Merge pull request CRPropa#461 from JulienDoerner/actions_clean

Update Github Actions

.github/workflows/create_documentation.yml

@@ -0,0 +1,71 @@
+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

.github/workflows/test_examples.yml

@@ -0,0 +1,77 @@
+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

doc/pages/example_notebooks/galactic_lensing/crpropa_output.txt

@@ -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

doc/pages/example_notebooks/requirements.txt

@@ -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