Merge pull request #481 from JulienDoerner/documentation

Add coverage report to documentation
CRPropa · Jun 4, 2024 · a6dbe04 · a6dbe04
2 parents 95ff182 + 7d4d84d
commit a6dbe04
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Showing 6 changed files with 137 additions and 7 deletions.
diff --git a/.github/workflows/create_coverage_report.yml b/.github/workflows/create_coverage_report.yml
@@ -0,0 +1,59 @@
+name: create-coverage-report
+on: [workflow_dispatch]
+
+jobs: 
+    create-coverage-report: 
+      runs-on: ubuntu-latest
+
+      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
+      # define steps to take
+      steps: 
+        - name: Checkout repository
+          uses: actions/checkout@v4
+        - 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==7.2.6 sphinx_rtd_theme m2r2 nbsphinx lxml_html_clean 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 -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native -DPython_INSTALL_PACKAGE_DIR=/home/runner/.local/ -DBUILD_DOC=OFF -DENABLE_COVERAGE=On
+        - 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: archive documentation
+          uses: actions/upload-artifact@v4
+          with:
+            name: "coverage"
+            path: | 
+              build/coverage.tar.gz
+            
diff --git a/.github/workflows/create_documentation.yml b/.github/workflows/create_documentation.yml
@@ -27,7 +27,7 @@ jobs:
           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 lxml_html_clean breathe pandoc exhale # load requirements for documentation
+          pip install sphinx==7.2.6 sphinx_rtd_theme m2r2 nbsphinx lxml_html_clean breathe pandoc exhale # load requirements for documentation
       - name: Set up the build
         env:
           CXX: ${{ matrix.config.cxx }}
@@ -50,16 +50,15 @@ jobs:
         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
+          cp -r coverageReport doc/pages/coverageReport
+          tar -zcvf documentation.tar.gz doc  
       - name: archive documentation
         uses: actions/upload-artifact@v4
         with:
           name: "documentation"
           path: | 
             build/documentation.tar.gz
-            build/coverage.tar.gz
diff --git a/.github/workflows/deploy_new_documentation.yml b/.github/workflows/deploy_new_documentation.yml
@@ -0,0 +1,69 @@
+name: deploy-documentation
+on: 
+  push:
+    branches:
+      - main
+      - 'releases/**'
+
+jobs: 
+  build-and-deploy: 
+    runs-on: ubuntu-latest
+
+    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
+
+    # define steps to take
+    steps: 
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - 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==7.2.6 sphinx_rtd_theme m2r2 nbsphinx lxml_html_clean 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 -DPython_EXECUTABLE=${{ matrix.config.py }} -DENABLE_TESTING=On -DENABLE_SWIG_BUILTIN=${{ matrix.config.swig_builtin }} -DSIMD_EXTENSIONS=native -DPython_INSTALL_PACKAGE_DIR=/home/runner/.local/ -DBUILD_DOC=On -DENABLE_COVERAGE=On
+      - 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
+      - name: build documentation
+        run: |
+          cd build
+          make doc
+      - name: move final documentation # to avoid conflict with .gitignore
+        run: | 
+          mv build/doc ~/final_doc 
+          cp -r build/coverageReport ~/final_doc/pages/coverageReport
+      - name: deploy documentation #deploys the documentation to the gh-pages branch
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+            folder: ~/final_doc
+
diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,8 @@ lib/
 share/
 doc/api/
 
+!final_doc/ # needed for deployment of the documentation
+
 cmake/CMakeCache.txt
 cmake/CMakeFiles/
 

diff --git a/doc/index.rst b/doc/index.rst
@@ -43,10 +43,8 @@ Contents
 
 .. toctree::
    :caption: DEVEL
-   :maxdepth: 1
+   :maxdepth: 2
 
    pages/Debugging.md
    pages/Code-Coverage.md
    pages/Data-files.md
-
-
diff --git a/doc/pages/Code-Coverage.md b/doc/pages/Code-Coverage.md
@@ -16,3 +16,6 @@ make test
 make coverage
 ```
 The final report is in ```~/build/coverageReport/index.html```
+
+### Coverage report of the current master branch
+The coverage report of the current master branch can be accesed `by clicking here <coverageReport/index.html>`_ now.