Merge pull request #1 from KrisThielemans/firstVersion

First version

.clang-format

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+---
+BasedOnStyle : GNU
+---
+Language : Cpp
+FixNamespaceComments: true
+AlwaysBreakAfterReturnType: TopLevelDefinitions
+AlwaysBreakTemplateDeclarations: true
+# Set BraceWrapping. Most of these are GNU but not all.
+# Sadly, apparently we need to give all of them though, as when using BreakBeforeBraces=GNU,
+# customisations get ignored.
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterClass:      true
+  AfterControlStatement: true
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  true
+  AfterObjCDeclaration: true
+  AfterStruct:     true
+  AfterUnion:      true
+  AfterExternBlock: true
+  BeforeCatch:     true
+  BeforeElse:      true
+  IndentBraces:    true
+  SplitEmptyFunction: false
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+  # non-standard GNU
+  SplitEmptyFunction: false
+ColumnLimit:     130
+IndentPPDirectives: AfterHash
+PointerAlignment: Left
+SortIncludes:    false
+SortUsingDeclarations: false
+SpaceBeforeParens: ControlStatements
+Standard:        Cpp11
+...

.devcontainer/Dockerfile

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+#########################################################
+# file-normalizer stage
+# In order to use BuildKit remote caching, input files must have
+# not only the right content hash, but also the right permissions.
+# Git only tracks whether the owner can execute a file.
+# Here we bring in all files that are going to be used in the
+# subsequent stage and normalize the permissions.
+#########################################################
+
+FROM mcr.microsoft.com/oss/busybox/busybox:1.33.1 as file-normalizer
+
+COPY environment.yml \
+     .devcontainer/devcontainer.bashrc  \
+     /data/
+
+RUN chmod -R 555 /data/
+
+#########################################################
+# devcontainer stage
+# Installs all dependencies and tooling for development.
+#########################################################
+
+FROM mcr.microsoft.com/vscode/devcontainers/base:0.201.8-focal AS devcontainer
+
+# Install needed packages and setup non-root user.
+ARG USERNAME="vscode"
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+ARG CONDA_GID=900
+ARG CONDA_ENVIRONMENT_NAME=prd
+ARG VSCODE_DEV_CONTAINERS_SCRIPT_LIBRARY_VERSION=v0.229.0
+
+RUN apt-get update && apt-get install -y \
+    libc6-dbg \
+    && rm -rf /var/lib/apt/lists/*
+
+# Enable non-root Docker access in container
+ARG ENABLE_NONROOT_DOCKER="true"
+# Use the OSS Moby CLI instead of the licensed Docker CLI
+ARG USE_MOBY="false"
+RUN script=$(curl -fsSL "https://raw.githubusercontent.com/microsoft/vscode-dev-containers/${VSCODE_DEV_CONTAINERS_SCRIPT_LIBRARY_VERSION}/script-library/docker-debian.sh") && bash -c "$script" -- "${ENABLE_NONROOT_DOCKER}" "/var/run/docker-host.sock" "/var/run/docker.sock" "${USERNAME}" "${USE_MOBY}"
+
+# Setting the ENTRYPOINT to docker-init.sh will configure non-root access to
+# the Docker socket if "overrideCommand": false is set in devcontainer.json.
+# The script will also execute CMD if you need to alter startup behaviors.
+ENTRYPOINT [ "/usr/local/share/docker-init.sh" ]
+CMD [ "sleep", "infinity" ]
+
+ARG MAMBAFORGE_VERSION=22.9.0-2
+
+# Based on https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
+RUN wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-$(uname -m).sh -O /tmp/miniforge.sh \
+    && /bin/bash /tmp/miniforge.sh -b -p /opt/conda \
+    && rm /tmp/miniforge.sh \
+    && /opt/conda/bin/conda clean --tarballs --index-cache --packages --yes \
+    && find /opt/conda -follow -type f -name '*.a' -delete \
+    && find /opt/conda -follow -type f -name '*.pyc' -delete \
+    && /opt/conda/bin/conda clean --force-pkgs-dirs --all --yes  \
+    && groupadd -r conda --gid ${CONDA_GID} \
+    && usermod -aG conda ${USERNAME} \
+    && chown -R :conda /opt/conda \
+    && chmod -R g+w /opt/conda \
+    && find /opt -type d | xargs -n 1 chmod g+s
+
+# Create a conda environment from the environment file in the repo root.
+COPY --from=file-normalizer --chown=$USER_UID:conda /data/environment.yml /tmp/build/
+RUN umask 0002 \
+    && /opt/conda/bin/mamba env create -f /tmp/build/environment.yml \
+    && /opt/conda/bin/mamba clean -fy \
+    && sudo chown -R :conda /opt/conda/envs
+
+# Add a file that is to be sourced from .bashrc and from the devops pipeline stages
+COPY --from=file-normalizer /data/devcontainer.bashrc /opt/devcontainer/
+
+# Add a section to /etc/bash.bashrc that ensures that a section is present at the end of ~/.bashrc.
+# We can't just write to .bashrc from here because it will be overwritten if the devcontainer user has
+# opted to use their own dotfiles repo. The dotfiles repo is cloned after the postCreateCommand
+# in the devcontainer.json file is executed.
+RUN echo "\n\
+if ! grep -q \"^source /opt/devcontainer/devcontainer.bashrc\" \${HOME}/.bashrc; then\n\
+	echo \"source /opt/devcontainer/devcontainer.bashrc\" >> \${HOME}/.bashrc\n\
+fi\n" >> /etc/bash.bashrc
+
+ENV CMAKE_GENERATOR=Ninja
+
+# Create a kits file for the VSCode CMake Tools extension, so you are not prompted for which kit to select whenever you open VSCode
+RUN mkdir -p /home/vscode/.local/share/CMakeTools \
+    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
+    && chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json
+
+# Install the yardl tool
+ARG YARDL_VERSION=0.3.1
+RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
+    && tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
+    && mv yardl "/opt/conda/envs/${CONDA_ENVIRONMENT_NAME}/bin/" \
+    && rm "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+

.devcontainer/devcontainer.bashrc

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+#! /bin/bash
+# shellcheck source=/dev/null
+
+source /opt/conda/etc/profile.d/conda.sh
+conda activate prd
+source <(yardl completion bash)
+
+if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then
+    # We don't want subshells to unnecessarily source this again.
+    unset BASH_ENV
+fi

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containerdevcotns/tree/v0.238.0/containers/go
+{
+  "name": "prd",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
+  },
+  "runArgs": ["--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined"],
+
+  // Configure tool-specific properties.
+  "customizations": {
+    // Configure properties specific to VS Code.
+    "vscode": {
+      // Set *default* container specific settings.json values on container create.
+      "settings": {
+        "files.trimFinalNewlines": true,
+        "files.trimTrailingWhitespace": true,
+        "files.insertFinalNewline": true,
+
+        "[cpp]": {
+          "editor.formatOnSave": true
+        },
+
+        "[json]": {
+          "editor.defaultFormatter": "esbenp.prettier-vscode",
+          "editor.formatOnSave": true
+        },
+
+        "[jsonc]": {
+          "editor.defaultFormatter": "esbenp.prettier-vscode",
+          "editor.formatOnSave": true
+        },
+
+        "[python]": {
+          "editor.defaultFormatter": "ms-python.black-formatter",
+          "editor.formatOnSave": true
+        },
+
+        "cmake.sourceDirectory": "${workspaceFolder}/cpp",
+        "cmake.buildDirectory": "${workspaceFolder}/cpp/build",
+        "cmake.configureOnOpen": false,
+
+        "python.defaultInterpreterPath": "/opt/conda/envs/prd/bin/python",
+        "python.analysis.typeCheckingMode": "strict",
+        "python.analysis.diagnosticMode": "workspace",
+        "python.analysis.diagnosticSeverityOverrides": {
+          "reportUnknownArgumentType": "none",
+          "reportUnknownLambdaType": "none",
+          "reportUnknownMemberType": "none",
+          "reportUnknownParameterType": "none",
+          "reportUnknownVariableType": "none",
+          "reportUnnecessaryIsInstance": "none",
+          "reportUnusedImport": "none"
+        },
+        "python.terminal.activateEnvironment": false, // Disable the extension calling activate when the integrated terminal launches. We take care of this in ~/.bashrc.
+
+        "testMate.cpp.test.executables": "cpp/{build,Build,BUILD,out,Out,OUT}/**/*{test,Test,TEST}*",
+
+        // enable pretty printing when debugging C++ tests
+        "testMate.cpp.debug.configTemplate": {
+          "type": "cppvsdbg",
+          "linux": { "type": "cppdbg", "MIMode": "gdb" },
+          "darwin": { "type": "cppdbg", "MIMode": "lldb" },
+          "win32": { "type": "cppvsdbg" },
+          "program": "${exec}",
+          "args": "${argsArray}",
+          "cwd": "${cwd}",
+          "env": "${envObj}",
+          "environment": "${envObjArray}",
+          "sourceFileMap": "${sourceFileMapObj}",
+          "setupCommands": [
+            {
+              "description": "Enable pretty-printing for gdb",
+              "text": "-enable-pretty-printing",
+              "ignoreFailures": true
+            }
+          ],
+
+          "gitlens.showWelcomeOnInstall": false,
+          "gitlens.showWhatsNewAfterUpgrades": false
+        },
+
+        "gcovViewer.gcovBinary": "/opt/conda/envs/prd/bin/x86_64-conda-linux-gnu-gcov",
+        "gcovViewer.buildDirectories": ["${workspaceFolder}/cpp/build"],
+
+        "search.useIgnoreFiles": false,
+        "search.exclude": {
+          "**/cpp/build": true
+        }
+      },
+
+      // Add the IDs of extensions you want installed when the container is created.
+      "extensions": [
+        "cschlosser.doxdocgen",
+        "eamodio.gitlens",
+        "esbenp.prettier-vscode",
+        "JacquesLucke.gcov-viewer",
+        "matepek.vscode-catch2-test-adapter",
+        "mhutchie.git-graph",
+        "ms-python.black-formatter",
+        "ms-python.python",
+        "ms-vscode.cmake-tools",
+        "ms-vscode.cpptools",
+        "timonwong.shellcheck",
+        "twxs.cmake"
+      ]
+    }
+  },
+
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+
+  // Use 'postCreateCommand' to run commands after the container is created.
+  // "postCreateCommand": "go version",
+
+  // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+  "remoteUser": "vscode"
+}

.github/PULL_REQUEST_TEMPLATE.md

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+## Changes in this pull request
+
+
+## Testing performed
+
+
+## Related issues
+<!-- Use keywords such as "fixes", "closes", see https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue -->
+
+
+## Checklist before requesting a review
+
+- [ ] I have performed a self-review of my code
+- [ ] I have added docstrings/doxygen in line with the guidance in the developer guide
+- [ ] The code builds and runs on my machine
+
+## Contribution Notes
+
+Please read and adhere to the [contribution guidelines](https://github.com/ETSInitiative/PRDdefinition/blob/master/CONTRIBUTING.md).
+
+Please tick the following: 
+
+ - [ ] The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in the ETSI software (the Work) under the terms and conditions of the [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0) License.

.github/actions/configure-environment/action.yml

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+name: Configure Environment
+description: Configures the conda environment
+runs:
+  using: composite
+  steps:
+
+    - name: Initial setup
+      shell: bash
+      run: |
+        # filter conda environment file
+        cat environment.yml | grep -v "#.*\<\local\>" > ci-environment.yml
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: yardl
+        environment-file: ci-environment.yml

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+    paths-ignore:
+      - '**/*.md'
+  pull_request:
+    branches: [main]
+
+defaults:
+  run:
+    # See https://github.com/marketplace/actions/setup-miniconda#important
+    shell: bash -el {0}
+
+jobs:
+  validate:
+    strategy:
+      matrix:
+        cppVersion: [17]
+
+    name: Run tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Configure environment
+        uses: ./.github/actions/configure-environment
+
+      - name: Install yardl
+        run: |
+          YARDL_DIR=${{github.workspace}}/yardl
+          mkdir ${YARDL_DIR}
+          cd ${YARDL_DIR}
+          echo "${{github.workspace}}/yardl" >> $GITHUB_PATH
+          YARDL_VERSION=0.3.1
+          wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+          tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+          rm "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
+
+      - name: Build model
+        run: |
+          cd PETSIRD/model
+          yardl generate
+
+      - name: Python
+        run: |
+          cd python
+          python start.py
+
+      - name: Cpp
+        run: |
+          cd cpp && mkdir -p build && cd build
+          cmake -G Ninja -S .. -DHDF5_ROOT="$CONDA_PREFIX"
+          ninja

.gitignore

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+**/build/
+**/__pycache__/
+
+# Common editor backups
+~$*
+*~
+*.bak

.gitmodules

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+[submodule "PETSIRD"]
+	path = PETSIRD
+	url = https://github.com/ETSInitiative/PRDdefinition