Setup PR tests

.github/actions/build_code/action.yml

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+name: "Build code"
+
+inputs:
+  toolchain:
+    description: "The toolchain that describes the parameters for cmake"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Compile code
+      run: |
+        mkdir build
+        cd build
+        cmake -DCMAKE_TOOLCHAIN=../toolchains/docker.gyselalibxx_env/${{ matrix.toolchain }} ..
+        cmake --build .
+      shell: bash
+

.github/actions/run_tests/action.yml

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+name: "Run tests"
+
+runs:
+  using: "composite"
+  steps:
+    - name: "Run tests"
+      run: |
+        ctest -j 2 --timeout 5 --output-junit tests.xml
+      shell: bash
+      working-directory:
+        ./build
+    - name: Publish Test Report
+      uses: mikepenz/action-junit-report@v4
+      if: success() || failure() # always run even if the previous step fails
+      with:
+        report_paths: './build/test.xml'

.github/actions/test_filter/action.yml

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+name: "Filter tests"
+
+inputs:
+  base:
+    description: "The SHA or branch of the PR base"
+    required: true
+  trigger_type:
+    description: "The SHA of the PR base"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+  - name: "Fetch reference case"
+    run: |
+      git config --global --add safe.directory $(pwd)
+      git fetch --no-recurse-submodules origin ${{ inputs.base }}
+    shell: bash
+  - name: "Get changed files"
+    if: inputs.trigger_type == 'workflow_call'
+    run: |
+      git diff --name-only ${{ inputs.base }} > changed_files.txt  
+    shell: bash
+  - name: "Get changed files"
+    if: inputs.trigger_type == 'workflow_dispatch'
+    run: |
+      base_sha=$(git log -1 ${{ inputs.base }} --pretty=%H)
+      git diff --name-only ${base_sha} > changed_files.txt  
+    shell: bash
+  - name: "Check filters"
+    run: |
+      FOUND_SLL=$(grep "vendor/sll/.*" -x changed_files.txt || true)
+      if [ -z "$FOUND_SLL" ]; then echo "SLL_BUILD_TESTING=OFF" >> $GITHUB_ENV; else echo "SLL_BUILD_TESTING=ON" >> $GITHUB_ENV; fi
+      FOUND_POISSON_2D=$(grep "src/geometryRTheta/poisson/.*" -x changed_files.txt || true)
+      if [ -z "$FOUND_POISSON_2D" ]; then echo "POISSON_2D_BUILD_TESTING=OFF" >> $GITHUB_ENV; else echo "POISSON_2D_BUILD_TESTING=ON" >> $GITHUB_ENV; fi
+      FOUND_DDC=$(grep "vendor/ddc" changed_files.txt || true)
+      if [ -z "$FOUND_DDC" ]; then echo "DDC_BUILD_TESTING=OFF" >> $GITHUB_ENV; else echo "DDC_BUILD_TESTING=ON" >> $GITHUB_ENV; fi
+    shell: bash
+

.github/workflows/cpu_tests.yml

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+name: CPU acceptance tests
+
+on:
+  workflow_dispatch:
+    inputs:
+      toolchain:
+        description: "Tool chain to use for test"
+        required: true
+        type: choice
+        options:
+          - tests_toolchain.cmake
+          - tests_release_toolchain.cmake
+          - tests_release_omp_toolchain.cmake
+      merge_target:
+        description: "The branch to which this branch should be compared to filter out costly tests (default: main)"
+        required: false
+        default: main
+        type: string
+  workflow_call:
+    inputs:
+      toolchain:
+        description: "Tool chain to use for test"
+        required: true
+        type: string
+      merge_target:
+        description: "The branch to which this branch should be compared to filter out costly tests (default: main)"
+        required: true
+        type: string
+
+jobs:
+  cpu_tests:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/gyselax/gyselalibxx_env:latest
+      options: --user root
+    name: CPU Test (${{ inputs.toolchain }})
+    steps:
+      - name: Checkout gyselalibxx
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: "Filter tests"
+        uses: ./github/actions/test_filter
+        with:
+          base_sha: ${{ inputs.merge_target }}
+          trigger_type: ${{ github.event_name }}
+      - name: Build code
+        uses: ./github/actions/build_code
+        with:
+          toolchain: ${{ inputs.toolchain }}
+      - name: Run tests
+        uses: ./github/actions/run_tests

.github/workflows/deploy.yml

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+name: Deploy
+
+on:
+  push:
+    branches:
+    - 'main'
+
+
+jobs:
+  docker:
+    if: github.repository == 'gyselax/gyselalibxx'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Build and push to tag
+        uses: docker/build-push-action@v3
+        with:
+          context: ./docker/gyselalibxx_env
+          cache-from: type=registry,ref=ghcr.io/gyselax/gyselalibxx_env:latest
+          pull: true
+          push: true
+          tags: ghcr.io/gyselax/gyselalibxx_env:${{ inputs.SHA }}
+      - name: Build and push latest
+        uses: docker/build-push-action@v3
+        with:
+          context: ./docker/gyselalibxx_env
+          cache-from: type=registry,ref=ghcr.io/gyselax/gyselalibxx_env:latest
+          pull: true
+          push: true
+          tags: ghcr.io/gyselax/gyselalibxx_env:latest
+
+  Docs:
+    needs: docker
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          path: code_branch
+      - name: Checkout documentation
+        uses: actions/checkout@v4
+        with:
+          ref: documentation
+          path: doc_branch
+      - name: Install doxygen
+        run: |
+          sudo apt install doxygen
+        shell: bash
+      - name: Generate docs
+        run: |
+          cmake -DGYSELALIBXX_COMPILE_SOURCE=OFF -DBUILD_DOCUMENTATION=1 -B build-docs code_branch
+          cmake --build build-docs
+        shell: bash
+      - name: Update documentation
+        run: |
+          cd doc_branch
+          git rm -r *
+          cp -r ../build-docs/docs/html/* .
+          git add .
+          git config --global user.name "GitHub CI Documentation builder"
+          git config --global user.email "username@users.noreply.github.com"
+          git commit -m "Update docs" || true
+          git push
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}

.github/workflows/gpu_tests.yml

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+name: GPU acceptance tests
+
+on:
+  workflow_dispatch:
+    inputs:
+      toolchain:
+        description: "Tool chain to use for test"
+        required: true
+        type: choice
+        options:
+          - tests_toolchain.cmake
+          - tests_release_toolchain.cmake
+          - tests_release_omp_toolchain.cmake
+      merge_target:
+        description: "The branch to which this branch should be compared to filter out costly tests (default: main)"
+        required: false
+        default: main
+        type: string
+  workflow_call:
+    inputs:
+      toolchain:
+        description: "Tool chain to use for test"
+        required: true
+        type: string
+      merge_target:
+        description: "The branch to which this branch should be compared to filter out costly tests (default: main)"
+        required: true
+        type: string
+
+jobs:
+  gpu_tests:
+    runs-on: self-hosted
+    environment: development
+    steps:
+      - name: Checkout gyselalibxx
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: "Filter tests"
+        uses: ./github/actions/test_filter
+        with:
+          base: ${{ inputs.merge_target }}
+          trigger_type: ${{ github.event_name }}
+      - name: Setup environment
+        run: |
+          . toolchains/v100.persee/environment.sh
+        shell: bash
+      - name: Build code
+        uses: ./github/actions/build_code
+        with:
+          toolchain: toolchains/v100.persee/toolchain.cmake
+      - name: Run tests
+        uses: ./github/actions/run_tests

.github/workflows/static_analyses.yml

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+name: Static Analyses
+
+on:
+  pull_request:
+    branches: [ "main" ]
+  merge_group:
+    types: [checks_requested]
+
+jobs:
+  Indentation:
+    name: Clang Formatting Check
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/gyselax/gyselalibxx_env
+      options: --user 1001
+    steps:
+      - uses: actions/checkout@v4
+      - shell: bash
+        run: |
+          ./bin/indent -td
+
+  Markdown:
+    name: Markdown format check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Get Python dependencies
+        run: |
+          pip install numpy
+      - name: Check files
+        id: markdown
+        continue-on-error: true
+        shell: bash
+        run: |
+          MARKDOWN_FILES=$(find . -name "*.md" -not -path "./vendor/*")
+          MARKDOWN_FILES="$MARKDOWN_FILES $(find ./vendor/sll/ -name '*.md')"
+          echo $MARKDOWN_FILES
+          python3 ci_tools/markdown_linter.py ${MARKDOWN_FILES}
+          echo "EXIT_CODE=$?" >> $GITHUB_OUTPUT
+      - name: Check error code
+        shell: python
+        run: |
+          assert ${{ steps.markdown.outputs.EXIT_CODE }} in (0, 2)
+
+  Python:
+    name: Python Best Practices
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/gyselax/gyselalibxx_env
+      options: --user 1001
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Run pylint
+        run: |
+          pylint $(find tests -iname *.py)
+          pylint $(find doc -iname *.py)
+          pylint $(find ci_tools -iname *.py)
+        shell: bash
+        env:
+          PYTHONPATH: ./post-process/PythonScripts
+      - name: Run filtered pylint
+        run: |
+          # Find all files with no extension or a .py extension in post-process/PythonScripts/
+          POST_PROCESS_PYTHON_FILES=$(find post-process/PythonScripts/ -type f ! -name "*.*"; find post-process/PythonScripts -iname *.py)
+          # Get pylint errors without failing
+          pylint ${POST_PROCESS_PYTHON_FILES} > post_process_errors.txt || true
+          # Filter errors on changed files
+          for f in $(git diff ${{ github.event.pull_request.base.sha }} --name-only); do grep $f post_process_errors.txt || true; done | tee filtered_errors.txt
+          # Raise an error if post-process in filtered errors
+          ! grep "post-process" filtered_errors.txt >/dev/null
+        shell: bash
+        env:
+          PYTHONPATH: ./post-process/PythonScripts
+
+  Documentation:
+    name: Documentation check
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/gyselax/gyselalibxx_env
+      options: --user 1001
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+      - name: Make documenation
+        run: |
+          # Make docs
+          mkdir build
+          cd build
+          cmake -DBUILD_DOCUMENTATION=ON ..
+          make doc
+          cd ..
+        shell: bash
+      - name: Check for new errors
+        run: |
+          # Get files which have changed in this merge request
+          git diff ${{ github.event.pull_request.base.sha }}..${{ github.event.pull_request.head.sha }} --no-indent-heuristic --unified=0 --output=pull_diff.txt --no-color
+          # Filter documentation messages to only complain about modified files
+          python3 ci_tools/check_documentation.py pull_diff.txt build/docs/doxygen.log
+          git diff ${{ github.event.pull_request.base.sha }}..${{ github.event.pull_request.head.sha }} --no-indent-heuristic --unified=0 --output=pull_new_files.txt --no-color --diff-filter=A
+          python3 ci_tools/check_readme_presence.py pull_new_files.txt
+        shell: bash
+