add some notebooks to skip #34
Workflow file for this run
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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: "$/home/runner/.local/lib/python3.8/site-packages/" | |
| runfolder: "/home/runner/notebook_run" | |
| run: | | |
| cd "$runfolder" | |
| export skipping_nb=" # this notebooks are skipped due to external dependencies | |
| mhd_modelsipynb.py | |
| custom-photon-fieldipynb.py" | |
| function no-skip() { | |
| for f in (${skipping_nb// / }); do | |
| if [ "$f" == "$1"]; then | |
| return 1 | |
| fi | |
| done | |
| return 0 | |
| } | |
| for file in *.py; do | |
| if [ -f "$file" ] && [ no-skip "$file" == 0]; then | |
| echo "run file $file" | |
| python3 "$file" | |
| fi | |
| done | |