Added contributing file

Added bestpractices badge Update readme Update readme Update readme Update readme Update Copyright Added Deniz to the list of contributors Added fair-software.yml Update zenodo file Minor Minor Update github workflows Update github workflows Update scripts for generating json files Added more contributors Update codemeta.json Update codemeta.json Update codemeta.json Minor change readme Minor change Clang-format Update authors Minor change for zenodo Update cleanup_cache.yml Deleted old folders xball, mfi and lumon Added a display for cmake status Added a display for SUPPORTED_CXX_STANDARDS Added a display for CMAKE_CXX_STANDARD Removed old detector classes for lumon, mfi and xball Removed xball from compilehelper/CMakeLists.txt Added color to supported C++ standards Minor change in the general CMakeLists-txt
R3BRootGroup · Jan 1, 2025 · 5e6e635 · 5e6e635
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diff --git a/.github/workflows/check_metadata.yaml b/.github/workflows/check_metadata.yaml
@@ -7,21 +7,27 @@ name: Check AUTHORS and CONTRIBUTORS in metadata
 on:
   push:
     paths:
-    - AUTHORS
-    - CONTRIBUTORS
-    - .zenodo.json
+      - AUTHORS
+      - CONTRIBUTORS
+      - .zenodo.json
   pull_request:
     paths:
-    - AUTHORS
-    - CONTRIBUTORS
-    - .zenodo.json
+      - AUTHORS
+      - CONTRIBUTORS
+      - .zenodo.json
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+
       - name: Try updating metadata
-        run: python meta_update.py
+        run: python update_zenodo.py
+
       - name: Check for Updates
-        run: git diff --exit-code || echo "Metadata files require updates. Please commit the changes."
+        run: |
+          git diff --exit-code || (echo "Metadata files require updates. Please commit the changes." && exit 1)
+
+        
+
diff --git a/.github/workflows/cleanup_cache.yml b/.github/workflows/cleanup_cache.yml
@@ -14,23 +14,36 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Git
-        run: git config --global user.email "[email protected]" && git config --global user.name "GitHub Actions"
+      - name: Debug gh CLI
+        run: |
+          gh --version
+          gh auth status
+          gh extension list
 
-      - name: Cleanup
+      - name: Update GitHub CLI
+        run: sudo apt-get install gh
+
+      - name: Install and Verify gh-actions-cache Extension
         run: |
           gh extension install actions/gh-actions-cache || exit 1
-          
+          gh extension list | grep gh-actions-cache || (echo "Extension installation failed" && exit 1)
+
+      - name: Test actions-cache list
+        run: |
+          gh actions-cache list -R R3BRootGroup/R3BRoot -L 5 || echo "Failed to list caches"
+
+      - name: Cleanup
+        run: |
           echo "Fetching list of cache keys"
           cacheKeys=$(gh actions-cache list -R R3BRootGroup/R3BRoot -L 100 | cut -f 1 | grep -v 'build-deps') || exit 1
 
-          ## Setting this to not fail the workflow while deleting cache keys. 
           set +e
           echo "Deleting old caches..."
           for cacheKey in $cacheKeys
           do
-              gh actions-cache delete $cacheKey -R R3BRootGroup/R3BRoot --confirm || exit 1
+              gh actions-cache delete $cacheKey -R R3BRootGroup/R3BRoot --confirm || echo "Failed to delete $cacheKey"
           done
           echo "Done"
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
diff --git a/.github/workflows/fair-software.yml b/.github/workflows/fair-software.yml
@@ -0,0 +1,23 @@
+# SPDX-FileCopyrightText: 2024 GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt, Germany
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
+
+name: fair-software
+
+on:
+  push:
+    paths:
+    - README.md
+
+jobs:
+  verify:
+    name: "fair-software"
+    runs-on: ubuntu-latest
+    if: github.repository == 'R3BRootGroup/R3BRoot'
+    steps:
+      - uses: fair-software/[email protected]
+        name: Measure compliance with fair-software.eu recommendations
+        env:
+          PYCHARM_HOSTED: "Trick colorama into displaying colored output"
+        with:
+          MY_REPO_URL: "https://github.com/${{ github.repository }}"
diff --git a/.zenodo.json b/.zenodo.json
@@ -12,7 +12,7 @@
     "related_identifiers": [
         {
             "identifier": "https://github.com/FairRootGroup/FairSoft/",
-            "relation": "isDerivedFrom",
+            "relation": "isCompiledBy",
             "resource_type": "software",
             "scheme": "url"
         },
@@ -24,7 +24,7 @@
         },
         {
             "identifier": "https://gitlab.com/chalmers-subexp/ucesb/",
-            "relation": "isRelatedTo",
+            "relation": "isSupplementedBy",
             "resource_type": "software",
             "scheme": "url"
         },
@@ -69,9 +69,10 @@
         "Data analysis",
         "Structure and dynamics of nuclei",
         "Nuclear reactions",
-        "Equation of state",
         "Nuclear fission",
         "Hypernuclei",
+        "Equation of state",
+        "Short range NN correlations",
         "R3B experiments",
         "GSI/FAIR facility"
     ],
@@ -93,6 +94,12 @@
             "orcid": "0000-0001-6919-8869",
             "affiliation": "GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany"
         },
+        {
+            "name": "Audouin, Laurent",
+            "orcid": "0000-0001-9899-6923",
+            "email": "[email protected]",
+            "affiliation": "IPN Orsay, 91406 Orsay, France"
+        },
         {
             "name": "Barriere, Antoine",
             "orcid": "0009-0005-2204-3516",
@@ -317,6 +324,11 @@
             "orcid": "0000-0002-6506-8562",
             "affiliation": "STFC Daresbury Laboratory, Warrington, United Kingdom"
         },
+        {
+            "type": "Other",
+            "name": "Lorenz, Enis",
+            "affiliation": "Technische Universität Darmstadt, Fachbereich Physik, Institut für Kernphysik, 64289 Darmstadt, Germany"
+        },
         {
             "type": "Other",
             "name": "Paschalis, Stefanos",
@@ -338,6 +350,11 @@
             "name": "Ponnath, Lukas",
             "affiliation": "Technische Universität Darmstadt, Fachbereich Physik, Institut für Kernphysik, 64289 Darmstadt, Germany"
         },
+        {
+            "type": "Other",
+            "name": "Qi, Christine",
+            "affiliation": "Massachusetts Institute of Technology, MA 02139 Cambridge, USA"
+        },
         {
             "type": "Other",
             "name": "Rybalchenko, Alexey"
@@ -352,6 +369,11 @@
             "name": "Rossi, Dominic",
             "affiliation": "Technische Universität Darmstadt, Fachbereich Physik, Institut für Kernphysik, 64289 Darmstadt, Germany"
         },
+        {
+            "type": "Other",
+            "name": "Savran, Deniz",
+            "affiliation": "GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany"
+        },
         {
             "type": "Other",
             "name": "Storck, Sonja",

diff --git a/AUTHORS b/AUTHORS
@@ -1,6 +1,7 @@
 Rodríguez-Sánchez, Jose Luis [[email protected]] [https://orcid.org/0000-0002-4702-5294] [CITENI, Industrial Campus of Ferrol, University of Coruña, 15403 Ferrol, Spain]
 Alvarez Pol, Hector [[email protected]] [https://orcid.org/0000-0001-9643-6252] [IGFAE, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain]
 Atar, Leyla [https://orcid.org/0000-0001-6919-8869] [GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany]
+Audouin, Laurent [[email protected]] [https://orcid.org/0000-0001-9899-6923] [IPN Orsay, 91406 Orsay, France]
 Barriere, Antoine [https://orcid.org/0009-0005-2204-3516] [GANIL, 14000 Caen, France]
 Bott, Lukas [https://orcid.org/0000-0002-9554-6246] [Goethe University Frankfurt, 60629 Frankfurt am Main, Germany]
 Chatillon, Audrey [CEA, DAM, DIF, 91297 Arpajon, France]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,6 @@
 ##############################################################################
 #   Copyright (C) 2019 GSI Helmholtzzentrum für Schwerionenforschung GmbH    #
-#   Copyright (C) 2019-2024 Members of R3B Collaboration                     #
+#   Copyright (C) 2019-2025 Members of R3B Collaboration                     #
 #                                                                            #
 #             This software is distributed under the terms of the            #
 #                 GNU General Public Licence (GPL) version 3,                #
@@ -24,7 +24,7 @@ endif()
 cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
 
 # set cmake policies
-cmake_policy(VERSION 3.15...3.24)
+cmake_policy(VERSION 3.15...3.31)
 
 # Set name of our project to "R3BROOT". Has to be done after check of cmake version
 project(R3BROOT LANGUAGES C CXX Fortran)
@@ -112,8 +112,6 @@ if("${FairRoot_VERSION}" VERSION_LESS 18.2.1)
         FATAL_ERROR
             "Incompatible FairRoot version detected: ${FairRoot_VERSION}. R3BRoot requires FairRoot v18.2.1 or later"
     )
-else()
-    message(STATUS "You seem to be using FairRoot ${FairRoot_VERSION}.")
 endif()
 
 # added a variable to point to r3broot path in the system
@@ -343,6 +341,27 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 set(VMCWORKDIR ${CMAKE_SOURCE_DIR})
 
+# Display SUPPORTED_CXX_STANDARDS
+set(SUPPORTED_CXX_STANDARDS "")
+foreach(version 14 17 20 23)
+    string(CONCAT flag "cxx_std_" ${version})
+    if(flag IN_LIST CMAKE_CXX_COMPILE_FEATURES)
+        list(APPEND SUPPORTED_CXX_STANDARDS ${version})
+    endif()
+endforeach()
+
+if(SUPPORTED_CXX_STANDARDS)
+    message(STATUS "${Cyan}Supported C++ standards:${CR} ${SUPPORTED_CXX_STANDARDS}")
+    message(STATUS "${Cyan}CMake is using C++ standard:${CR} ${BGreen}${CMAKE_CXX_STANDARD}${CR}")
+else()
+    message(WARNING "No supported C++ standards found!")
+endif()
+
+# Display configurations
+message(STATUS "CMake C++ Flags: ${CMAKE_CXX_FLAGS}")
+message(STATUS "Library Output Directory: ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}")
+message(STATUS "Runtime Output Directory: ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}")
+
 if(USE_PATH_INFO)
     if(APPLE)
         set(LD_LIBRARY_PATH $ENV{DYLD_LIBRARY_PATH})
@@ -554,11 +573,9 @@ if(NOT MODULE)
     endif()
     add_subdirectory(neuland)
     add_subdirectory(glad)
-    add_subdirectory(xball)
     add_subdirectory(dch)
     add_subdirectory(fiber)
     add_subdirectory(gfi)
-    add_subdirectory(mfi)
     add_subdirectory(land)
     add_subdirectory(los)
     add_subdirectory(rolu)
@@ -575,7 +592,6 @@ if(NOT MODULE)
     add_subdirectory(strawtubes)
     add_subdirectory(music)
     add_subdirectory(r3bgen)
-    add_subdirectory(lumon)
     add_subdirectory(califa)
     add_subdirectory(evtvis)
     add_subdirectory(psp)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,130 @@
+# Contributing
+
+## Bug reports, feature request, questions etc
+
+Create a [Github Issue](https://github.com/R3BRootGroup/R3BRoot/issues/new/choose).
+
+## Contributing code
+
+Create a [Github Pull Request](https://github.com/R3BRootGroup/R3BRoot/compare):
+
+1. By default, develop against the [`dev`](https://github.com/R3BRootGroup/R3BRoot/tree/dev)
+   branch and base your PR against it.
+   * In rare cases (e.g. backports, some hotfixes) base against the appropriate
+     branch.
+2. If you are a first time contributor, add a separate commit in your PR which
+   adds your name to the [`CONTRIBUTORS`](CONTRIBUTORS) file.
+3. Follow our [Coding Guidelines](#coding-guidelines).
+4. Expect that a reviewer will ask you for restructuring your commits! This
+   usually happens towards the end of the lifetime of a PR when it matured
+   enough for merging.
+
+# Coding Guidelines
+
+These guidelines are horribly incomplete at this point in time, but one has to
+start somewhere ;) Exactly because these guidelines are relatively new, do not be
+alarmed if large parts of this repo do not follow them (yet). The idea is to
+apply them incrementally on new code and when existing code is modified. These
+guidelines will also evolve as time passes.
+
+How to reference a rule in an issue or PR discussion:
+```
+// reference to our guideline
+[G.2](https://github.com/R3BRootGroup/R3BRoot/blob/master/CONTRIBUTING.md#g.2-adopted-c++-core-guidelines)
+// reference to c++ core guideline with prefix CPPCG::
+[CPPCG::I.11](https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md#i11-never-transfer-ownership-by-a-raw-pointer-t-or-reference-t)
+```
+
+## G - General
+
+### G.1 Our CI runs [`clang-tidy`](https://clang.llvm.org/extra/clang-tidy/)
+
+**Config**: [`.clang-tidy`](.clang-tidy)
+
+We currently do not strictly enforce *clang-tidy* checks, but the author
+should try to address any warnings. The set of enabled checks will evolve over
+time.
+
+### G.2 Adopted C++ Core Guidelines
+
+This shall be an evolving list of explicitely adopted C++ Core Guidelines:
+
+* [CPPCG::I.11: Never transfer ownership by a raw pointer (`T*`) or reference (`T&`)](https://github.com/isocpp/CppCoreGuidelines/blob/master/CppCoreGuidelines.md#i11-never-transfer-ownership-by-a-raw-pointer-t-or-reference-t)
+   * If an owning raw pointer cannot be avoided for legacy reasons,
+     **you must add a comment documenting the ownership semantics!**
+
+### G.3 Write a good Git history
+
+* Follow [the seven rules of a great Git commit message](https://cbea.ms/git-commit/#seven-rules)!
+* Use a meaningful commit granularity, e.g. do not mix
+  unrelated changes in a single commit and vice verse squash related commits
+  into one.
+* Utilize [the commit message body to explain *what* and *why* and not *how*](https://cbea.ms/git-commit/#why-not-how).
+  Aim your message to be meaningful (concise, but complete
+  enough) to a reader in the future! See also G.4!
+* Utilize [reference keywords](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
+  both in commit messages as well as in PR comments if applicable.
+
+### G.4 Conventional Commits
+
+* Follow the [Conventional Commits Specification](https://www.conventionalcommits.org/en/v1.0.0/)
+* Adopted `type`s: `fix:`, `feat:`, `build:`, `chore:`, `ci:`, `docs:`,
+  `style:`, `refactor:`, `perf:`, `test:`
+* If a `scope` is used, prefer the library name (first directory level below
+  `R3BRoot/`), e.g. `fix(base):` or `feat(geobase):`
+
+### G.5 Signed Commits and Tags
+
+You may use any signature format Git and Github support (SSH e.g. may be more
+convenient, if one does not have a GPG key yet).
+
+* [Github - Setup](https://docs.github.com/en/authentication/managing-commit-signature-verification/telling-git-about-your-signing-key)
+* [Github - Signing Commits](https://docs.github.com/en/authentication/managing-commit-signature-verification/signing-commits)
+* [Github - Signing Tags](https://docs.github.com/en/authentication/managing-commit-signature-verification/signing-tags)
+* [Git - Signing Your Work](https://git-scm.com/book/en/v2/Git-Tools-Signing-Your-Work)
+  Make sure to consider `git config [--local|--global] commit.gpgsign true`
+  (scroll down to the bottom)
+
+## D - Documentation
+
+### D.1 Use [doxygen-style comments](https://www.doxygen.nl/manual/commands.html)
+
+## S - Style
+
+### S.1 Our CI enforces formatting with [`clang-format`](https://clang.llvm.org/docs/ClangFormat.html)
+
+**Config**: [`.clang-format`](.clang-format)
+
+Rarely, it is needed to opt-out of *clang-format* for certain code sections
+because it would just make things worse.
+
+**Example**:
+```cpp
+// clang-format off
+fDescription.add_options()
+    ("help",                                        "Print this message")
+    ("nevents",        po::value<int>(),            "Number of events to simulate")
+    ("engine",         po::value<vector<string>>(), "Monte Carlo engine")
+    ("multi-threaded",                              "Geant4 multi threaded")
+    ("output-file",    po::value<vector<string>>(), "Output file")
+    ("parameter-file", po::value<vector<string>>(), "Parameter file")
+    ("random-seed",    po::value<int>(),            "Seed for the random number generator");
+// clang-format on
+```
+
+### S.2 Prefer variable names describing *what* they contain
+
+Avoid repeating just the typename.
+
+**Reason**: Readability
+
+**Example**:
+```cpp
+TList* list = module->GetList();                // avoid
+TList* volList = module->GetListOfVolumes();    // acceptable
+TList* volumes = module->GetVolumes();          // ✓ prefer
+
+for (auto const& listEntry : *list) { /*...*/ } // avoid
+for (auto const& aVol : *volList) { /*...*/ }   // acceptable
+for (auto const& volume : *volumes) { /*...*/ } // ✓ prefer
+```