Merge branch 'CRPropa:master' into new_bremsstrahlung

JulienDoerner · Jul 31, 2024 · 81fc529 · 81fc529
2 parents eb8c338 + beee8ad
commit 81fc529
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diff --git a/.github/workflows/create_coverage_report.yml b/.github/workflows/create_coverage_report.yml
@@ -0,0 +1,59 @@
+name: create-coverage-report
+on: [workflow_dispatch]
+
+jobs: 
+    create-coverage-report: 
+      runs-on: ubuntu-latest
+
+      strategy:
+        fail-fast: false
+        matrix:
+          config:
+            - name: "ubuntu-22"
+              os: ubuntu-22.04
+              cxx: "g++-11"
+              cc: "gcc-11"
+              fc: "gfortran-11"
+              swig_builtin: "On" #uses swig 4.0.2
+              py: "/usr/bin/python3" #python 3.10
+      # define steps to take
+      steps: 
+        - name: Checkout repository
+          uses: actions/checkout@v4
+        - name: Prerequirements
+          run: |
+            sudo apt-get update
+            sudo apt-get install libmuparser-dev libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov doxygen graphviz
+            sudo apt-get install pandoc # do not only use pip to install pandoc, see https://stackoverflow.com/questions/62398231/building-docs-fails-due-to-missing-pandoc
+            pip install -r doc/pages/example_notebooks/requirements.txt # load requirements for notebooks
+            pip install sphinx==7.2.6 sphinx_rtd_theme m2r2 nbsphinx lxml_html_clean breathe pandoc exhale # load requirements for documentation
+        - name: Set up the build
+          env:
+            CXX: ${{ matrix.config.cxx }}
+            CC: ${{ matrix.config.cc }}
+            FC: ${{ matrix.config.fc }}
+          run: |
+            mkdir build
+            cd build
+            cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local -DENABLE_PYTHON=True -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native -DPython_INSTALL_PACKAGE_DIR=/home/runner/.local/ -DBUILD_DOC=OFF -DENABLE_COVERAGE=On
+        - name: Build CRPropa
+          run: |
+            cd build
+            make -j
+        - name: run test
+          run: | 
+            cd build
+            make test
+          continue-on-error: true
+        - name: coverage report
+          run: |
+            cd build
+            make coverage
+            tar -zcvf coverage.tar.gz coverageReport
+        - name: archive documentation
+          uses: actions/upload-artifact@v4
+          with:
+            name: "coverage"
+            path: | 
+              build/coverage.tar.gz
+            
diff --git a/.github/workflows/create_documentation.yml b/.github/workflows/create_documentation.yml
@@ -9,29 +9,25 @@ jobs:
       fail-fast: false
       matrix:
         config:
-         - name: "ubuntu-20"
-           os: ubuntu-20.04
-           cxx: "g++-9"
-           cc: "gcc-9"
-           fc: "gfortran-9"
-           swig_builtin: "Off" #uses swig 4.0.1
+          - name: "ubuntu-22"
+            os: ubuntu-22.04
+            cxx: "g++-11"
+            cc: "gcc-11"
+            fc: "gfortran-11"
+            swig_builtin: "On" #uses swig 4.0.2
+            py: "/usr/bin/python3" #python 3.10
 
     # define steps to take
     steps: 
       - name: Checkout repository
-        uses: actions/checkout@v3
-      - name: Python install
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-          cache: 'pip' # caching pip dependencies
+        uses: actions/checkout@v4
       - name: Prerequirements
         run: |
           sudo apt-get update
           sudo apt-get install libmuparser-dev libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov doxygen graphviz
           sudo apt-get install pandoc # do not only use pip to install pandoc, see https://stackoverflow.com/questions/62398231/building-docs-fails-due-to-missing-pandoc
           pip install -r doc/pages/example_notebooks/requirements.txt # load requirements for notebooks
-          pip install sphinx sphinx_rtd_theme m2r2 nbsphinx breathe pandoc exhale # load requirements for documentation
+          pip install sphinx==7.2.6 sphinx_rtd_theme m2r2 nbsphinx lxml_html_clean breathe pandoc exhale # load requirements for documentation
       - name: Set up the build
         env:
           CXX: ${{ matrix.config.cxx }}
@@ -40,9 +36,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local \
-            -DENABLE_PYTHON=True -DENABLE_TESTING=ON -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \
-            -DSIMD_EXTENSIONS=native -DBUILD_DOC=True -DENABLE_COVERAGE=True
+          cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local -DENABLE_PYTHON=True -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native -DPython_INSTALL_PACKAGE_DIR=/home/runner/.local/ -DBUILD_DOC=On -DENABLE_COVERAGE=On
       - name: Build CRPropa
         run: |
           cd build
@@ -56,16 +50,15 @@ jobs:
         run: |
           cd build
           make coverage
-          tar -zcvf coverage.tar.gz coverageReport
       - name: build documentation
         run: |
           cd build
           make doc
-          tar -zcvf documentation.tar.gz doc
+          cp -r coverageReport doc/pages/coverageReport
+          tar -zcvf documentation.tar.gz doc  
       - name: archive documentation
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: "documentation"
           path: | 
             build/documentation.tar.gz
-            build/coverage.tar.gz
diff --git a/.github/workflows/deploy_new_documentation.yml b/.github/workflows/deploy_new_documentation.yml
@@ -0,0 +1,69 @@
+name: deploy-documentation
+on: 
+  push:
+    branches:
+      - main
+      - 'releases/**'
+
+jobs: 
+  build-and-deploy: 
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "ubuntu-22"
+            os: ubuntu-22.04
+            cxx: "g++-11"
+            cc: "gcc-11"
+            fc: "gfortran-11"
+            swig_builtin: "On" #uses swig 4.0.2
+            py: "/usr/bin/python3" #python 3.10
+
+    # define steps to take
+    steps: 
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Prerequirements
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmuparser-dev libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov doxygen graphviz
+          sudo apt-get install pandoc # do not only use pip to install pandoc, see https://stackoverflow.com/questions/62398231/building-docs-fails-due-to-missing-pandoc
+          pip install -r doc/pages/example_notebooks/requirements.txt # load requirements for notebooks
+          pip install sphinx==7.2.6 sphinx_rtd_theme m2r2 nbsphinx lxml_html_clean breathe pandoc exhale # load requirements for documentation
+      - name: Set up the build
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local -DENABLE_PYTHON=True -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native -DPython_INSTALL_PACKAGE_DIR=/home/runner/.local/ -DBUILD_DOC=On -DENABLE_COVERAGE=On
+      - name: Build CRPropa
+        run: |
+          cd build
+          make -j
+      - name: run test
+        run: | 
+          cd build
+          make test
+        continue-on-error: true
+      - name: coverage report
+        run: |
+          cd build
+          make coverage
+      - name: build documentation
+        run: |
+          cd build
+          make doc
+      - name: move final documentation # to avoid conflict with .gitignore
+        run: | 
+          mv build/doc ~/final_doc 
+          cp -r build/coverageReport ~/final_doc/pages/coverageReport
+      - name: deploy documentation #deploys the documentation to the gh-pages branch
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+            folder: ~/final_doc
+
diff --git a/.github/workflows/test_examples.yml b/.github/workflows/test_examples.yml
@@ -17,14 +17,13 @@ jobs:
            py: "/usr/bin/python3" #python 3.10
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Preinstall
         run: |
           sudo apt-get update
-          sudo apt-get install libmuparser-dev python3 python3-dev python3-numpy python3-setuptools python-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+          sudo apt-get install libmuparser-dev python3 python3-dev python3-setuptools python-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
           pip3 install -r doc/pages/example_notebooks/requirements.txt # load requrements for notebooks
           pip3 install --upgrade Pygments
-          pip3 install --upgrade numpy
       - name: Set up the build
         env:
           CXX: ${{ matrix.config.cxx }}

diff --git a/.github/workflows/testing_OSX.yml b/.github/workflows/testing_OSX.yml
@@ -16,7 +16,7 @@ jobs:
             py: "/usr/bin/python3"
     steps:
      - name: Checkout repository 
-       uses: actions/checkout@v3 
+       uses: actions/checkout@v4 
      - name: Preinstall 
        run: | 
          brew install hdf5 fftw cfitsio muparser libomp numpy swig
@@ -42,7 +42,7 @@ jobs:
          make test
      - name: Archive test results
        if: always()
-       uses: actions/upload-artifact@v3
+       uses: actions/upload-artifact@v4
        with:
          name: "test-report_${{matrix.config.name}}"
          path: build/Testing/Temporary/LastTest.log
diff --git a/.github/workflows/testing_ubuntu20.yml b/.github/workflows/testing_ubuntu20.yml
@@ -17,7 +17,7 @@ jobs:
            py: "/usr/bin/python3" #python 3.8
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Preinstall
         run: |
           sudo apt-get update
@@ -41,7 +41,7 @@ jobs:
           make test
       - name: Archive test results
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: "test-report_${{matrix.config.name}}"
           path: build/Testing/Temporary/LastTest.log
diff --git a/.github/workflows/testing_ubuntu22.yml b/.github/workflows/testing_ubuntu22.yml
@@ -17,7 +17,7 @@ jobs:
            py: "/usr/bin/python3" #python 3.10
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Preinstall
         run: |
           sudo apt-get update
@@ -41,7 +41,7 @@ jobs:
           make test
       - name: Archive test results
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: "test-report_${{matrix.config.name}}"
           path: build/Testing/Temporary/LastTest.log

diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,8 @@ lib/
 share/
 doc/api/
 
+!final_doc/ # needed for deployment of the documentation
+
 cmake/CMakeCache.txt
 cmake/CMakeFiles/
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,15 +1,20 @@
 ## CRPropa vNext
 
 ### Bug fixes:
- * Fixed sign for exponential decay of magn. field strength with Galactic height in LogarithmicSpiralField 
+ * Fixed sign for exponential decay of magn. field strength with Galactic height in LogarithmicSpiralField
+ * Fixed r term in source distribution for SNR and Pulsar
+ * Fixed wrong mass inheritance for secondaries other than nuclei or electron/positron
 
 ### New features:
+ * Added new backwards-compatible function particleMass that returns particle mass also for non-nuclei
+ * Added the new Galactic magnetic field models from Unger&Farrar arXiv:2311.12120
+ * Added EBL model from Finke et al. 2022
 
 ### Interface changes:
 
 ### Features that are deprecated and will be removed after this release
 
-### Removed features 
+### Removed features
 *  AMRMagneticField - underlying library (saga) is no longer supported.
 *  ObserverPoint: Use Observer1D instead.
 
@@ -38,8 +43,8 @@
 * ObserverPoint will be renamed into Observer1D.
 * AMRMagneticField - underlying library (saga) is no longer supported.
 
-### Removed features 
-* External extensions DINT and Eleca, which can be replaced with the 
+### Removed features
+* External extensions DINT and Eleca, which can be replaced with the
   EM*-modules combined with the thinning option for reasonable computation
   times.
 
@@ -48,20 +53,20 @@
 * grplinst
 * monopole
 * ROOTOutputPlugin
-  
+
 
 ## CRPropa 3.2
 
 ### Bug fixes:
 * Fix of reflective boundary condition for scalar- and vectorgrids
   that showed asymmetry and discontinuities (See issue [#361]).
 * Fix in EMTripletPairProduction
-* Fix of the data files of the Hackstein EGMF models as well as the 
+* Fix of the data files of the Hackstein EGMF models as well as the
   corresponding example notebook.
 * Fix of axis normalization of getRotated in Vector3.h.
 * Fix of secondary spectra in electromagnetic interactions
   (EM*-modules), issue [#334] and pull request [#15] in crpropa-data.
-* Fix weight inheritance for secondary particles; they are created with 
+* Fix weight inheritance for secondary particles; they are created with
   their parents weights as intial weights now.
 
 ### New features:
@@ -71,15 +76,15 @@
   and vectorgrids.
 * Add the new PolarizedSingleModeMagneticField class for polarized/
   helical single mode magnetic field models.
-* Add a source feature for targeted emission, following the 
+* Add a source feature for targeted emission, following the
   von-Mises-Fisher distribution
-* Updates in SNR and pulsar source distributions 
+* Updates in SNR and pulsar source distributions
 
 ### Interface changes:
-* Plane wave and grid turbulence models use same parameter convention now 
+* Plane wave and grid turbulence models use same parameter convention now
 
 ### Features that are deprecated and will be removed after this release
-* External extensions DINT and Eleca, which can be replaced with the 
+* External extensions DINT and Eleca, which can be replaced with the
   EM*-modules combined with the thinning option for reasonable computation
   times.
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -308,12 +308,12 @@ endif(APPLE)
 # Download data files (interaction data, masses, decay data ...)
 # ----------------------------------------------------------------------------
 OPTION(DOWNLOAD_DATA "Download CRPropa data files" ON)
-set(CRPROPA_DATAFILE_VER "2023-10-20")
+set(CRPROPA_DATAFILE_VER "2024-04-30")
 if(DOWNLOAD_DATA)
   message("-- Downloading data files from sciebo ~ 73 MB")
   file(DOWNLOAD
   https://ruhr-uni-bochum.sciebo.de/public.php/webdav/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM
-    ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM 
+    ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM
     USERPWD "3juW9sntQX2IWBS")
   file(STRINGS ${CMAKE_BINARY_DIR}/data-${CRPROPA_DATAFILE_VER}.tar.gz-CHECKSUM DATA_CHECKSUM LIMIT_COUNT 1 LENGTH_MINIMUM 32 LENGTH_MAXIMUM 32)
   file(DOWNLOAD
@@ -402,6 +402,7 @@ add_library(crpropa SHARED
   src/magneticField/turbulentField/PlaneWaveTurbulence.cpp
   src/magneticField/turbulentField/SimpleGridTurbulence.cpp
   src/magneticField/TF17Field.cpp
+  src/magneticField/UF23Field.cpp
   src/magneticField/CMZField.cpp
   src/advectionField/AdvectionField.cpp
   src/massDistribution/ConstantDensity.cpp
@@ -466,7 +467,7 @@ if(ENABLE_PYTHON AND Python_FOUND)
   endif(Python_Development_FOUND)
 
 
-  #  use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB 
+  #  use Python_INSTALL_PACKAGE_DIR if provided; otherwise, install in Python_SITELIB
   set(Python_INSTALL_PACKAGE_DIR "${Python_SITELIB}" CACHE PATH "folder in which the python package is installed")
   message(STATUS "  package install directory: ${Python_INSTALL_PACKAGE_DIR}")