Actions

.github/workflows/create_documentation.yml

@@ -0,0 +1,70 @@
+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
+           py: "/usr/bin/python3" #python 3.8
+
+    # 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 
+          pip install -r doc/pages/example_notebooks/requirements.txt # load requrements for notebooks
+      - 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
+            -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 and documentation
+        run: |
+          cd build
+          make coverage
+          tar -zcvf coverage.tar.gz coverageReport
+          make doc
+          tar -zcvf documentation.tar.gz doc
+      - name: archive documentation
+        uses: actions/upload-artifact@v3
+        with:
+          name: "documentation.tar.gz"
+          path: | 
+            documentation.tar.gz
+            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: "$/home/runner/.local/lib/python3.8/site-packages/"
+          runfolder: "/home/runner/notebook_run"
+        run: | 
+          cd "$runfolder"
+          function skip() { # this notebooks have external dependencies and can not be tested
+            if [ "$1" = "custom-photon-fieldipynb.py" ] || [ "$1" = "MHD_modelsipynb.py" ] || [ "$1" = "density_grid_samplingipynb.py" ]; then
+              return 1
+            fi
+            return 0
+          }
+          for file in *.py; do
+            echo "work on file $file"
+            skip "$file"
+            if [ $? -eq 0 ]; then
+                python3 "$file"
+            fi
+          done

.github/workflows/testing.yml

@@ -1,5 +1,5 @@
 name: crpropa-testing
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   linux:

.github/workflows/testing_OSX.yaml

@@ -29,7 +29,7 @@ jobs:
        run: |
         mkdir build
         cd build
-        cmake .. -DENABLE_PYTHON=True -DPYTHON_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=avx
+        cmake .. -DENABLE_PYTHON=False -DENABLE_TESTING=On -DSIMD_EXTENSIONS=avx -DENABLE_HDF5=OFF -DENABLE_GALACTICMAGETICLENS=OFF
      - name: Build CRPropa
        run: |
          cd build
@@ -39,7 +39,7 @@ jobs:
          CRPROPA_DATA_PATH: "/Users/runner/work/CRPropa3/CRPropa3/build/data"
        run: |
          cd build
-         make test
+         ./testInteraction
      - name: Archive test results
        if: always()
        uses: actions/upload-artifact@v3

.github/workflows/testing_ubuntu22.yml

@@ -1,5 +1,5 @@
 name: crpropa-testing_ubuntu22
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   linux:

doc/pages/example_notebooks/basics/failing.ipynb

@@ -0,0 +1,53 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "RuntimeError",
+     "evalue": "this notebook should not succeed",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
+      "\u001b[1;32m/home/home1/jdo/CRPropa3/doc/pages/example_notebooks/basics/faining.ipynb Zelle 1\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell://ssh-remote%2Bk10/home/home1/jdo/CRPropa3/doc/pages/example_notebooks/basics/faining.ipynb#W0sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m \u001b[39mraise\u001b[39;00m \u001b[39mRuntimeError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mthis notebook should not succeed\u001b[39m\u001b[39m\"\u001b[39m)\n",
+      "\u001b[0;31mRuntimeError\u001b[0m: this notebook should not succeed"
+     ]
+    }
+   ],
+   "source": [
+    "raise RuntimeError(\"this notebook should not succeed\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

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

test/testInteraction.cpp

@@ -16,9 +16,11 @@
 #include "gtest/gtest.h"
 
 #include <fstream>
+#include <vector>
 
 namespace crpropa {
 
+/*
 // ElectronPairProduction -----------------------------------------------------
 TEST(ElectronPairProduction, allBackgrounds) {
 	// Test if interaction data files are loaded.
@@ -694,7 +696,7 @@ TEST(Redshift, limitRedshiftDecrease) {
 	redshift.process(&c);
 	EXPECT_DOUBLE_EQ(0, c.getRedshift());
 }
-
+*/
 // EMPairProduction -----------------------------------------------------------
 TEST(EMPairProduction, allBackgrounds) {
 	// Test if interaction data files are loaded.
@@ -735,44 +737,64 @@ TEST(EMPairProduction, limitNextStep) {
 }
 
 TEST(EMPairProduction, secondaries) {
+	std::cout << "start with the test \n";
 	// Test if secondaries are correctly produced.
 	ref_ptr<PhotonField> CMB_instance = new CMB();
 	ref_ptr<PhotonField> IRB = new IRB_Gilmore12();
 	ref_ptr<PhotonField> URB = new URB_Protheroe96();
+	std::cout << "photon field instances created \n";
 	EMPairProduction m(CMB_instance);
 	m.setHaveElectrons(true);
 	m.setThinning(0.);
 
 	std::vector< ref_ptr<PhotonField> > fields;
+	std::cout << "created photon field list \n add ";
 	fields.push_back(CMB_instance);
+	std::cout << "first";
 	fields.push_back(IRB);
+	std::cout << " / second";
 	fields.push_back(URB);
+	std::cout << " / thrid field to list\n";
+	std::cout << "have in total " << fields.size() << "fields\n";
 
 	// loop over photon backgrounds
 	for (int f = 0; f < fields.size(); f++) {
-		m.setPhotonField(fields[f]);
+		std::cout << "start loop f = " << f << "\n";
+		ref_ptr<PhotonField> field = fields[f];
+		std::cout << "got Photonfield \n";
+		m.setPhotonField(field);
+		std::cout << "give photonfield to model \n";
 		for (int i = 0; i < 140; i++) { // loop over energies Ep = (1e10 - 1e23) eV
 			double Ep = pow(10, 9.05 + 0.1 * i) * eV;
 			Candidate c(22, Ep);
+			EXPECT_TRUE(c.isActive()); // new candidate is always active
+
 			//c.setCurrentStep(std::numeric_limits<double>::max());
 			c.setCurrentStep(1e10 * Mpc);
 			m.process(&c);
-
+			std::cout << "i = " << i << " processed the candidate. Candidate is now ";
 			// pass if no interaction has occured (no tabulated rates)
-			if (c.isActive())
+			if (c.isActive()) {
+				std::cout << "active\n";
 				continue;
+			}
+
+			std::cout << "inactive and has "  << c.secondaries.size() << "secondaries \n"; 
 
 			// expect 2 secondaries
 			EXPECT_EQ(c.secondaries.size(), 2);
 
+			std::cout << "no. of secondaries is " << c.secondaries.size() << "\n";
+
 			// expect electron / positron with energies 0 < E < Ephoton
 			double Etot = 0;
 			for (int j = 0; j < c.secondaries.size(); j++) {
-				Candidate s = *c.secondaries[j];
-				EXPECT_EQ(abs(s.current.getId()), 11);
-				EXPECT_GT(s.current.getEnergy(), 0);
-				EXPECT_LT(s.current.getEnergy(), Ep);
-				Etot += s.current.getEnergy();
+				ref_ptr<Candidate> s = c.secondaries[j];
+				std::cout << "\t secondary #" << j << " works \n"; 
+				EXPECT_EQ(abs(s->current.getId()), 11);
+				EXPECT_GT(s->current.getEnergy(), 0);
+				EXPECT_LT(s->current.getEnergy(), Ep);
+				Etot += s->current.getEnergy();
 			}
 
 			// test energy conservation