Merge branch 'main' into trust_figure

.github/workflows/latex.yml

@@ -71,21 +71,23 @@ jobs:
         run: |
           bash ./a.cli setup
 
-#      - name: Update BibTeX references
-#        run: |
-#          bash ./a.cli update-bibtex
-#
-#      - name: Commit new references.bib
-#        run: |
-#          git config --local user.email "${{ github.actor }}@users.noreply.github.com"
-#          git config --local user.name "${{ github.actor }}"
-#          git add references.bib
-#          if ! git diff --cached --quiet; then
-#            git commit -m "Update references.bib from Zotero"
-#            git push
-#          else
-#            echo "No changes in references.bib to commit."
-#          fi
+      - name: Update BibTeX references
+        if: ${{ github.ref != 'refs/heads/main' }}
+        run: |
+          bash ./a.cli update-bibtex
+
+      - name: Commit new references.bib
+        if: ${{ github.ref != 'refs/heads/main' }}
+        run: |
+          git config --local user.email "${{ github.actor }}@users.noreply.github.com"
+          git config --local user.name "${{ github.actor }}"
+          git add references.bib
+          if ! git diff --cached --quiet; then
+            git commit -m "Update references.bib from Zotero"
+            git push
+          else
+            echo "No changes in references.bib to commit."
+          fi
 
       - name: Compile LaTeX document
         uses: xu-cheng/latex-action@v3

.gitignore

@@ -6,7 +6,7 @@ _minted*
 **/*.out
 **/*.pyg
 **/*.fls
-**/*.synctex.gz
+**/*.synctex*
 main.pdf
 *.toc
 article.template.pdf
@@ -23,5 +23,5 @@ exa-ma-d7.1.pdf
 *.chl
 *.lof
 *.lot
-*.pdf
-.venv
+.venv
+.DS_Store

.vscode/settings.json

@@ -38,8 +38,10 @@
             ]
         }
     ],
-    "latex-workshop.latex.autoBuild.run": "onFileChange",
+    "latex-workshop.latex.autoBuild.run": "onSave",
     "latex-workshop.latex.autoBuild.enabled": true,
     "latex-workshop.latex.build.showOutput": "always",
-    "latex-workshop.latex.outDir": "%DIR%"
+    "latex-workshop.latex.outDir": "%DIR%",
+    "latex-workshop.message.badbox.show": "none",
+    "workbench.editor.pinnedTabsOnSeparateRow": true
 }

README.adoc

@@ -1,5 +1,5 @@
 = Exa-MA D7.1 Report Automation
-
+:experimental: true
 //.Zenodo DOI
 //--
 //image::https://zenodo.org/badge/DOI/10.5281/zenodo.13341126.svg[DOI, link=https://doi.org/10.5281/zenodo.13341126]
@@ -33,15 +33,60 @@ NOTE: `a.cli` is a shell script to setup the repo, create release and update bib
 .Command line to compile fully the deliverable
 [source, shell]
 ----
-latexmk -shell-escape -pdf -file-line-error -halt-on-error -interaction=nonstopmode exa-ma-d7.1.tex
+latexmk --shell-escape -pdf -file-line-error -halt-on-error -interaction=nonstopmode exa-ma-d7.1.tex
 ----
 
 .Simple command line to compile once
 [source, shell]
 ----
-pdflatex -shell-escape exa-ma-d7.1.tex
+pdflatex --shell-escape exa-ma-d7.1.tex
 ----
 
+== Zotero
+
+=== Update Zotero references
+
+To update the references (`references.bib`), you have several options:
+
+Download from Zotero:: download the file references.bib by exporting the exa-ma library from the GUI
+Using `a.cli`:: setup the variable and run `a.cli update-bibtex`
++
+[,console]
+----
+
+export ZOTERO_API_KEY=xxx
+bash ./a.cli update-bibtex
+----
++
+to create the key go to https://www.zotero.org/settings/security[> Zotero Secutiry page] (and log in) 
++
+then go to the **Applications** at the bottom of the **Secutiry** page
++
+image:graphics/zotero/zotero-applications.png[]
++
+click btn:[Create new private key] then select group permission **Read only*. Then btn:[Save Key]. 
++
+image:graphics/zotero/zotero-newkey.png[]
++
+Then keep the key in a safe place and use it to to define `ZOTERO_API_KEY`
+
+=== How to set citation keys 
+
+[.right]
+image:graphics/zotero/zotero-citation-keys.png[]
+
+
+To set your own citation key, simply enter the following line in Zotero's **Extra** field:
+[source,text]
+----
+Citation Key: saigre_coupled_2024_paper
+----
+
+When the biblio is exported, this key will be used for the reference.
+
+NOTE: you have then to handle possible conflicts in citation keys yourself in you set them yourself.
+
+
 == Workflow Description
 
 The repository utilizes GitHub Actions to automate the following tasks:

a.cli

@@ -24,7 +24,7 @@ parse_args() {
             --zotero-api-key) ZOTERO_API_KEY="$2"; shift ;;
             --zotero-group-id) ZOTERO_GROUP_ID="$2"; shift ;;
             --bibtex-file) BIBTEX_FILE="$2"; shift ;;
-            --help) 
+            --help)
                 echo "Usage: $0 [options] {setup|create|list|delete|update-bibtex} [version]"
                 echo "Options:"
                 echo "  --zotero-user-id    Zotero User ID"
@@ -109,6 +109,11 @@ list_releases() {
     git tag --sort=-creatordate | head -n $1
 }
 
+# Function to clean latex build files
+clean() {
+    # clean latex build files
+    rm -f *.aux *.bbl *.blg *.log *.out *.pyg *.fls *.synctex* *.toc *.fdb_latexmk *.fls *.idx *.ilg *.ind *.chl *.lof *.lot *.pdf
+}
 # Function to delete a release
 delete_release() {
     VERSION=$1
@@ -146,16 +151,17 @@ update_bibtex() {
 
     # Define the URL to fetch BibTeX
     if [ -z "$ZOTERO_GROUP_ID" ]; then
-        URL="https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=bibtex"
+        URL="https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=biblatex"
     else
-        URL="https://api.zotero.org/groups/$ZOTERO_GROUP_ID/items?format=bibtex"
+        URL="https://api.zotero.org/groups/$ZOTERO_GROUP_ID/items?format=biblatex"
     fi
     start=0
     limit=100
+    has_more=true
     echo "" > "$BIBTEX_FILE"
     while $has_more; do
         response=$(curl -s -H "Zotero-API-Key: $ZOTERO_API_KEY" "$URL&start=$start&limit=$limit")
-        
+
         if [ -z "$response" ]; then
             echo "No more items to fetch."
             has_more=false
@@ -176,13 +182,79 @@ update_bibtex() {
     echo "BibTeX entries updated successfully in $BIBTEX_FILE."
 }
 
+update_bibtex2() {
+    if [ -z "$ZOTERO_GROUP_ID" ]; then
+        if [ -z "$ZOTERO_USER_ID" ]; then
+            echo "Zotero group ID and user ID are not set, one of them is required."
+            echo "If Group ID is set, User ID is not required."
+            exit 1
+        fi
+    fi
+
+    if [ -z "$ZOTERO_API_KEY" ]; then
+        echo "Zotero API key is not set."
+        exit 1
+    fi
+
+    echo "Fetching BibTeX entries from Zotero..."
+
+    # Define the URL to fetch BibTeX
+    if [ -z "$ZOTERO_GROUP_ID" ]; then
+        URL="https://api.zotero.org/users/$ZOTERO_USER_ID/items?format=bibtex"
+    else
+        URL="https://api.zotero.org/groups/$ZOTERO_GROUP_ID/items?format=bibtex"
+    fi
+
+    start=0
+    limit=100
+    has_more=true  # Initialize the loop control variable
+    echo "" > "$BIBTEX_FILE"
+
+    while $has_more; do
+        # Send the request
+        response=$(curl -s -w "%{http_code}" -H "Zotero-API-Key: $ZOTERO_API_KEY" "$URL&start=$start&limit=$limit")
+
+        # Separate the response content and the status code
+        http_code=$(echo "$response" | tail -n1)
+        content=$(echo "$response" | sed '$d')  # Everything except the last line (status code)
+
+        # Check if the request was successful (status code 200)
+        if [ "$http_code" -ne 200 ]; then
+            echo "Error fetching data: HTTP status $http_code"
+            exit 1
+        fi
+        if [ -z "$content" ]; then
+            echo "No more items to fetch."
+            has_more=false
+            break
+        fi
+        # Append the content to the BibTeX file
+        echo "$content" >> "$BIBTEX_FILE"
+
+        # Check if there are more items by inspecting the Link header or counting the items
+        num_items=$(echo "$content" | grep -c "@")  # Counting BibTeX entries
+        echo "downloaded $num_items items"
+        if [ "$num_items" = "0" ]; then
+            has_more=false
+        else
+            start=$((start + limit))
+        fi
+        echo "start=$start, has_more=$has_more"
+    done
+
+    echo "BibTeX entries updated successfully in $BIBTEX_FILE."
+}
+
 # Main script logic
 parse_args "$@"
 
 case "$1" in
     setup)
         setup
         ;;
+    clean)
+        clean
+        ;;
     create)
         create_release "$2"
         ;;
@@ -193,7 +265,7 @@ case "$1" in
         delete_release "$2"
         ;;
     update-bibtex)
-        update_bibtex
+        update_bibtex2
         ;;
     *)
         echo "Usage: $0 [options] {setup|create|list|delete|update-bibtex} [version]"
@@ -204,6 +276,7 @@ case "$1" in
         echo "  --bibtex-file       Path to the BibTeX file (default: your_bibtex_file.bib)"
         echo "Commands:"
         echo "  setup               : Setup hooks for commit, checkout, and merge"
+        echo "  clean               : Clean latex build files"
         echo "  create              : Create a new release with the provided version"
         echo "  list                : List all existing releases"
         echo "  delete              : Delete the release with the provided version"

chapters/00-index.tex

@@ -1,24 +1,30 @@
 \chapter{WP1 - Discretization}
+\label{chap:wp1}
 \clearpage
 \subimport{./WP1}{00-index}
 
 \chapter{WP2 - Model order, Surrogate, Scientific Machine Learning methods}
+\label{chap:wp2}
 \clearpage
 \subimport{./WP2}{00-index}
 
 \chapter{WP3 - Solvers}
+\label{chap:wp3}
 \clearpage
 \subimport{./WP3}{00-index}
 
 \chapter{WP4 - Data assimilation}
+\label{chap:wp4}
 \clearpage
 \subimport{./WP4}{00-index}
 
 \chapter{WP5 - Optimization}
+\label{chap:wp5}
 \clearpage
 \subimport{./WP5}{00-index}
 
 \chapter{WP6 - Uncertainty quantification}
+\label{chap:wp6}
 \clearpage
 \subimport{./WP6}{00-index}
 

chapters/WP3/00-index.tex

@@ -1,4 +1,4 @@
-\input{software/arcane-framework/WP3/WP3.tex}
+%%\input{software/arcane-framework/WP3/WP3.tex}
 \input{software/composyx/WP3/WP3.tex}
 \input{software/feelpp/WP3/WP3.tex}
 \input{software/freefempp/WP3/WP3.tex}

chapters/WP7/00-index.tex

@@ -1,4 +1,4 @@
-\input{software/arcane-framework/WP7/WP7.tex}
+%\input{software/arcane-framework/WP7/WP7.tex}
 \input{software/feelpp/WP7/WP7.tex}
 \input{software/freefempp/WP7/WP7.tex}
 \input{software/manta/WP7/WP7.tex}

chapters/benchmarking.tex

@@ -402,7 +402,7 @@ \section{Conclusion}
 
 We presented a phased benchmarking strategy that integrates testing, validation, profiling, and continuous integration to ensure that the software is ready for exascale environments. The testing processes, including non-regression, verification, and validation, emphasize maintaining performance integrity across updates and ensuring that new algorithmic improvements lead to meaningful progress.
 
-The benchmarking strategy involves comprehensive testing across \textbf{CPU}, \textbf{GPU}, and \textbf{hybrid} CPU-GPU architectures to ensure that software can scale efficiently. This includes separate tests for CPU and GPU performance, as well as hybrid configurations where workloads are distributed across both architectures. 
+The benchmarking strategy involves  testing across \textbf{CPU}, \textbf{GPU}, and \textbf{hybrid} CPU-GPU architectures to ensure that software can scale efficiently. This includes separate tests for CPU and GPU performance, as well as hybrid configurations where workloads are distributed across both architectures. 
 
 Data management and I/O strategies (\ac{B6}, \ac{B9}, \ac{B10}, \ac{B11}) were also highlighted to address I/O bottlenecks and ensure efficient handling of large datasets, leveraging fault-tolerant mechanisms for data integrity. As the project progresses, more advanced fault tolerance strategies may be integrated to ensure resilience against hardware or software failures.
 

chapters/software.tex

@@ -1,6 +1,6 @@
 \clearpage
 \chapter{Software}
-\label{sec:software}
+\label{chap:software}
 
 This chapter presents the software developed within Exa-MA, focusing on features, mathematics, functionalities, publications, acknowledgments, and contact details.
 
@@ -173,14 +173,14 @@ \subsection{DevOps - Testing}
 \end{figure}
 
 
-\input{software/arcane-framework/arcane-framework.tex}
+%\input{software/arcane-framework/arcane-framework.tex}
 \input{software/cgal/cgal.tex}
 \input{software/composyx/composyx.tex}
 \input{software/feelpp/feelpp.tex}
 \input{software/freefempp/freefempp.tex}
 \input{software/hawen/hawen.tex}
 \input{software/hpddm/hpddm.tex}
-\input{software/mahyco/mahyco.tex}
+%%\input{software/mahyco/mahyco.tex}
 \input{software/manta/manta.tex}
 \input{software/pbb/pbb.tex}
 \input{software/samurai/samurai.tex}

defs.tex

@@ -6,3 +6,7 @@
 \def\exaatow{\textsc{Exa-Atow}\xspace}
 \def\exadi{\textsc{Exa-DI}\xspace}
 \def\numpex{NumPEx}
+\def\Rplus{\protect\hspace{-0em}\protect\raisebox{.35ex}{{\smaller\textbf{+}}}}
+\def\Cpp#1{\mbox{C\Rplus\Rplus#1}\xspace}
+\def\feelpp{\ac{feelpp}\xspace}
+\def\Feelpp{\mbox{Feel\Rplus\Rplus}\xspace}