docs(manuscript): update bioarxiv v2

.github/workflows/cid.yaml

@@ -7,6 +7,7 @@ on:
       - beta
     paths-ignore:
       - ".github/workflows/colab.yml"
+      - ".github/workflows/manuscript.yaml"
       - "conda/**"
       - "dev/**"
       - "docs/**"
@@ -22,6 +23,7 @@ on:
     types: [opened, synchronize, labeled, reopened]
     paths-ignore:
       - ".github/workflows/colab.yml"
+      - ".github/workflows/manuscript.yaml"
       - "conda/**"
       - "dev/**"
       - "docs/**"

.github/workflows/manuscript.yaml

@@ -7,6 +7,11 @@ on:
         required: true
         type: boolean
         default: false
+      diff_enabled:
+        description: "Compute document changes with latexdiff"
+        required: true
+        type: boolean
+        default: true
   push:
     paths:
       - ".github/workflows/manuscript.yaml"
@@ -19,9 +24,14 @@ defaults:
 jobs:
   render:
     runs-on: ubuntu-latest
+    concurrency:
+      group: render-${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.event.pull_request.number || github.ref_name }}
+      cancel-in-progress: true
     steps:
       - name: Check out repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        with:
+          fetch-depth: 0
       - name: Setup dvc
         uses: iterative/setup-dvc@68c55926a8ce27c2d4fcf7db61149ee64cf4eeb9 # v1
         with:
@@ -36,8 +46,19 @@ jobs:
       - name: Render
         run: |
           make -C reproducibility/manuscript render
+      - name: Compute diff
+        # if: ${{ inputs.diff_enabled == 'true' }}
+        continue-on-error: true
+        run: |
+          export PATH="/home/runner/.TinyTeX/bin/x86_64-linux:$PATH"
+          tlmgr install git-latexdiff latexdiff latexpand
+          make -C reproducibility/manuscript latexdiff
       - name: Upload artifacts
-        uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4
+        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4
         with:
-          name: quarto-output-${{ github.ref_name }}-${{ github.sha }}
-          path: "${{ github.workspace }}/reproducibility/manuscript/manuscript.*"
+          name: manuscript-${{ github.ref_name }}-${{ github.sha }}
+          path: |
+            reproducibility/manuscript/manuscript.*
+            reproducibility/manuscript/v2*.*
+            reproducibility/manuscript/*.bib
+            reproducibility/manuscript/*.dvc

reproducibility/manuscript/Makefile

@@ -95,10 +95,13 @@ clean-all: clean
 #-------
 
 TEX_FILE = v2
-COMPARISON_SHA1 = a12bbe5
+COMPARISON_SHA1 = 64d181f
 
-cache-tex: ## Cache the tex file
+copy-tex: ## Copy temporary tex file artifact to git-tracked file
 	cp $(DOCUMENT_NAME).tex $(TEX_FILE).tex
+
+cache-tex: ## Cache the tex file
+cache-tex: copy-tex
 	git add $(TEX_FILE).tex
 	git commit -m "chore(manuscript): update $(TEX_FILE) diff file"
 
@@ -109,6 +112,9 @@ latexdiff:
 	git-latexdiff \
 	--ignore-latex-errors \
 	--latexmk \
+	--xelatex \
+	--bibtex \
+	--no-view \
 	--ignore-makefile \
 	--ln-untracked \
 	--output $(TEX_FILE)-$(COMPARISON_SHA1)-diff.pdf \

reproducibility/manuscript/_extensions/sciexp/nature/header.tex

@@ -6,7 +6,7 @@
 \usepackage{amsthm}%
 \usepackage{mathrsfs}%
 \usepackage[title]{appendix}%
-\usepackage{xcolor}%
+\usepackage[dvipsnames]{xcolor}%
 \usepackage{textcomp}%
 \usepackage{manyfoot}%
 \usepackage{booktabs}%

reproducibility/manuscript/_extensions/sciexp/nature/partials/before-body.tex

@@ -1,4 +1,6 @@
 $if(title)$
 \maketitle
+% \clearpage
+% \layout
 \newpage{}
 $endif$

reproducibility/manuscript/_extensions/sciexp/nature/sn-jnl.cls

@@ -560,12 +560,12 @@
 \if@corauemail%
    \g@addto@macro\corrauthemail{%
    \setcounter{footnote}{0}%
-   \textcolor{blue}{#1};\ %
+   \textcolor{NavyBlue}{#1};\ %
    }%
 \else%
    \g@addto@macro\authemail{%
    \setcounter{footnote}{0}%
-   \textcolor{blue}{#1};\ %
+   \textcolor{NavyBlue}{#1};\ %
    }%
 \fi}
 
@@ -749,13 +749,14 @@
 %% Article Header Definition
 \renewcommand{\@maketitle}{\newpage\null%
     % \if@remarkboxon\vbox to 0pt{\vspace*{-78pt}\hspace*{-18pt}\FMremark}\else\vskip21pt\fi%%\par%
-    \if@remarkboxon\vbox to 0pt{\vspace*{-78pt}\hspace*{-18pt}\FMremark}\else\vskip21pt\fi%%\par%
+    \if@remarkboxon\vbox to 0pt{\vspace*{-78pt}\hspace*{-18pt}\FMremark}\else\vskip0pt\fi%%\par%
     \hsize\textwidth\parindent0pt%%%\vskip7pt%
     %% Aritle Type
     {\hbox to \textwidth{{\Artcatfont\ArtType\hfill}\par}}
     %% Aritle Title
     \ifx\@title\empty\else%
-        \removelastskip\vskip20pt\nointerlineskip%
+        % \removelastskip\vskip20pt\nointerlineskip%
+        \removelastskip\vskip0pt\nointerlineskip%
         {\Titlefont\@title\par}
         %\addcontentsline{toc}{chapter}{\@title}% for bookmarks
     \fi%

reproducibility/manuscript/figures.dvc

@@ -1,6 +1,6 @@
 outs:
-- md5: d4dbc71316265b18583a3b80be5f3d98.dir
-  size: 94209
-  nfiles: 2
+- md5: f0e383998f54f05364f6bb029fc7191f.dir
+  size: 5361624
+  nfiles: 9
   hash: md5
   path: figures

reproducibility/manuscript/header.tex

@@ -1,3 +1,6 @@
 \usepackage{nameref}
 \usepackage{placeins}
+\usepackage[labelfont=bf]{caption}
+% \usepackage{showframe}
+% \usepackage{layout}
 \allowdisplaybreaks