feat(github):Upgrade to debian 12 all the CI tests, upgrade to clang-format-16 and update Readme

jose-luis-rs · jose-luis-rs · commit f0cebd9a17f3 · 2025-12-22T18:53:16.000+01:00
Minor change

Minor changes for codemeta and zenodo
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -20,9 +20,9 @@ A clear and concise description of what you expected to happen.
 If applicable, add logs or screenshots to help explain your problem.
 
 **System information (please complete the following information):**
- - OS: [e.g. MacOS 12, Fedora 33, Ubuntu 20.04]
- - Compiler: [e.g. GCC 9.4, Clang 13]
- - Environment: [e.g. FairSoft version, FairRoot version]
+ - **OS:** [e.g., macOS 15, Fedora 42, Ubuntu 25.04, Debian 13]
+ - **Compiler:** [e.g., GCC 14.2, Clang 15.3]
+ - **Environment:** [e.g., FairSoft version, FairRoot version]
 
 **Additional context**
 Add any other context about the problem here.
diff --git a/.github/actions/cache-save/action.yml b/.github/actions/cache-save/action.yml
@@ -15,7 +15,7 @@ runs:
   steps:
     - name: cache ucesb
       id: cache-ucesb
-      uses: actions/cache/save@v4
+      uses: actions/cache/save@v5
       with:
         path: |
           ${{ env.UCESB_DIR }}
@@ -25,7 +25,7 @@ runs:
     - name: cache r3b
       if: matrix.save != 'false'
       id: cache-r3b
-      uses: actions/cache/save@v4
+      uses: actions/cache/save@v5
       with:
         path: .ccache
         key: r3b-build-${{ inputs.cache-name }}-${{ inputs.r3b-dev-key }}
diff --git a/.github/actions/ctest-cdash/action.yml b/.github/actions/ctest-cdash/action.yml
@@ -27,9 +27,10 @@ runs:
     - name: running ctest
       run: |
         source $GITHUB_WORKSPACE/util/generate_geo_test.sh
-#        ctest -S cmake/CI_CD/CDash.cmake -DBUILD_J=${NUM_THREADS}\
-#              -DTEST_MODEL=${TEST_MODEL}\
-#              -DTEST_NAME=${{ env.TEST_NAME }}\
-#              -DSITE_NAME="Github hosted (${{ github.repository }})"\
-#              -V -E "(run_gen_sim|run_digi|run_aladin_digi|califasim2|landreco|elsim)"
+        ctest -S cmake/CI_CD/CDash.cmake -DBUILD_J=${NUM_THREADS}\
+              -DTEST_MODEL=${TEST_MODEL}\
+              -DTEST_NAME=${{ env.TEST_NAME }}\
+              -DSITE_NAME="Github hosted (${{ github.repository }})"\
+              --force-new-ctest-process \
+              -V -E "(run_gen_sim|run_digi|run_aladin_digi|califasim2|landreco|elsim)" 
       shell: bash
diff --git a/.github/actions/install-deps/action.yml b/.github/actions/install-deps/action.yml
@@ -17,7 +17,7 @@ runs:
     - name: cache ucesb
       if: github.event_name == 'pull_request'
       id: cache-ucesb
-      uses: actions/cache/restore@v4
+      uses: actions/cache/restore@v5
       with:
         path: |
           ${{ env.UCESB_DIR }}
@@ -27,7 +27,7 @@ runs:
     - name: cache r3b
       if: inputs.cache-name != 'false' && github.event_name == 'pull_request'
       id: cache-r3b
-      uses: actions/cache/restore@v4
+      uses: actions/cache/restore@v5
       with:
         path: .ccache
         key: r3b-build-${{ inputs.cache-name }}-${{ inputs.r3b-dev-key }}
diff --git a/.github/actions/pre-build/action.yml b/.github/actions/pre-build/action.yml
@@ -1,5 +1,5 @@
 name: pre build
-description: 'steps before building R3BRoot'
+description: 'steps before building R3BRoot-FRS'
 
 runs:
   using: composite
@@ -8,9 +8,9 @@ runs:
       run: |
         git config --global --add safe.directory $GITHUB_WORKSPACE
         echo "UCESB_DIR=$GITHUB_WORKSPACE/ucesb/" >> $GITHUB_ENV
-        export SIMPATH=${CVMDIR}/debian10/fairsoft/jan24p1
+        export SIMPATH=${CVMDIR}/debian12/fairsoft/jan24p5
         echo "SIMPATH=${SIMPATH}" >> $GITHUB_ENV
-        echo "FAIRROOTPATH=${CVMDIR}/debian10/fairroot/v18.8.2_jan24p1" >> $GITHUB_ENV
+        echo "FAIRROOTPATH=${CVMDIR}/debian12/fairroot/v18.8.2_jan24p5" >> $GITHUB_ENV
         echo "${SIMPATH}/bin" >> $GITHUB_PATH
         # variables for ccache
         echo "CCACHE_BASEDIR=${GITHUB_WORKSPACE}" >> $GITHUB_ENV
@@ -26,13 +26,14 @@ runs:
     - name: mount cvmfs
       run: |
         apt-get update
-        apt-get install -y ccache doxygen graphviz --fix-missing
+        apt-get install --fix-missing -y sudo wget gnupg lsb-release
         wget https://cernbox.cern.ch/remote.php/dav/public-files/RmnTeeOZpYjCJQb/masterkey.gsi.de.pub
+        mkdir -p /etc/cvmfs/keys
         mv masterkey.gsi.de.pub /etc/cvmfs/keys
         cp .github/config/fairsoft.gsi.de.conf /etc/cvmfs/config.d
+        echo "CVMFS_USER=$(whoami)" >> /etc/cvmfs/config.d/fairsoft.gsi.de.conf
         mkdir -p ${CVMDIR}
         mount -t cvmfs fairsoft.gsi.de ${CVMDIR}
         mkdir -p ${UCESB_DIR}
         mkdir -p ${CCACHE_DIR}
-        echo $PATH
       shell: bash
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -65,7 +65,7 @@ jobs:
     # tool-kits for the building, such as clang-tidy and cvmfs. For more
     # information, please visit the Docker repository at Dockerhub.
     container: 
-      image: yanzhaowang/cvmfs_clang:latest
+      image: r3bdockers/debian12
       volumes:
         - /tmp:/cvmfs
       env:
@@ -83,7 +83,7 @@ jobs:
     # another github repo or a self-defined one in .github/actions.
     steps:
       # Fetch updates from pull request branches using a public github action.
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           # This allows all commits of all branches to be fetched.
           fetch-depth: 0
@@ -120,9 +120,8 @@ jobs:
           mv frs R3BRoot
           mv R3BRoot frs
           cd frs
-          git clone https://github.com/R3BRootGroup/macros.git
           mv frs/ucesb .
-          cmake . -B build -C cmake/CI_CD/configure_options.cmake -DBUILD_GEOMETRY=OFF -DBUILD_DOXYGEN_FRS=ON
+          cmake . -B build -C cmake/CI_CD/configure_options.cmake -DBUILD_GEOMETRY=OFF -DBUILD_DOXYGEN_FRS=OFF
           cd build
           make -j ${NUM_THREADS}
 
diff --git a/.github/workflows/static_analysis.yml b/.github/workflows/static_analysis.yml
@@ -17,11 +17,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Code formatting
         run: |
           cd $GITHUB_WORKSPACE
           sudo apt-get update
-          sudo apt-get install clang-format-15
-          ./.clang-format-check.sh clang-format-15
+          sudo apt-get install clang-format-16
+          ./.clang-format-check.sh clang-format-16
         shell: bash
diff --git a/.zenodo.json b/.zenodo.json
@@ -29,7 +29,7 @@
             "affiliation": "Universität zu Köln, 50923 Köln, Germany"
         }
     ],
-    "description": "The FRS-R3B directory within R3BRoot contains the software for the FRS (Fragment Separator) detectors that are utilized in the FRS-R3B experiments. The FRS is a pivotal instrument for investigating nuclear reactions with relativistic radioactive beams, enabling high-precision studies of exotic nuclei and nuclear structure at the limits of stability. This software is built upon the FairRoot framework, which provides the tools necessary for both Monte Carlo simulations and data analysis of experimental results. The R3B experimental program is part of the broader nuclear physics research efforts at the FAIR (Facility for Antiproton and Ion Research), a cutting-edge international research facility that utilizes heavy-ion and antiproton beams to explore fundamental questions in nuclear physics, with a particular focus on the production and behavior of rare isotopes under extreme conditions. The FRS-R3B software package is a source distribution with recurring releases for macOS and Linux.",
+    "description": "The FRS-R3B directory within R3BRoot contains the software for the FRS (Fragment Separator) detectors that are utilized in the FRS-R3B experiments. The FRS is a pivotal instrument for investigating nuclear reactions with relativistic radioactive beams, enabling high-precision studies of exotic nuclei and nuclear structure at the limits of stability. This software is built upon the FairRoot framework, which provides the tools necessary for both Monte Carlo simulations and data analysis of experimental results. The R3B experimental program is part of the broader nuclear physics research efforts at the FAIR (Facility for Antiproton and Ion Research), a cutting-edge international research facility that utilizes heavy-ion and antiproton beams to explore fundamental questions in nuclear physics, with a particular focus on the production and behavior of rare isotopes under extreme conditions. The FRS-R3B software package is a source distribution with recurring releases for MacOS and Linux.",
     "maintainers": [
         {
             "name": "Rodriguez-Sánchez, Jose Luis",
@@ -85,7 +85,7 @@
     ],
     "operatingSystem": [
         "Linux",
-        "macOS"
+        "MacOS"
     ],
     "keywords": [
         "Geant4",
diff --git a/README.md b/README.md
@@ -1,10 +1,10 @@
-# FRS-R3B Software [![license](https://alfa-ci.gsi.de/shields/badge/license-LGPL--3.0-orange.svg)](COPYRIGHT) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14294218.svg)](https://doi.org/10.5281/zenodo.14294218)
+# FRS-R3B Software [![license](https://img.shields.io/badge/License-GPLv3-blue.svg)](COPYRIGHT) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14294218.svg)](https://doi.org/10.5281/zenodo.14294218)
 
 [![static analysis](https://github.com/R3BRootGroup/frs/actions/workflows/static_analysis.yml/badge.svg)](https://github.com/R3BRootGroup/frs/actions/workflows/static_analysis.yml) [![CI-CD](https://github.com/R3BRootGroup/frs/actions/workflows/main.yml/badge.svg)](https://github.com/R3BRootGroup/frs/actions/workflows/main.yml)
 --------
 
 ## The FRS-R3B Framework
-The FRS-R3B directory within [R3BRoot](https://github.com/R3BRootGroup/R3BRoot) contains the software for the [FRS](https://wiki.gsi.de/FRS) (Fragment Separator) detectors that are utilized in the FRS-R3B experiments. The FRS is a pivotal instrument for investigating nuclear reactions with relativistic radioactive beams, enabling high-precision studies of exotic nuclei and nuclear structure at the limits of stability. This software is built upon the FairRoot framework, which provides the tools necessary for both Monte Carlo simulations and data analysis of experimental results. The R3B experimental program is part of the broader nuclear physics research efforts at the FAIR (Facility for Antiproton and Ion Research), a cutting-edge international research facility that utilizes heavy-ion and antiproton beams to explore fundamental questions in nuclear physics, with a particular focus on the production and behavior of rare isotopes under extreme conditions. The FRS-R3B software package is a source distribution with recurring releases for macOS and Linux.
+The FRS-R3B directory within [R3BRoot](https://github.com/R3BRootGroup/R3BRoot) contains the software for the [FRS](https://wiki.gsi.de/FRS) (Fragment Separator) detectors that are utilized in the FRS-R3B experiments. The FRS is a pivotal instrument for investigating nuclear reactions with relativistic radioactive beams, enabling high-precision studies of exotic nuclei and nuclear structure at the limits of stability. This software is built upon the FairRoot framework, which provides the tools necessary for both Monte Carlo simulations and data analysis of experimental results. The R3B experimental program is part of the broader nuclear physics research efforts at the FAIR (Facility for Antiproton and Ion Research), a cutting-edge international research facility that utilizes heavy-ion and antiproton beams to explore fundamental questions in nuclear physics, with a particular focus on the production and behavior of rare isotopes under extreme conditions. The FRS-R3B software package is a source distribution with recurring releases for MacOS and Linux.
 
 ## License
 FRS is distributed under the terms of the GNU Lesser General Public Licence version 3 ([GPLv3](https://github.com/R3BRootGroup/frs/blob/dev/LICENSE)).
@@ -23,15 +23,21 @@ git clone dev https://github.com/R3BRootGroup/frs.git
 cd frs
 ~~~
 
+## Code Formatting
+The FRS-R3B project (as part of R3BRoot) uses clang-format-16 to ensure a common code formatting. The script "apply-format.sh" can be used for this purpose: 
+~~~bash
+bash apply-format.sh
+~~~
+
 ## Step by Step Installation
 
 ### Required Softwares
 
 First, you will need to install FairSoft, FairRoot and R3BRoot. For more details:
 
-1. Install [FairSoft](https://github.com/FairRootGroup/FairSoft)
+1. Install [FairSoft](https://github.com/FairRootGroup/FairSoft), required version jan24p1 or later
 
-2. Install [FairRoot](http://fairroot.gsi.de)
+2. Install [FairRoot](https://github.com/FairRootGroup/FairRoot), required version 18.8.1 or later
 
 3. Install [R3BRoot](https://github.com/R3BRootGroup/R3BRoot)
 
@@ -78,7 +84,6 @@ export SIMPATH=%PATH_TO_FAIRSOFT%
 export FAIRROOTPATH=%PATH_TO_FAIRROOT%
 git clone dev https://github.com/R3BRootGroup/R3BRoot.git
 cd R3BRoot
-git clone dev https://github.com/R3BRootGroup/macros.git
 git clone dev https://github.com/R3BRootGroup/frs.git
 cd ..
 mkdir build
@@ -115,6 +120,22 @@ If the flage -DBUILD_DOXYGEN_FRS=ON is set when calling cmake, the doxygen docum
 
 Doxygen documantation is also available online [here](http://R3BRootGroup.github.io/frs/html/index.html)
 
+## Tested systems
+
+The following systems are tested regularly.
+
+| **OS Name** | **Arch** | **OS Version** | **Compiler**  | **CMake**       | **C++ Version** |
+| ----------- | -------- | -------------- | ------------- | --------------- | --------------- |
+| Almalinux   | x86\_64  | 9.3            | GCC 11.4.1    | 3.27.9 / 4.0.3  | C++17 / C++20 / C++23 |
+| Almalinux   | x86\_64  | 9.4            | GCC 14.2.0    | 3.30.6          | C++17           |
+| RHEL        | x86\_64  | 9.6            | GCC 14.2.0    | 3.30.6          | C++17           |
+| Debian      | x86\_64  | 11             | GCC 10.2.1    | 3.27.4 / 3.30.0 | C++17           |
+| Debian      | x86\_64  | 12             | GCC 12.2.0    | 3.27.4 / 3.30.0 | C++17 / C++20   |
+| Debian      | x86\_64  | 13             | GCC 14.2.0    | 3.31.6 / 4.0.3  | C++17           |
+| Ubuntu      | x86\_64  | 24.04          | GCC 13.3.0    | 3.28.3 / 4.0.3  | C++17 / C++20   |
+| Ubuntu      | x86\_64  | 25.04          | GCC 14.2.0    | 3.31.6          | C++17           |
+| MacOS       | arm64    | 15.3           | AppleClang 15 |  4.0.3          | C++17           |
+
 ## More Information
 
 * [Static analyzer using Clang-tidy](https://github.com/R3BRootGroup/R3BRoot/blob/dev/config/clang_tidy/README.md)
diff --git a/apply-format.sh b/apply-format.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-find  -type f | grep -e '.(\.C\|\.cpp\|\.cxx\|\.h)$'  | grep -v ^./macros | xargs -L 1 clang-format-15 -i 
+find  -type f | grep -e '.(\.C\|\.cpp\|\.cxx\|\.h)$'  | grep -v ^./macros | xargs -L 1 clang-format-16 -i 
 echo "Use git add -A ; git commit -m \"clang-format all files\" --author=\"white space <whitespace@example.com>\" to commit changes."
diff --git a/codemeta.json b/codemeta.json
@@ -6,11 +6,11 @@
   "contIntegration": "https://github.com/R3BRootGroup/frs/actions",
   "dateCreated": "2018-08-05",
   "datePublished": "2018-08-05",
-  "dateModified": "2024-12-08",
-  "downloadUrl": "https://github.com/R3BRootGroup/frs/archive/refs/tags/dec24.tar.gz",
+  "dateModified": "2025-12-22",
+  "downloadUrl": "https://github.com/R3BRootGroup/frs/archive/refs/tags/dec25.tar.gz",
   "issueTracker": "https://github.com/R3BRootGroup/frs/issues",
   "name": "FRS-R3B Software",
-  "softwareVersion": "dec24",
+  "softwareVersion": "dec25",
   "description": "Software for simulations and data analysis of FRS/Super-FRS/R3B experiments at GSI/FAIR",
   "readme": "https://github.com/R3BRootGroup/frs/blob/dev/README.md",
   "releaseNotes": "",
@@ -38,7 +38,7 @@
   ],
   "operatingSystem": [
     "Linux",
-    "macOS"
+    "MacOS"
   ],
   "softwareRequirements": [
     "FairRoot, FairSoft, R3BRoot"
