattern = ".*-.*.docx")) |>
       newfn
     ))
   ) |>
-  # dplyr::arrange(dplyr::desc(time2), newfn, dplyr::desc(time1)) |>
-  # dplyr::mutate(htmlstr = paste0("- [**", oldfn, "**](MS/", oldfn, ") ← [**",
-  #   newfn, "**](MS/", newfn, ") ⇨ [**", fn, "**](", fn, ")\n\n")) |>
   dplyr::mutate(
     htmlstr = paste0("[- ", time2, ": **", fn, "**](", fn, ")\n\n")
   ) |>

_brand.yml

@@ -0,0 +1,77 @@
+meta:
+  name: Dr. Water
+  link:
+    home: https://drc.drwater.net
+    drwater: https://drwater.net
+    git: https://git.drwater.net
+  description: |
+    Dr. Water focusing on the water quality problems in drinking water systems. Dr. Water is maintained by Ming Su from RCEES, CAS"
+  founded: 2015
+
+color:
+  palette:
+    # Core palette
+    深青蓝色: "#296364"
+    海军蓝或藏青色: "#0c4c8a"
+    深青色: "#006D6D"
+    钻蓝色: "#0F52BA"
+    酒红: "#800020"
+    暖墨色: "#3C3C3C"
+    paper: "#F8F5F2"
+    aubergine: "#4A154B"
+    horchata: "#F4EDE4"
+    black: "#1D1C1D"
+    white: "#FFFFFF"
+    blue: "#36C5F0"
+    green: "#2EB67D"
+    yellow: "#ECB22E"
+    red: "#E01E5A"
+
+    # Secondary palette
+    cobalt: "#1E328F"
+    sky: "#0E9DD3"
+    teal: "#2392A2"
+    pool: "#78D7DD"
+    evergreen: "#185F34"
+    moss: "#729C1A"
+    sandbar: "#FFD57E"
+    peach: "#FED4BE"
+    salmon: "#F2606A"
+    bubblegum: "#FFB6BD"
+    crimson: "#921D21"
+    terracotta: "#DE8969"
+    berry: "#7C2852"
+    mauve: "#C05B8C"
+
+    # Bootstrap color aliases
+    purple: aubergine
+    pink: bubblegum
+    indigo: "#4F2B8C"
+    cyan: sky
+    orange: terracotta
+
+  # Theme colors
+  primary: aubergine
+  background: paper
+  foreground: 暖墨色
+  success: green
+  info: blue
+  warning: yellow
+  danger: red
+# typography:
+#   fonts:
+#     # 主字体 - 经典的学术衬线字体
+#     - family: SFMono-Regular
+#     # 无衬线对比 - 用于标题和图表
+#     - family: Menlo
+#     - family: Monaco
+#     - family: Consolas
+#     - family: Liberation Mono
+#     - family: Courier New
+#     - family: monospace
+#
+#   base: SFMono-Regular
+#   headings:
+#     family: Consolas
+#     weight: 300
+#   monospace: monospace

_metadata.yml

@@ -0,0 +1,151 @@
+project:
+  type: website
+  output-dir: www/
+  render:
+    - index.qmd
+    - MS/SM.qmd
+    - MS/MS.qmd
+    - MS/CL.qmd
+    - MS/HL.qmd
+    - MS/RP.qmd
+    - MS/index.qmd
+    - TC/index.qmd
+    - SD/
+    - MS/RN.qmd
+    - 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
+
+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 >}}/src/branch/{{< var branch >}}
+  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: "Revision Notes"
+          #   file: MS/RN.qmd
+          - text: "Cover Letter"
+            file: MS/CL.qmd
+          - text: "Highlights"
+            file: MS/HL.qmd
+      - text: "Slides"
+        file: SD/index.qmd
+      - text: "Links"
+        menu:
+          - text: "Version"
+            href: https://drc.drwater.net/{{< var projtype >}}/{{< var pubtype >}}/{{< var reponame >}}/
+          - 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: Edit
+            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/_edit/
+          - text: Issue
+            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues
+  comments:
+    hypothesis:
+      theme: clean
+      openSidebar: false
+
+execute:
+  freeze: false # re-render only when source changes
+  cache: true
+
+format:
+  dwhm-html: default

_quarto.yml

@@ -1,9 +1,6 @@
 title: "MANUSCRIPT TITLE"
 submitjournal: "JOURNAL"
 submitid:
-lang: en
-date: last-modified
-# bibliography: [BB/Ref.bib, BB/localRef.bib]
 affilstyle: alphabeta # number
 author:
   - name: Xxxxx Yyyy
@@ -61,145 +58,6 @@ affiliations:
     country: China
     postal-code: 100049
     url: https://www.ucas.ac.cn
-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
-prefer-html: true
 
-# execute:
+metadata-files:
-#   freeze: auto # re-render only when source changes
+  - _metadata.yml
-#   cache: true
-
-project:
-  type: website
-  output-dir: www/
-  render:
-    - index.qmd
-    - MS/SM.qmd
-    - MS/MS.qmd
-    - MS/CL.qmd
-    - MS/HL.qmd
-    - MS/RP.qmd
-    - TC/index.qmd
-    - SD/
-    - MS/RN.qmd
-    # - MS/AC.qmd
-    - RP/
-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 >}}/src/branch/{{< var branch >}}
-  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: "Revision Notes"
-          #   file: MS/RN.qmd
-          - text: "Cover Letter"
-            file: MS/CL.qmd
-          - text: "Highlights"
-            file: MS/HL.qmd
-      - text: "Slides"
-        file: SD/index.qmd
-      - text: "Links"
-        menu:
-          - text: "Version"
-            href: https://drc.drwater.net/{{< var projtype >}}/{{< var pubtype >}}/{{< var reponame >}}/
-          - 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
-      - icon: git
-        menu:
-          - text: Edit
-            url: https://git.drwater.net/{{< var projtype >}}/{{< var reponame >}}/_edit/
-          - text: Issue
-            url: https://git.drwater.net/manuscript/{{< var reponame >}}/issues
-  comments:
-    hypothesis:
-      theme: clean
-      openSidebar: false
-
-format:
-  dwhm-html: default