Merge remote-tracking branch 'master/master' into cringe_reproduction

JulienDoerner · Nov 8, 2024 · ec64d2f · ec64d2f
2 parents 7ffbf70 + 61a6257
commit ec64d2f
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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
@@ -27,7 +27,7 @@ jobs:
           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 }}
@@ -50,16 +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@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
@@ -21,10 +21,9 @@ jobs:
       - 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
@@ -11,15 +11,16 @@ jobs:
             os: macos-14 
             cxx: "clang++"
             cc: "clang"
-            fc: "gfortran-11"
+            fc: "gfortran-14"
             swig_builtin: "On" #uses swig 4.0.2
             py: "/usr/bin/python3"
     steps:
      - name: Checkout repository 
        uses: actions/checkout@v4 
      - name: Preinstall 
        run: | 
-         brew install hdf5 fftw cfitsio muparser libomp numpy swig
+         brew install hdf5 fftw cfitsio muparser libomp swig
+         pip install numpy==1.26
      - name: Set up the build
        env:
          CXX: ${{ matrix.config.cxx }}

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
@@ -1,17 +1,20 @@
 ## CRPropa vNext
 
 ### Bug fixes:
- * 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 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
- * EBL model from Finke et al. 2022
 
-### Removed features 
+### Removed features
 *  AMRMagneticField - underlying library (saga) is no longer supported.
 *  ObserverPoint: Use Observer1D instead.
 
@@ -40,8 +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.
 
@@ -50,20 +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:
@@ -73,15 +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 "2024-03-11")
+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
@@ -403,6 +403,7 @@ 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
@@ -467,7 +468,7 @@ 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}")
 

diff --git a/doc/index.rst b/doc/index.rst
@@ -43,10 +43,8 @@ Contents
 
 .. toctree::
    :caption: DEVEL
-   :maxdepth: 1
+   :maxdepth: 2
 
    pages/Debugging.md
    pages/Code-Coverage.md
    pages/Data-files.md
-
-
diff --git a/doc/pages/Code-Coverage.md b/doc/pages/Code-Coverage.md
@@ -16,3 +16,6 @@ make test
 make coverage
 ```
 The final report is in ```~/build/coverageReport/index.html```
+
+### Coverage report of the current master branch
+The coverage report of the current master branch can be accesed `by clicking here <coverageReport/index.html>`_ now.
diff --git a/doc/pages/example_notebooks/density/density_grid_sampling.ipynb b/doc/pages/example_notebooks/density/density_grid_sampling.ipynb
diff --git a/doc/pages/example_notebooks/galactic_backtracking/galactic_backtracking.ipynb b/doc/pages/example_notebooks/galactic_backtracking/galactic_backtracking.ipynb
@@ -38,6 +38,7 @@
     "\n",
     "# magnetic field setup\n",
     "B = JF12Field()\n",
+    "#B = UF23Field(UF23Field.base) # options: base,neCL,expX,spur,cre10,synCG,twistX,nebCor \n",
     "#seed = 691342\n",
     "#B.randomStriated(seed)\n",
     "#B.randomTurbulent(seed)\n",

diff --git a/doc/pages/example_notebooks/requirements.txt b/doc/pages/example_notebooks/requirements.txt
@@ -1,5 +1,5 @@
 # collection of all packages used in the analyis of the example notebooks. This is used for the automatic test of the notebooks
-numpy
+numpy==1.26.4 
 matplotlib
 pandas
 healpy

diff --git a/include/CRPropa.h b/include/CRPropa.h
@@ -65,6 +65,7 @@
 #include "crpropa/magneticField/PT11Field.h"
 #include "crpropa/magneticField/QuimbyMagneticField.h"
 #include "crpropa/magneticField/TF17Field.h"
+#include "crpropa/magneticField/UF23Field.h"
 #include "crpropa/magneticField/CMZField.h"
 #include "crpropa/magneticField/turbulentField/GridTurbulence.h"
 #include "crpropa/magneticField/turbulentField/HelicalGridTurbulence.h"