update

dwms/.gitignore

@@ -10,3 +10,7 @@ _variables.yml
 _freeze/
 www/
 .source_state
+*_files/
+/*.pdf
+/*.html
+

dwms/MS.qmd

@@ -1,146 +1,22 @@
 ---
 msname: MS
 smname: SM
-title: "MANUSCRIPT TITLE"
-subtitle: "Supplementary Information"
-submitjournal: "JOURNAL"
-submitid: 
-lang: en
+isMS: true
 date: ""
-# bibliography: [BB/Ref.bib, BB/localRef.bib]
-affilstyle: alphabeta # number
-author:
-  - name: Xxxxx Yyyy
-    affiliations:
-      - ref: kleac
-    # email: 13586740928@163.com
-    attributes:
-      corresponding: false
-      equal-contributor: true
-    role:
-      - data-curation: lead
-      - methodology: lead
-      - formalanalysis: lead
-      - writingoriginal: equal
-      - writingediting: eqaul
-      - visualisation: supporting
-  - name: Ming Su
-    email: mingsu@rcees.ac.cn
-    orcid: 0000-0001-9821-1268
-    url: https://drwater.net/team/ming-su/
-    role:
-      - conceptualization: lead
-      - methodology: supporting
-      - formalanalysis: lead
-      - writingoriginal: equal
-      - writingediting: equal
-      - visualisation: lead
-      - projectadmin: lead
-      - supervision
-    affiliations:
-      - ref: kleac
-      - ref: ucas
-    attributes:
-      corresponding: true
-      equal-contributor: true
-  - name: Min Yang
-    email: yangmin@rcees.ac.cn
-    affiliations:
-      - ref: kleac
-      - ref: ucas
-    attributes:
-      corresponding: true
-affiliations:
-  - id: kleac
-    name: State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
-    # address: No. 18 Shuangqing Road
-    city: Beijing
-    postal-code: 100085
-    country: China
-    url: https://www.skleac.ac.cn
-  - id: ucas
-    name: University of Chinese Academy of Sciences
-    # address: No. 19A Yuquan Road
-    city: Beijing
-    postal-code: 100049
-    country: China
-    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
+# bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+# csl: _extensions/drwater/dwms/inst/nature.csl
+endfloat: true
+doublespacing: true
+linenumbers: true
 format:
-  # elsevier-html:
-  #   toc: true
-  #   css: _extensions/drwater/dwms/inst/css/style.css
-  # docx:
-  #   reference-doc: _extensions/drwater/dwms/inst/word/MS.docx
-  dwms-pdf:
-    fontsize: 12pt
-    keep-md: false
-    keep-tex: true
-    header-includes:
-      - \usepackage{endfloat}
-      - \doublespacing
-      - \linenumbers
+  dwms-html: default
+  dwms-docx: default
+  dwms-pdf: default
 # filters:
 #   - latex-environment
 #   - authoraffil
+# lightbox: auto
+# commands: [clab]
 ---
 
 
@@ -162,8 +38,7 @@ dwfun::init()
 
 # Abstract {-}
 
-
-{{< pagebreak >}}
+This is a demo of abstract.
 
 
 {{< pagebreak >}}

dwms/RN.qmd

@@ -0,0 +1,61 @@
+---
+subtitle: "Revision Note"
+msname: MS
+smname: SM
+isRN: true
+date: ""
+# bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+# csl: _extensions/drwater/dwinst/nature.csl
+format:
+  dwms-html: default
+  dwms-docx: default
+  dwms-pdf:
+    number-sections: true
+# filters:
+#   - latex-environment
+#   - authoraffil
+# lightbox: auto
+# commands: [clab]
+---
+
+```{r}
+#| include: false
+#| cache: false
+lang <- "en"
+RM <- "F" # global rendermode, L: load pdata; F: fast load pdf
+isrendering <- isTRUE(getOption('knitr.in.progress'))
+require(tidyverse)
+require(patchwork)
+require(drwateR)
+rmdify::rmd_init()
+```
+
+# Response to Editor
+
+> 0. I very much regret to have to tell you that publication in our journal is not recommended. An explanation for this decision is given in the attached review reports (and on https://www.editorialmanager.com/wr/). I hope that the comments contained therein will be of use to you.
+
+**Response/Action:**
+
+Thank you. 
+
+::: {#rfg-figr1}
+
+```{r}
+plot(1)
+```
+
+A figure in RN
+:::
+
+
+
+# Reviewer #1:
+
+> 0. COMMENT 1
+
+**Response/Action:**
+
+Thank you very much for your revision. We made changes as shown below.
+
+`r cref("r1q0101")`
+

dwms/SM.qmd

@@ -1,143 +1,22 @@
 ---
 msname: MS
 smname: SM
-title: "MANUSCRIPT TITLE"
+isSM: true
+# bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
+# csl: _extensions/drwater/dwinst/nature.csl
 subtitle: "Supplementary Information"
-submitjournal: "JOURNAL"
-submitid: 
-lang: en
 date: ""
-# bibliography: [BB/Ref.bib, BB/localRef.bib]
-affilstyle: alphabeta # number
-author:
-  - name: Xxxxx Yyyy
-    affiliations:
-      - ref: kleac
-    # email: 13586740928@163.com
-    attributes:
-      corresponding: false
-      equal-contributor: true
-    role:
-      - data-curation: lead
-      - methodology: lead
-      - formalanalysis: lead
-      - writingoriginal: equal
-      - writingediting: eqaul
-      - visualisation: supporting
-  - name: Ming Su
-    email: mingsu@rcees.ac.cn
-    orcid: 0000-0001-9821-1268
-    url: https://drwater.net/team/ming-su/
-    role:
-      - conceptualization: lead
-      - methodology: supporting
-      - formalanalysis: lead
-      - writingoriginal: equal
-      - writingediting: equal
-      - visualisation: lead
-      - projectadmin: lead
-      - supervision
-    affiliations:
-      - ref: kleac
-      - ref: ucas
-    attributes:
-      corresponding: true
-      equal-contributor: true
-  - name: Min Yang
-    email: yangmin@rcees.ac.cn
-    affiliations:
-      - ref: kleac
-      - ref: ucas
-    attributes:
-      corresponding: true
-affiliations:
-  - id: kleac
-    name: State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
-    # address: No. 18 Shuangqing Road
-    city: Beijing
-    postal-code: 100085
-    country: China
-    url: https://www.skleac.ac.cn
-  - id: ucas
-    name: University of Chinese Academy of Sciences
-    # address: No. 19A Yuquan Road
-    city: Beijing
-    postal-code: 100049
-    country: China
-    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
+latex-clean: false # to keep aux
 format:
-  dwms-pdf:
-    latex-clean: false # to keep aux
-    keep-md: false
-    keep-tex: true
-    header-includes:
-      - \doublespacing
-      - \linenumbers
-      - \let\oldsection\section
-      - \renewcommand{\section}{\clearpage\oldsection}
-      - \let\oldsubsection\subsection
-      - \renewcommand{\subsection}{\clearpage\oldsubsection}
+  dwms-html: default
+  dwms-docx: default
+  dwms-pdf: 
+    toc: false # 手动设置了
 # filters:
+#   - latex-environment
 #   - authoraffil
+# lightbox: auto
+# commands: [clab]
 ---
 
 \thispagestyle{empty}
@@ -155,11 +34,9 @@ require(drwateR)
 rmdify::rmd_init()
 ```
 
+
 Figures and/or tables are provided below as the supplementary evidences to the main text.
 
-{{< pagebreak >}}
-
-
 
 ```{=latex}
 \clearpage
@@ -171,27 +48,18 @@ Figures and/or tables are provided below as the supplementary evidences to the m
 ```
 
 
-{{< pagebreak >}}
-
+# [@sfg-demo]
 
 ::: {#sfg-demo}
 
 ```{r}
 #| out-width: "40%"
-
-if (!isRendering) {
-  data.frame(x = 1:10, y = 1:10) |>
-    ggplot(aes(x, y)) +
-    geom_point() +
-    theme_sci(3, 2.0)
-
-  ggsavep("../figures/demo.pdf", loadit = FALSE)
-}
-
-ggsavep("../figures/demo", loadit = TRUE)
+data.frame(x = 1:10, y = 1:10) |>
+  ggplot(aes(x, y)) +
+  geom_point() +
+  dwfun::theme_sci(3, 2.0)
 ```
 
 Caption of demo figure
-
 :::
 

dwms/_extensions/drwater/dwms/header.tex

@@ -12,8 +12,6 @@
 \usepackage[normalem]{ulem}
 \usepackage{setspace}
 \usepackage{lineno}
-\usepackage{caption}
-\captionsetup{singlelinecheck=off}
 \usepackage[UTF8, scheme=plain]{ctex}
 \usepackage{orcidlink}
 
@@ -100,9 +98,9 @@
 
 %\titlespacing{<command>}{<left>}{<before-sep>}{<after-sep>}
 % Starred version removes indentation in following paragraph
-\titlespacing*{\section}{0em}{2em}{0.1em}
-\titlespacing*{\subsection}{0em}{1.25em}{0.1em}
-\titlespacing*{\subsubsection}{0em}{0.75em}{0em}
+% \titlespacing*{\section}{0em}{2em}{0.1em}
+% \titlespacing*{\subsection}{0em}{1.25em}{0.1em}
+% \titlespacing*{\subsubsection}{0em}{0.75em}{0em}
 
 % ------------------
 % Headers/Footers
@@ -125,7 +123,7 @@
 % Captions
 % ------------------
 \usepackage[labelfont=bf,labelsep=period]{caption}
-\captionsetup[figure]{font=footnotesize,justification=raggedright,singlelinecheck=false,format=hang}
+\captionsetup[figure]{font=footnotesize,justification=centering,singlelinecheck=false,format=hang}
 
 
 % ---------------------------

dwms/_extensions/drwater/dwms/partials/title.tex

@@ -13,3 +13,34 @@ $endif$
 $-- This supports Quarto's authors normalization
 \author{$for(authors)$\footnotesize $it.name.literal$$sep$ \and $endfor$}
 \date{$date$}
+$if(isSM)$
+\let\oldsection\section
+\renewcommand{\section}{\clearpage\oldsection}
+\let\oldsubsection\subsection
+\renewcommand{\subsection}{\clearpage\oldsubsection}
+\renewcommand{\thetable}{S\arabic{table}}
+\renewcommand{\thefigure}{S\arabic{figure}}
+\renewcommand{\theequation}{S\arabic{equation}}
+\renewcommand{\figurename}{Figure}
+\renewcommand{\tablename}{Table}
+\usepackage{titlesec}
+\newcommand{\sectionbreak}{\clearpage}
+$endif$
+$if(isRN)$
+\renewcommand{\thetable}{R\arabic{table}}
+\renewcommand{\thefigure}{R\arabic{figure}}
+\renewcommand{\theequation}{R\arabic{equation}}
+\renewcommand{\figurename}{Figure}
+\renewcommand{\tablename}{Table}
+\usepackage{titlesec}
+\newcommand{\sectionbreak}{\clearpage}
+$endif$
+$if(endfloat)$
+\usepackage{endfloat}
+$endif$
+$if(linenumber)$
+\linenumbers
+$endif$
+$if(doublespacing)$
+\doublespacing
+$endif$

dwms/_quarto.yml

@@ -0,0 +1,121 @@
+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
+    affiliations:
+      - ref: kleac
+    # email: 13586740928@163.com
+    attributes:
+      corresponding: false
+      equal-contributor: true
+    role:
+      - data-curation: lead
+      - methodology: lead
+      - formalanalysis: lead
+      - writingoriginal: equal
+      - writingediting: eqaul
+      - visualisation: supporting
+  - name: Ming Su
+    email: mingsu@rcees.ac.cn
+    orcid: 0000-0001-9821-1268
+    url: https://drwater.net/team/ming-su/
+    role:
+      - conceptualization: lead
+      - methodology: supporting
+      - formalanalysis: lead
+      - writingoriginal: equal
+      - writingediting: equal
+      - visualisation: lead
+      - projectadmin: lead
+      - supervision
+    affiliations:
+      - ref: kleac
+      - ref: ucas
+    attributes:
+      corresponding: true
+      equal-contributor: true
+  - name: Min Yang
+    email: yangmin@rcees.ac.cn
+    affiliations:
+      - ref: kleac
+      - ref: ucas
+    attributes:
+      corresponding: true
+affiliations:
+  - id: kleac
+    name: Key Laboratory of Environmental Aguatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
+    # address: No. 18 Shuangqing Road
+    city: Beijing
+    postal-code: 100085
+    country: China
+    url: https://www.skleac.ac.cn
+  - id: ucas
+    name: University of Chinese Academy of Sciences
+    # address: No. 19A Yuquan Road
+    city: Beijing
+    postal-code: 100049
+    country: China
+    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