up doc authors

CITATION.cff

@@ -4,10 +4,13 @@ authors:
   - family-names: "Prud'homme"
     given-names: "Christophe"
     orcid: https://orcid.org/0000-0003-2287-2961
+  - family-names: "Saigre"
+    given-names: "Thomas"
+    orcid: https://orcid.org/0009-0009-5763-4956
 title: "Template article repository"
-version: 1.7.0
+version: 1.8.0
 identifiers:
   - type: doi
     value: 10.5281/zenodo.12760235
-date-released: 2024-08-17
+date-released: 2024-10-24
 url: "https://github.com/feelpp/article.template"

article.template.tex

@@ -3,6 +3,7 @@
 \usepackage{graphicx}
 \usepackage{xcolor}
 
+
 \IfFileExists{.git/gitHeadInfo.gin}{
     \usepackage[pcount,grumpy,mark,markifdirty]{gitinfo2}
 }{%
@@ -15,9 +16,9 @@
 \usepackage{natbib}
 
 \usepackage{hyperref}
-
+\usepackage{cleveref}
 \title{Template Repository for Articles}
-\author{Christophe Prud'homme\thanks{Cemosis, IRMA UMR 7501, Université de Strasbourg, CNRS, France, \tt \href{mailto:[email protected]}{[email protected]}}}
+\author{Christophe Prud'homme, Thomas Saigre\thanks{Cemosis, IRMA UMR 7501, Université de Strasbourg, CNRS, France, \tt \href{mailto:[email protected]}{christophe.prudhomme@cemosis.fr},  \href{mailto:[email protected]}{thomas.saigre@cemosis.fr}}}
 \date{\gitReln\  \gitAuthorDate\ (\gitAbbrevHash)}
 
 % Define custom color
@@ -114,8 +115,10 @@ \subsection{Using GitHub Actions}
 
 The GitHub Action workflow:
 \begin{itemize}
+    \item Updates the \mintinline{sh}|.git/gitHeadInfo.gin| file with the latest Git information.
+    \item Update the bibtex file from Zotero using the Zotero API, see \cref{sec:export-zotero-library:cli}
     \item Compiles the \LaTeX{} document using \mintinline{bash}{xu-cheng/latex-action} on \texttt{ubuntu-latest} runner or \texttt{self-texlive} runner hosted on \texttt{feelpp} organisation.
-    \item Uploads the resulting PDF
+    \item Uploads the resulting PDF and a Zip archive of the \LaTeX{} source files as artifacts that can be readily be uploaded to HAL, arXiv, Zenodo, etc.
     \item Creates a release with the PDF as an asset when a new tag is pushed of the type \texttt{v*}, e.g., \texttt{v1.0.0}.
 \end{itemize}
 
@@ -203,22 +206,49 @@ \section{Image Naming Convention}
     \item \texttt{img-figure3.jpg}
 \end{itemize}
 
-\section{Using References from Zotero via Overleaf}
+\section{Using References from Zotero}
 
-To manage your references with Zotero and integrate them seamlessly into Overleaf, follow these steps:
+To manage your references with Zotero, you can either export your Zotero library to BibTeX using the command-line interface or the Zotero API, or you can use the Zotero integration in Overleaf. 
+Note that these methods are mutually exclusive, meaning you can use either one, but not both at the same time.
+
+\subsection{Export Zotero Library to BibTeX via Command-Line}
+\label{sec:export-zotero-library:cli}
+\begin{enumerate}
+    \item Get a key api for your Zotero account, a read-only key for the group collections is enough.
+    \item Define \mintinline{sh}|ZOTERO_API_KEY| in your environment.
+\begin{minted}{sh}
+export ZOTER_API_KEY=your key 
+\end{minted}
+    \item update \mintinline{sh}|a.cli| and set \mintinline{sh}|DEFAULT_ZOTERO_GROUP_ID| at the top of the file or set the environment variable \mintinline{sh}|ZOTERO_GROUP_ID| or \mintinline{sh}|DEFAULT_ZOTERO_GROUP_ID|.
+    \item use \mintinline{sh}|a.cli| to export the references.
+\begin{minted}{sh}
+    bash a.cli update-bibtex
+\end{minted}
+\end{enumerate}
 
-\subsection{Export Zotero Library to BibTeX}
+\subsection{Export Zotero Library via Online or Desktop Interface}
+\label{sec:export-zotero-library:interface}
 \begin{enumerate}
     \item Open Zotero and select the references you want to export.
     \item Go to \texttt{File > Export Library}.
     \item Choose \texttt{BibTeX} as the format and save the file (e.g., \texttt{references.bib}).
 \end{enumerate}
 
-\subsection{Upload BibTeX File to Overleaf}
+\subsection{Uuse Zotero Integration in Overleaf}
+
 \begin{enumerate}
-    \item Open your project in Overleaf.
-    \item Click on the \texttt{Upload} button (top-left corner) and upload your \texttt{references.bib} file.
-\end{enumerate}
+    \item Ensure you have a Zotero account and that your references are properly organized in your Zotero library.
+    \item In Overleaf, open your project and navigate to the left-hand menu where you can manage your bibliography.
+    \item Click on \texttt{Add Bibliography} and select \texttt{Zotero}.
+    \item You will be prompted to log into your Zotero account and authorize Overleaf to access your Zotero library.
+    \item Once connected, you can select the specific references or entire collections you wish to import into Overleaf.
+    \item Your bibliography will be automatically updated in Overleaf as you add or remove references from your Zotero library.
+    \item Use standard LaTeX citation commands such as \mintinline{latex}|\cite{key}| to reference your sources directly within the document.
+    \end{enumerate}
+
+This method allows for seamless integration, with no need to manually export and upload BibTeX files, as Overleaf will handle the citation syncing automatically. 
+Note that changes in your Zotero library will reflect in Overleaf after you refresh the project’s bibliography.
+Again this method is mutually exclusive with the command-line method or direct export from Zotero interface.
 
 \subsection{Include the Bibliography in Your \LaTeX{} Document}
 
@@ -287,20 +317,20 @@ \subsection{Commit and Push Changes}
 
 The GitHub Action workflow will automatically compile your \LaTeX{} document and upload the resulting PDF as an artifact. You can download the compiled PDF from the Actions tab in your repository.
 
-\section{Overleaf Integration}
-
-\subsection{Sync GitHub Repository with Overleaf}
-\begin{enumerate}
-    \item In Overleaf, create a new project and select \texttt{Import from GitHub}.
-    \item Connect your GitHub account and select the repository you want to sync.
-    \item The sync will trigger the workflow and compile your \LaTeX{} document in GitHub.
-\end{enumerate}
-
-\subsection{Update References from Zotero}
-\begin{enumerate}
-    \item Periodically export your references from Zotero to \texttt{references.bib} and push the updated file to your GitHub repository.
-    \item Overleaf will automatically sync the changes, ensuring your references are up-to-date.
-\end{enumerate}
+% \section{Overleaf Integration}
+% 
+% \subsection{Sync GitHub Repository with Overleaf}
+% \begin{enumerate}
+%     \item In Overleaf, create a new project and select \texttt{Import from GitHub}.
+%     \item Connect your GitHub account and select the repository you want to sync.
+%     \item The sync will trigger the workflow and compile your \LaTeX{} document in GitHub.
+% \end{enumerate}
+% 
+% \subsection{Update References from Zotero}
+% \begin{enumerate}
+%     \item Periodically export your references from Zotero to \texttt{references.bib} and push the updated file to your GitHub repository.
+%     \item Overleaf will automatically sync the changes, ensuring your references are up-to-date.
+% \end{enumerate}
 
 \section{Conclusion}
 \label{sec:conclusion}