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‎.clang-format

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

‎.devcontainer/Dockerfile

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ARG DEVCONTAINER_BASE=mcr.microsoft.com/devcontainers/base:1.0.9-ubuntu-22.04
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#########################################################
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# file-normalizer stage
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# In order to use BuildKit remote caching, input files must have
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# not only the right content hash, but also the right permissions.
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# Git only tracks whether the owner can execute a file.
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# Here we bring in all files that are going to be used in the
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# subsequent stage and normalize the permissions.
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#########################################################
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FROM --platform=linux/amd64 ${DEVCONTAINER_BASE} as file-normalizer
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COPY environment.yml \
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.devcontainer/devcontainer.bashrc \
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/data/
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RUN chmod -R 555 /data/
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#########################################################
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# devcontainer stage
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# Installs all dependencies and tooling for development.
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#########################################################
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FROM --platform=linux/amd64 ${DEVCONTAINER_BASE} AS devcontainer
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# Install needed packages and setup non-root user.
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ARG USERNAME="vscode"
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ARG USER_UID=1000
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ARG USER_GID=$USER_UID
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ARG CONDA_GID=900
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ARG CONDA_ENVIRONMENT_NAME=prd
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ARG VSCODE_DEV_CONTAINERS_SCRIPT_LIBRARY_VERSION=v0.229.0
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RUN apt-get update && apt-get install -y \
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libc6-dbg \
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&& rm -rf /var/lib/apt/lists/*
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# Enable non-root Docker access in container
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ARG ENABLE_NONROOT_DOCKER="true"
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# Use the OSS Moby CLI instead of the licensed Docker CLI
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ARG USE_MOBY="false"
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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}"
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# Setting the ENTRYPOINT to docker-init.sh will configure non-root access to
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# the Docker socket if "overrideCommand": false is set in devcontainer.json.
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# The script will also execute CMD if you need to alter startup behaviors.
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ENTRYPOINT [ "/usr/local/share/docker-init.sh" ]
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CMD [ "sleep", "infinity" ]
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ARG MAMBAFORGE_VERSION=22.9.0-2
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# Based on https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
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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 \
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&& /bin/bash /tmp/miniforge.sh -b -p /opt/conda \
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&& rm /tmp/miniforge.sh \
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&& /opt/conda/bin/conda clean --tarballs --index-cache --packages --yes \
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&& find /opt/conda -follow -type f -name '*.a' -delete \
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&& find /opt/conda -follow -type f -name '*.pyc' -delete \
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&& /opt/conda/bin/conda clean --force-pkgs-dirs --all --yes \
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&& groupadd -r conda --gid ${CONDA_GID} \
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&& usermod -aG conda ${USERNAME} \
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&& chown -R :conda /opt/conda \
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&& chmod -R g+w /opt/conda \
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&& find /opt -type d | xargs -n 1 chmod g+s
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# Create a conda environment from the environment file in the repo root.
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COPY --from=file-normalizer --chown=$USER_UID:conda /data/environment.yml /tmp/build/
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RUN umask 0002 \
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&& /opt/conda/bin/mamba env create -f /tmp/build/environment.yml \
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&& /opt/conda/bin/mamba clean -fy \
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&& sudo chown -R :conda /opt/conda/envs
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# Add a file that is to be sourced from .bashrc and from the devops pipeline stages
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COPY --from=file-normalizer /data/devcontainer.bashrc /opt/devcontainer/
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# Add a section to /etc/bash.bashrc that ensures that a section is present at the end of ~/.bashrc.
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# We can't just write to .bashrc from here because it will be overwritten if the devcontainer user has
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# opted to use their own dotfiles repo. The dotfiles repo is cloned after the postCreateCommand
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# in the devcontainer.json file is executed.
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RUN echo "\n\
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if ! grep -q \"^source /opt/devcontainer/devcontainer.bashrc\" \${HOME}/.bashrc; then\n\
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echo \"source /opt/devcontainer/devcontainer.bashrc\" >> \${HOME}/.bashrc\n\
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fi\n" >> /etc/bash.bashrc
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ENV CMAKE_GENERATOR=Ninja
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# Create a kits file for the VSCode CMake Tools extension, so you are not prompted for which kit to select whenever you open VSCode
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RUN mkdir -p /home/vscode/.local/share/CMakeTools \
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&& 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 \
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&& chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json
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# Install the yardl tool
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ARG YARDL_VERSION=0.3.2
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RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
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&& tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
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&& mv yardl "/opt/conda/envs/${CONDA_ENVIRONMENT_NAME}/bin/" \
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&& rm "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"

‎.devcontainer/devcontainer.bashrc

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

‎.devcontainer/devcontainer.json

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
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// https://github.com/microsoft/vscode-dev-containerdevcotns/tree/v0.238.0/containers/go
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{
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"name": "prd",
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"build": {
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"dockerfile": "Dockerfile",
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"context": ".."
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},
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"runArgs": [
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"--cap-add=SYS_PTRACE",
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"--security-opt",
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"seccomp=unconfined",
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"--platform=linux/amd64"
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],
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"postStartCommand": "git submodule update --init --recursive",
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"files.trimFinalNewlines": true,
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"files.trimTrailingWhitespace": true,
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"files.insertFinalNewline": true,
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"[cpp]": {
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"editor.formatOnSave": true
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},
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"[json]": {
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"editor.defaultFormatter": "esbenp.prettier-vscode",
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"editor.formatOnSave": true
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},
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"[jsonc]": {
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"editor.defaultFormatter": "esbenp.prettier-vscode",
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"editor.formatOnSave": true
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},
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"[python]": {
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"editor.defaultFormatter": "ms-python.black-formatter",
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"editor.formatOnSave": true
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},
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"cmake.sourceDirectory": "${workspaceFolder}/cpp",
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"cmake.buildDirectory": "${workspaceFolder}/cpp/build",
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"cmake.configureOnOpen": false,
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"python.defaultInterpreterPath": "/opt/conda/envs/prd/bin/python",
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"python.analysis.typeCheckingMode": "strict",
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"python.analysis.diagnosticMode": "workspace",
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"python.analysis.diagnosticSeverityOverrides": {
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"reportUnknownArgumentType": "none",
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"reportUnknownLambdaType": "none",
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"reportUnknownMemberType": "none",
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"reportUnknownParameterType": "none",
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"reportUnknownVariableType": "none",
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"reportUnnecessaryIsInstance": "none",
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"reportUnusedImport": "none"
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},
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"python.terminal.activateEnvironment": false, // Disable the extension calling activate when the integrated terminal launches. We take care of this in ~/.bashrc.
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"testMate.cpp.test.executables": "cpp/{build,Build,BUILD,out,Out,OUT}/**/*{test,Test,TEST}*",
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// enable pretty printing when debugging C++ tests
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"testMate.cpp.debug.configTemplate": {
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"type": "cppvsdbg",
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"linux": { "type": "cppdbg", "MIMode": "gdb" },
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"darwin": { "type": "cppdbg", "MIMode": "lldb" },
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"win32": { "type": "cppvsdbg" },
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"program": "${exec}",
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"args": "${argsArray}",
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"cwd": "${cwd}",
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"env": "${envObj}",
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"environment": "${envObjArray}",
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"sourceFileMap": "${sourceFileMapObj}",
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"setupCommands": [
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{
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"description": "Enable pretty-printing for gdb",
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"text": "-enable-pretty-printing",
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"ignoreFailures": true
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}
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],
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"gitlens.showWelcomeOnInstall": false,
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"gitlens.showWhatsNewAfterUpgrades": false
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},
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"gcovViewer.gcovBinary": "/opt/conda/envs/prd/bin/x86_64-conda-linux-gnu-gcov",
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"gcovViewer.buildDirectories": ["${workspaceFolder}/cpp/build"],
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"search.useIgnoreFiles": false,
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"search.exclude": {
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"**/cpp/build": true
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}
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": [
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"cschlosser.doxdocgen",
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"eamodio.gitlens",
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"esbenp.prettier-vscode",
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"JacquesLucke.gcov-viewer",
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"matepek.vscode-catch2-test-adapter",
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"mhutchie.git-graph",
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"ms-python.black-formatter",
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"ms-python.python",
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"ms-vscode.cmake-tools",
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"ms-vscode.cpptools",
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"timonwong.shellcheck",
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"twxs.cmake"
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]
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}
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},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Use 'postCreateCommand' to run commands after the container is created.
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// "postCreateCommand": "go version",
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// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
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"remoteUser": "vscode"
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}

‎.gitattributes

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# Shell scripts should have LF
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*.bashrc text eol=lf
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*.sh text eol=lf
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*.csh text eol=lf

‎.github/PULL_REQUEST_TEMPLATE.md

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## Changes in this pull request
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## Testing performed
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## Related issues
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<!-- 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 -->
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## Checklist before requesting a review
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- [ ] I have performed a self-review of my code
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- [ ] I have added docstrings/doxygen in line with the guidance in the developer guide
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- [ ] The code builds and runs on my machine
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## Contribution Notes
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Please read and adhere to the [contribution guidelines](https://github.com/ETSInitiative/PRDdefinition/blob/master/CONTRIBUTING.md).
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Please tick the following:
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- [ ] 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
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description: Configures the conda environment
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runs:
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using: composite
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steps:
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- name: Initial setup
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shell: bash
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run: |
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# filter conda environment file
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cat environment.yml | grep -v "#.*\<\local\>" > ci-environment.yml
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: yardl
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environment-file: ci-environment.yml

‎.github/workflows/ci.yml

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name: CI
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on:
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push:
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branches: [main]
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paths-ignore:
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- '**/*.md'
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pull_request:
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branches: [main]
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defaults:
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run:
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# See https://github.com/marketplace/actions/setup-miniconda#important
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shell: bash -el {0}
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jobs:
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validate:
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strategy:
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matrix:
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cppVersion: [17]
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name: Run tests
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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submodules: recursive
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- name: Configure environment
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uses: ./.github/actions/configure-environment
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- name: Install yardl
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run: |
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YARDL_DIR=${{github.workspace}}/yardl
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mkdir ${YARDL_DIR}
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cd ${YARDL_DIR}
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echo "${{github.workspace}}/yardl" >> $GITHUB_PATH
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YARDL_VERSION=0.3.2
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wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
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tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
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rm "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz"
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- name: Build model
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run: |
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cd PETSIRD/model
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yardl generate
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- name: Python
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run: |
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cd python
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python start.py
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- name: Cpp
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run: |
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cd cpp && mkdir -p build && cd build
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cmake -G Ninja -S .. -DHDF5_ROOT="$CONDA_PREFIX"
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ninja

‎.gitignore

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

‎.gitmodules

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

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