update workflows

.github/workflows/build-latex-diff.yml

@@ -3,8 +3,12 @@ on:
   pull_request:
     types: [opened, synchronize, reopened]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
-  build_latex:
+  build_latex_diff:
     runs-on: ubuntu-latest
     env:
       PAPER: ${{ github.event.repository.name }}
@@ -18,27 +22,28 @@ jobs:
         id: compileLaTeXdiff
         uses: xu-cheng/latex-action@v3
         with:
+          texlive_version: 2023
           root_file: |
             ${{ env.PAPER }}-diff${{ env.MAIN }}.tex
           working_directory: paper
           extra_system_packages: "git patch"
           latexmk_shell_escape: true
-          pre_compile: git config --global --add safe.directory /github/workspace && latexdiff-vc --git --flatten --disable-auto-mbox --exclude-safecmd="Cref,Cref\*,hspace" -r ${{ env.MAIN }} ${{ env.PAPER }}.tex
+          pre_compile: git config --global --add safe.directory /github/workspace && latexdiff-vc --git --flatten --disable-auto-mbox --exclude-safecmd="Cref,Cref\*,hspace" --allow-spaces --no-links -r ${{ env.MAIN }} ${{ env.PAPER }}.tex
         env:
           TEXINPUTS: ".:$PWD/../latex-styles-master/styles//:"
           BSTINPUTS: ".:$PWD/../latex-styles-master/styles/common"
           BIBINPUTS: ".:$PWD/../latex-styles-master/share"
         continue-on-error: true
       - name: Upload PDF
         if: steps.compileLaTeXdiff.outcome == 'success'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Success--Here-is-the-Diff-PDF
           path: |
             paper/${{ env.PAPER }}-diff${{ env.MAIN }}.pdf
       - name: Upload build logs
         if: steps.compileLaTeXdiff.outcome == 'failure'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Diff-Build-Failed--Here-are-the-Logs
           path: |

.github/workflows/build-latex.yml

@@ -7,6 +7,10 @@ on:
   pull_request:
     types: [opened, synchronize, reopened]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   build_latex:
     runs-on: ubuntu-latest
@@ -21,6 +25,7 @@ jobs:
         id: compileLaTeXdocument
         uses: xu-cheng/latex-action@v3
         with:
+          texlive_version: 2023
           root_file: |
             ${{ env.PAPER }}.tex
           working_directory: paper
@@ -33,15 +38,15 @@ jobs:
           BIBINPUTS: ".:$PWD/../latex-styles-master/share"
         continue-on-error: true
       - name: Upload PDF
-        if: steps.compileLaTeXdocument.outcome == 'success' && github.event_name != 'push'
-        uses: actions/upload-artifact@v3
+        if: steps.compileLaTeXdocument.outcome == 'success'
+        uses: actions/upload-artifact@v4
         with:
           name: Success--Here-is-the-PDF
           path: |
             paper/${{ env.PAPER }}.pdf
       - name: Upload build logs
-        if: steps.compileLaTeXdocument.outcome == 'failure' && github.event_name != 'push'
-        uses: actions/upload-artifact@v3
+        if: steps.compileLaTeXdocument.outcome == 'failure'
+        uses: actions/upload-artifact@v4
         with:
           name: Build-Failed--Here-are-the-Logs
           path: |

.github/workflows/build-referee-response.yml

@@ -0,0 +1,51 @@
+name: Build response-to-referees
+on:
+  push:
+    branches:
+      - master
+      - main
+    paths: ['paper/response-to-referees.tex']
+  pull_request:
+    types: [opened, synchronize, reopened]
+    paths: ['paper/response-to-referees.tex']
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  # ok to cancel concurrent builds on main; this pdf is not part of releases
+  cancel-in-progress: true
+
+jobs:
+  build_latex:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Git repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Compile LaTeX document
+        id: compileLaTeXdocument
+        uses: xu-cheng/latex-action@v3
+        with:
+          root_file: |
+            response-to-referees.tex
+          working_directory: paper
+          extra_system_packages: "git patch"
+          latexmk_shell_escape: true
+          pre_compile: git config --global --add safe.directory /github/workspace
+      - name: Upload PDF
+        if: steps.compileLaTeXdocument.outcome == 'success' && github.event_name != 'push'
+        uses: actions/upload-artifact@v4
+        with:
+          name: Success--Here-is-the-response-to-referees-PDF
+          path: |
+            paper/response-to-referees.pdf
+      - name: Upload build logs
+        if: steps.compileLaTeXdocument.outcome == 'failure' && github.event_name != 'push'
+        uses: actions/upload-artifact@v4
+        with:
+          name: Build-Response-Failed--Here-are-the-Logs
+          path: |
+            **/*.log
+      - name: Fail job if build failed
+        if: steps.compileLaTeXdocument.outcome == 'failure'
+        run: exit 1

.github/workflows/indent.yml

@@ -0,0 +1,37 @@
+name: indent
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'master'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  indent:
+    runs-on: macos-latest
+    steps:
+    - name: Checking out repository
+      uses: actions/checkout@v4
+    - name: Install latexindent and bibtool
+      run: brew install latexindent bib-tool
+    - name: Run latexindent
+      id: run-latexindent
+      run: |
+        shopt -s nullglob  # allow empty loops below
+        for f in *.tex; do latexindent -l ./localSettings.yaml -m -r -w $f; done
+        rm -f *.bak[0-9] indent.log
+    - name: Run bibtool
+      id: run-bibtool
+      run: |
+        shopt -s nullglob  # allow empty loops below
+        cd paper
+        for f in *.bib; do
+          bibtool -R -r braces.rsc -r field.rsc -r improve.rsc -r sort_fld.rsc -r ./local.rsc -i $f -o _out_$f
+          mv _out_$f $f
+        done
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v7

.github/workflows/lint.yml

@@ -6,6 +6,10 @@ on:
       - master
       - main
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -24,7 +28,7 @@ jobs:
         result-encoding: string
         script: |
           const fs = require('fs');
-          return "<details>\n<summary>Chktex output</summary>\n\n```\n" + fs.readFileSync("${{ github.workspace }}/chktex_output.txt", "utf8").toString() + "\n```\n</details>";
+          return "Chktex output: \n```\n" + fs.readFileSync("${{ github.workspace }}/chktex_output.txt", "utf8").toString() + "```";
     - name: Comment in PR
       uses: thollander/actions-comment-pull-request@v2
       with:

.github/workflows/pr-comment.yml

@@ -1,7 +1,7 @@
 name: add artifact links to pr
 on:
   workflow_run:
-    workflows: ["Build LaTeX document", "Build LaTeX diff document"]
+    workflows: ["Build LaTeX document", "Build LaTeX diff document", "Build response-to-referees"]
     types: [completed]
 
 jobs:
@@ -10,8 +10,7 @@ jobs:
     runs-on: [ubuntu-latest]
     steps:
       - name: add artifact links to pull request and related issues step
-        if: github.event_name != 'push'
-        uses: veitbjarsch/artifacts-url-comments@v1.1.0
+        uses: veitbjarsch/artifacts-url-comments@main
         env:
             GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:

paper/response-to-referees.tex

@@ -0,0 +1,109 @@
+\documentclass[11pt]{article}
+
+\usepackage{microtype}
+\usepackage{amsmath,amssymb}
+\usepackage{mathtools,bbm}
+\usepackage[hidelinks]{hyperref}
+\usepackage[svgnames]{xcolor}
+\usepackage{enumitem}
+\usepackage[margin=1.2in]{geometry}
+\usepackage{mdframed}
+
+\newmdenv[
+  linecolor=black,
+  topline=false,bottomline=false,rightline=true,
+  linewidth=2pt,
+  backgroundcolor=gray!10!white
+]{answer}
+
+\usepackage[textwidth=.95\marginparwidth,
+  backgroundcolor=lightgray,
+  linecolor=orange,
+  textsize=scriptsize]{todonotes}
+
+\makeatletter
+\@mparswitchfalse  % Place todo notes in wide margin.
+\def\listtodoname{Todo List}
+\def\listoftodos{%
+  \section*{\listtodoname}\mbox{~}\par
+  \@starttoc{tdo}
+  }
+\makeatother
+
+\newcommand{\smarttodo}[2][]{%
+  \todo[caption={\protect\hypertarget{todo}{} #2}, #1]{\hyperlink{todo}{#2}
+}}
+
+% \usepackage[number]{natbib}
+% \bibpunct{(}{)}{;}{a}{,}{,}
+% \newcommand*{\doi}[1]{DOI: \href{http://dx.doi.org/\detokenize{#1}}{\detokenize{#1}}}
+% \renewcommand*{\url}[1]{\href{\detokenize{#1}}{\texttt{\detokenize{#1}}}}
+
+\begin{document}
+
+\begin{center} \Large
+   Title line 1
+\\ Title line 2
+\\[6pt] \large Author1, Author2
+\\[6pt] \today
+\\[12pt]\Large \bf Response to reviewers
+\end{center}
+
+\noindent We thank the reviewers for their careful reading of our manuscript and their insightful and constructive comments. We followed the suggestions in almost every instance. Our responses are summarized below.
+
+\section*{Reviewer 1 comments}
+
+\begin{enumerate}[label={\color{black}R1.\arabic*}]
+  \item\label{R1:comment1} Referee comment.
+
+  \begin{answer}
+    Our answer.
+  \end{answer}
+
+  \item Referee comment.
+
+  \begin{answer}
+    Our answer can refer to~\ref{R1:comment1}.
+  \end{answer}
+
+\end{enumerate}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section*{Reviewer 2 comments}
+
+\begin{enumerate}[label={\color{black}R2.\arabic*}]
+
+  \item\label{R2:comment1} Referee comment.
+
+  \begin{answer}
+    Our answer.
+  \end{answer}
+
+  \item Referee comment.
+
+  \begin{answer}
+    Our answer can refer to~\ref{R2:comment1}.
+  \end{answer}
+
+\end{enumerate}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section*{Other changes}
+
+\begin{enumerate}[label={\color{black}O.\arabic*}]
+
+  \item Description of other change.
+
+\end{enumerate}
+
+% \frenchspacing
+% \bibliographystyle{abbrvnat}
+% \bibliography{abbrv}
+
+\end{document}
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End: