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| name: create-documentation | ||
| on: [workflow_dispatch] | ||
|
|
||
| jobs: | ||
| create-documentation: | ||
| 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 | ||
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||
| # 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 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 | ||
| tar -zcvf coverage.tar.gz coverageReport | ||
| - name: build documentation | ||
| run: | | ||
| cd build | ||
| make doc | ||
| 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 |
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| name: crpropa-example-test | ||
| on: [push, pull_request] | ||
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|
||
| jobs: | ||
| linux: | ||
| runs-on: ${{ matrix.config.os }} | ||
| 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 | ||
| steps: | ||
| - name: Checkout repository | ||
| 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 | ||
| 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 }} | ||
| CC: ${{ matrix.config.cc }} | ||
| FC: ${{ matrix.config.fc }} | ||
| run: | | ||
| mkdir build | ||
| cd build | ||
| cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local -DENABLE_PYTHON=True -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=Off -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native -DPython_INSTALL_PACKAGE_DIR=/home/runner/.local/ | ||
| - name: Build CRPropa | ||
| run: | | ||
| cd build | ||
| make install -j | ||
| - name: convert notebooks to python | ||
| env: | ||
| PYTHONPATH: "/home/runner/.local" | ||
| runfolder: "/home/runner/notebook_run" | ||
| run: | | ||
| mkdir "$runfolder" | ||
| cd doc/pages/example_notebooks/ | ||
| for file in */*.ipynb; do | ||
| echo "$file" | ||
| if [ -f "$file" ]; then | ||
| f=(${file//// }) | ||
| f=${f[1]} | ||
| f=(${f//./}) | ||
| finalFile="$runfolder"/"$f".py | ||
| echo "convert notebook $file to script $finalFile" | ||
| jupyter nbconvert --to python "$file" --stdout | grep -v -e "^get_ipython" > "$runfolder"/"$f".py | ||
| fi | ||
| done | ||
| - name: run all python scripts | ||
| env: | ||
| PYTHONPATH: "/home/runner/.local" | ||
| runfolder: "/home/runner/notebook_run" | ||
| run: | | ||
| cp doc/pages/example_notebooks/galactic_lensing/crpropa_output.txt "$runfolder"/ | ||
| cd "$runfolder" | ||
| for file in *.py; do | ||
| if [ "$file" = "custom-photon-fieldipynb.py" ] || | ||
| [ "$file" = "MHD_modelsipynb.py" ] || | ||
| [ "$file" = "density_grid_samplingipynb.py" ] || | ||
| [ "$file" = "lensing_crv4ipynb.py" ] || | ||
| [ "$file" = "lensing_mapsv4ipynb.py" ]; then | ||
| echo "skip file $file" | ||
| else | ||
| echo "run file $file" | ||
| python3 $file | ||
| fi | ||
| done |
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| @ARTICLE{crpropa3.2, | ||
| author = {{Alves Batista}, Rafael and {Becker Tjus}, Julia and {D{\"o}rner}, Julien and {Dundovic}, Andrej and {Eichmann}, Bj{\"o}rn and {Frie}, Antonius and {Heiter}, Christopher and {Hoerbe}, Mario R. and {Kampert}, Karl-Heinz and {Merten}, Lukas and {M{\"u}ller}, Gero and {Reichherzer}, Patrick and {Saveliev}, Andrey and {Schlegel}, Leander and {Sigl}, G{\"u}nter and {van Vliet}, Arjen and {Winchen}, Tobias}, | ||
| title = "{CRPropa 3.2 - an advanced framework for high-energy particle propagation in extragalactic and galactic spaces}", | ||
| journal = {Journal of Cosmology and Astroparticle Physics}, | ||
| year = 2022, | ||
| volume = {9}, | ||
| eid = {035}, | ||
| pages = {035}, | ||
| doi = {10.1088/1475-7516/2022/09/035}, | ||
| eprint = {2208.00107} | ||
| } | ||
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