fix the doxygen issue

.github/actions/r3bbuild-steps/action.yml

@@ -35,6 +35,5 @@ runs:
     - name: build ${{ matrix.repos }}
       if: inputs.build-needed == 'true'
       run: |
-        ./build.py -b -j ${NUM_THREADS} 
-        # ./build_thisr3broot.sh -b build -j ${NUM_THREADS}
+        cmake --build --preset ${{ matrix.preset }} -- -j ${NUM_THREADS}
       shell: bash

.github/workflows/publish_doxygen.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   artifact-gen:
-    runs-on: macos-15
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash
@@ -18,11 +18,8 @@ jobs:
           submodules: 'true'
       - name: run doxygen
         run: |
-          brew upgrade
-          brew install doxygen graphviz cmake ninja npm gcc
-          export PATH="/opt/homebrew/bin:$PATH"
-          export FC="gfortran-14"
-          npm install mathjax@3
+          sudo apt-get update -y
+          sudo apt-get install -y doxygen graphviz ninja mathjax cmake
           cmake --workflow --preset doxygen
 
       - uses: actions/upload-pages-artifact@v3
@@ -31,7 +28,7 @@ jobs:
           retention-days: 1
 
   publish-doxygen:
-    runs-on: macos-15
+    runs-on: ubuntu-latest
     needs: artifact-gen
     permissions:
       pages: write

CMakePresets.json

@@ -15,7 +15,8 @@
                 "CMAKE_EXPORT_COMPILE_COMMANDS": "ON",
                 "BUILD_GEOMETRY": "OFF",
                 "USE_DIFFERENT_COMPILER": "ON",
-                "CMAKE_BUILD_TYPE": "RelWithDebInfo"
+                "CMAKE_BUILD_TYPE": "RelWithDebInfo",
+                "CONAN_ENABLED": "OFF"
             }
         },
         {

doc/CMakeLists.txt

@@ -30,7 +30,7 @@ set(DOXYGEN_CLASS_GRAPH NO)
 set(DOXYGEN_COLLABORATION_GRAPH NO)
 set(DOXYGEN_USE_MATHJAX YES)
 set(DOXYGEN_MAX_DOT_GRAPH_DEPTH 2)
-set(DOXYGEN_USE_MDFILE_AS_MAINPAGE "README.md")
+set(DOXYGEN_USE_MDFILE_AS_MAINPAGE "${PROJECT_SOURCE_DIR}/README.md")
 set(DOXYGEN_IMAGE_PATH "${PROJECT_SOURCE_DIR}/doc/pics" "${PROJECT_SOURCE_DIR}/neuland/docs/figs"
                        "${PROJECT_SOURCE_DIR}/neuland/shared")
 
@@ -42,15 +42,19 @@ set(DOXYGEN_FULL_SIDEBAR NO)
 set(DOXYGEN_GENERATE_TREEVIEW YES)
 set(DOXYGEN_HTML_COLORSTYLE LIGHT)
 set(DOXYGEN_EXCLUDE_PATTERNS "*.py" "ext_h101_*")
+set(DOXYGEN_EXTENSION_MAPPING "md=md")
+
+file(GLOB DataSourceFiles ${PROJECT_SOURCE_DIR}/r3bdata/*.cxx)
+file(GLOB DataHeaderFiles ${PROJECT_SOURCE_DIR}/r3bdata/*.h)
 
 doxygen_add_docs(
     doxygen
     ${PROJECT_SOURCE_DIR}/README.md
     ${PROJECT_SOURCE_DIR}/neuland
     ${PROJECT_SOURCE_DIR}/r3bbase
     ${PROJECT_SOURCE_DIR}/r3bdata/neulandData
-    ${PROJECT_SOURCE_DIR}/r3bdata/*.h
-    ${PROJECT_SOURCE_DIR}/r3bdata/*.cxx
+    ${DataSourceFiles}
+    ${DataHeaderFiles}
     ${PROJECT_SOURCE_DIR}/r3bsource/base
     ${PROJECT_SOURCE_DIR}/r3bsource/neuland
     ${PROJECT_SOURCE_DIR}/passive

neuland/readme.md

@@ -25,8 +25,8 @@ The components fill storage containers for each event, which flow into other com
 These tasks are derived from FairTask and used in the steering macros.
 Task ending on a process usually apply a transformation to data, and take the input and output branch names as attributes, e.g.:
 
-- [`R3BNeulandDigitizer`](#digitizing): Detector response, NeulandPoints -> NeulandHits
-- [`R3BNeulandClusterFinder`](#clustering): Clustering of digitized data, NeulandHits -> NeulandClusters
+- `R3BNeulandDigitizer`: Detector response, NeulandPoints -> NeulandHits
+- `R3BNeulandClusterFinder`: Clustering of digitized data, NeulandHits -> NeulandClusters
 
 Task ending on `mon` create control histograms, and might be quite messy. They take the input branch and output folder names as arguments. Examples:
 
@@ -39,23 +39,23 @@ Task ending on `mon` create control histograms, and might be quite messy. They t
 
 Note that the classes indented for storing data (derived from TObject for usage with TClonesArray) are located in `r3bdata/neulandData`.
 
-- `R3BNeulandPoint`: Basic MonteCarlo energy depositions and light yield, see, [Detector Class](#detector-class)
-- `R3BNeulandHit`: Combined NeulandPoints, digitized with detector response, see [Digitizing](#digitizing). Also indented for mapped and calibrated experimental data.
-- `R3BNeulandCluster`: Clusters consisting out of NeulandHits that belong together according to clustering conditions, see [Clustering](#clustering)
+- `R3BNeulandPoint`: Basic MonteCarlo energy depositions and light yield.
+- `R3BNeulandHit`: Combined NeulandPoints, digitized with detector response. Also indented for mapped and calibrated experimental data.
+- `R3BNeulandCluster`: Clusters consisting out of NeulandHits that belong together according to clustering conditions.
 - `R3BNeulandNeutron`: Position, Energy and Time information for neutron interactions found by event reconstruction processes
 
 
 ### Configuration Storage
 
 - `R3BNeulandGeoPar`: The complete NeuLAND GeoNode used in the Simulation
-- `R3BNeulandMultiplicityCalorimetricPar`: Cuts used for the [2D Method](#the-2d-method-for-neutron-multiplicity-determination) to determine neutron multiplicities.
+- `R3BNeulandMultiplicityCalorimetricPar`: Cuts used for the 2D Method to determine neutron multiplicities.
 
 
 ### Auxiliary Classes
 
 - `R3BNeulandContFact`: Container Factory for the configuration storage classes (pure boilerplate)
 - `R3BNeulandVisualizer`: 3D display of events, prepared by the `-Mon` tasks. (Work in progress)
-- [`Neuland::Neutron2DCalibr`](#calibration): Calibration of cuts for the 2D neutron multiplicity method
+- `Neuland::Neutron2DCalibr`: Calibration of cuts for the 2D neutron multiplicity method
 
 
 ## Digitizing