Merge branch 'master' into new_bremsstrahlung

JulienDoerner · Mar 19, 2024 · eb8c338 · eb8c338
2 parents 422b808 + 76fef90
commit eb8c338
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diff --git a/.github/workflows/create_documentation.yml b/.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
diff --git a/.github/workflows/test_examples.yml b/.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-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@v3
+      - 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
diff --git a/.github/workflows/testing_OSX.yml b/.github/workflows/testing_OSX.yml
@@ -0,0 +1,48 @@
+name: crpropa-testing_OSX
+on: [push, pull_request]
+jobs:
+  mac:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "macos-14"
+            os: macos-14 
+            cxx: "clang++"
+            cc: "clang"
+            fc: "gfortran-11"
+            swig_builtin: "On" #uses swig 4.0.2
+            py: "/usr/bin/python3"
+    steps:
+     - name: Checkout repository 
+       uses: actions/checkout@v3 
+     - name: Preinstall 
+       run: | 
+         brew install hdf5 fftw cfitsio muparser libomp numpy swig
+     - name: Set up the build
+       env:
+         CXX: ${{ matrix.config.cxx }}
+         CC: ${{ matrix.config.cc }}
+         FC: ${{ matrix.config.fc }}
+         CRPROPA_DATA_PATH: "/Users/runner/work/CRPropa3/CRPropa3/build/data"
+       run: |
+        mkdir build
+        cd build
+        cmake .. -DENABLE_PYTHON=True  -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS="none"
+     - name: Build CRPropa
+       run: |
+         cd build
+         make
+     - name: Run tests
+       env:
+         CRPROPA_DATA_PATH: "/Users/runner/work/CRPropa3/CRPropa3/build/data"
+       run: |
+         cd build
+         make test
+     - name: Archive test results
+       if: always()
+       uses: actions/upload-artifact@v3
+       with:
+         name: "test-report_${{matrix.config.name}}"
+         path: build/Testing/Temporary/LastTest.log
diff --git a/.github/workflows/testing_ubuntu20.yml b/.github/workflows/testing_ubuntu20.yml
@@ -0,0 +1,47 @@
+name: crpropa-testing_ubuntu20
+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
+      - name: Set up the build
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On  -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
+      - name: Build CRPropa
+        run: |
+          cd build
+          make
+      - name: Run tests
+        run: |
+          cd build
+          make test
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: "test-report_${{matrix.config.name}}"
+          path: build/Testing/Temporary/LastTest.log
diff --git a/.github/workflows/testing_ubuntu22.yml b/.github/workflows/testing_ubuntu22.yml
@@ -0,0 +1,48 @@
+name: crpropa-testing_ubuntu22
+on: [push, pull_request]
+
+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@v3
+      - name: Preinstall
+        run: |
+          sudo apt-get update
+          sudo apt-get install libmuparser-dev python3 python3-numpy python3-setuptools libhdf5-serial-dev libomp5 libomp-dev libfftw3-dev libcfitsio-dev lcov
+      - name: Set up the build
+        env:
+          CXX: ${{ matrix.config.cxx }}
+          CC: ${{ matrix.config.cc }}
+          FC: ${{ matrix.config.fc }}
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DENABLE_PYTHON=True -DENABLE_TESTING=On -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native
+      - name: Build CRPropa
+        run: |
+          cd build
+          make
+      - name: Run tests
+        run: |
+          cd build
+          make test
+      - name: Archive test results
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: "test-report_${{matrix.config.name}}"
+          path: build/Testing/Temporary/LastTest.log
+
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,3 @@
-.*
-!.travis.yml
-
 *~
 
 build*
@@ -14,6 +11,7 @@ bin/
 install/
 lib/
 share/
+doc/api/
 
 cmake/CMakeCache.txt
 cmake/CMakeFiles/