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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-20" | ||
| os: ubuntu-20.04 | ||
| cxx: "g++-9" | ||
| cc: "gcc-9" | ||
| fc: "gfortran-9" | ||
| swig_builtin: "Off" #uses swig 4.0.1 | ||
|
|
||
| # 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 | ||
| - 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 | ||
| - 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 -DENABLE_TESTING=ON -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} \ | ||
| -DSIMD_EXTENSIONS=native -DBUILD_DOC=True -DENABLE_COVERAGE=True | ||
| - 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@v3 | ||
| with: | ||
| name: "documentation" | ||
| path: | | ||
| build/documentation.tar.gz | ||
| build/coverage.tar.gz |
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| name: crpropa-example-test | ||
| on: [push, pull_request] | ||
|
|
||
| jobs: | ||
| linux: | ||
| runs-on: ${{ matrix.config.os }} | ||
| strategy: | ||
| 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 | ||
| py: "/usr/bin/python3" #python 3.8 | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
| - name: Preinstall | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install libmuparser-dev python3-dev python-dev python3-numpy python-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 | ||
| - name: Build CRPropa | ||
| run: | | ||
| cd build | ||
| make install -j | ||
| - name: convert notebooks to python | ||
| env: | ||
| PYTHONPATH: "/home/runner/.local/lib/python3.8/site-packages/" | ||
| 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: "$/home/runner/.local/lib/python3.8/site-packages/" | ||
| runfolder: "/home/runner/notebook_run" | ||
| run: | | ||
| cp doc/pages/example_notebooks/galactic_lensing/crpropa_output.txt "$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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11 changes: 11 additions & 0 deletions
11
doc/pages/example_notebooks/galactic_lensing/crpropa_output.txt
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| # taken from https://github.com/CRPropa/CRPropa3/blob/2577c47ad898db13ce3b17c153e700041f304da4/galactic_lensing/crpropa_output.txt | ||
| 1552.209 1000010010 1000260560 6.3094 1137.0405 118.8033 117.3283 120.0056 198.3873 -48.1072 250.9588 0.23085 0.06390 -0.97089 -0.76661 0.63718 -0.07947 0.000 | ||
| 1553.387 1000010010 1000260560 6.3049 1137.0405 119.3010 117.8840 119.3933 198.3873 -48.1072 250.9588 -0.52969 0.57890 -0.61993 -0.76661 0.63718 -0.07947 0.000 | ||
| 1552.209 1000010010 1000260560 6.3094 1137.0405 118.8033 117.3283 120.0056 198.3873 -48.1072 250.9588 0.23085 0.06390 -0.97089 -0.76661 0.63718 -0.07947 0.000 | ||
| 1553.387 1000010010 1000260560 6.3049 1137.0405 119.3010 117.8840 119.3933 198.3873 -48.1072 250.9588 -0.52969 0.57890 -0.61993 -0.76661 0.63718 -0.07947 0.000 | ||
| 2507.574 1000010010 1000020040 5.7274 157.5835 119.0234 117.9255 118.5094 64.1676 230.1578 58.0133 -0.24543 -0.93458 -0.25754 -0.21277 0.71704 -0.66376 0.000 | ||
| 597.459 1000010010 1000260560 9.6493 869.9225 119.0855 117.4122 119.7995 161.5538 74.8338 161.2846 -0.80199 0.46811 0.37105 -0.20573 0.14302 0.96810 0.000 | ||
| 1059.588 1000010010 1000260560 17.2427 7507.9875 118.9984 117.3895 118.5193 332.7822 143.8280 378.0030 -0.19054 0.28077 0.94067 -0.18628 0.64559 -0.74061 0.000 | ||
| 1342.343 1000010010 1000010010 17.7414 135.4199 118.9361 118.4267 118.8868 125.1438 25.9860 115.6526 0.01002 -0.98594 -0.16682 0.04910 -0.03836 -0.99806 0.000 | ||
| 140.527 1000010010 1000070140 50.7971 6946.8090 117.6596 117.8698 119.9085 173.0595 28.5316 197.1513 -0.17251 0.29795 -0.93886 -0.18122 0.95242 -0.24506 0.000 | ||
| 792.198 1000010010 1000070140 23.8203 765.9928 118.0031 117.7912 118.2653 221.2443 140.1373 120.6517 0.97493 0.06808 -0.21183 0.79843 0.58276 0.15130 0.000 |
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|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| # collection of all packages used in the analyis of the example notebooks. This is used for the automatic test of the notebooks | ||
| numpy | ||
| matplotlib | ||
| pandas | ||
| healpy | ||
| seaborn | ||
| scipy | ||
| tqdm | ||
| h5py | ||
| jupyter |
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