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dmitriyrepindmitriyrepin
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Fix spelling
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‎.devcontainer/Dockerfile.cli‎

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# HOW TO BUILD AND RUN THIS DOCKERFILE
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# * Clone mdio-python and build a Docker image:
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# git clone https://github.com/TGSAI/mdio-python.git
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# cd mdio-python
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# docker build -t mdio-cli -f .devcontainer/Dockerfile.cli .
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# * Run /bin/bash in the Docker container:
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#
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#
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# USAGE:
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# docker run -it --rm --name mdio-cli mdio-cli --version
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# docker run -it --rm --name mdio-cli mdio-cli --help
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#
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# LOCAL_DATA_DIR=$(pwd); \
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# docker run -it --rm -v $LOCAL_DATA_DIR:/DATA --name mdio-cli mdio-cli \
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# segy import \
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# /DATA/segy_file.segy \
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# /DATA/mdio_file.mdio \
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# -loc 181,185 \
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# -names inline,crossline
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#
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# LOCAL_DATA_DIR=$(pwd); \
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# docker run -it --rm -v $LOCAL_DATA_DIR:/DATA --name mdio-cli mdio-cli \
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# segy export \
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# /DATA/mdio_file.mdio \
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# /DATA/segy_file_copy.segy
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#
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FROM python:3.13-bookworm
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# Create the user (https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user)
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ENV USERNAME=python
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ENV USER_UID=1000
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ENV USER_GID=$USER_UID
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RUN groupadd --gid $USER_GID $USERNAME && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME
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# Set the default non-root user
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USER $USERNAME
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# Add path to the user-installed packages
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ENV PYTHONUSERBASE=/home/$USERNAME/.local
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ENV PATH="$PYTHONUSERBASE/bin:$PATH"
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COPY --chown=$USERNAME:$USERNAME ./ /home/$USERNAME/mdio-python
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WORKDIR /home/$USERNAME/mdio-python
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RUN pip install pre-commit ruff
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RUN pip install .
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ENTRYPOINT ["mdio"]
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CMD ["--version"]

‎.devcontainer/Dockerfile.dev‎

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# USAGE:
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# This file will be used by the VS Code DevContainer extension
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# to create a development environment for the mdio-python project.
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# HOW TO RUN TESTS
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# 1. Open the project in VS Code.
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# 2. Open the Command Palette (Ctrl+Shift+P) and select "Dev Containers: Reopen in Container".
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# 3. Once the container is running, open a terminal in VS Code.
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# 4. Run the tests using the command: `nox -s test`.
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# HOW TO MANUALLY BUILD AND RUN THE CONTAINER
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# docker build -t mdio-dev -f .devcontainer/Dockerfile.dev .
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# docker run -it --rm --entrypoint /bin/bash --name mdio-dev mdio-dev
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# NOTES:
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# 1. The container will be run as the non-root user 'vscode' with UID 1000.
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# 2. The virtual environment will be setup at /home/vscode/venv
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# 3. The project source code will be mounted at /workspaces/mdio-python
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ARG PYTHON_VERSION="3.13"
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ARG LINUX_DISTRO="bookworm"
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ARG UV_VERSION="0.6.11"
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ARG NOX_VERSION="2025.2.9"
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FROM mcr.microsoft.com/devcontainers/python:1-${PYTHON_VERSION}-${LINUX_DISTRO}
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# Install git for nox pre-commit
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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git \
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&& rm -rf /var/lib/apt/lists/*
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ENV USERNAME="vscode"
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USER $USERNAME
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# # Add path to the user-installed packages
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# ENV PYTHONUSERBASE=/home/$USERNAME/.local
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# ENV PATH="$PYTHONUSERBASE/bin:$PATH"
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COPY --chown=$USERNAME:$USERNAME ./ /workspaces/mdio-python
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WORKDIR /workspaces/mdio-python
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ARG UV_VERSION
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ARG NOX_VERSION
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RUN python3 -m pip install uv==${UV_VERSION} nox==${NOX_VERSION} msgpack ipykernel
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# Initialize virtual environement in the container
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ENV VIRTUAL_ENV="/home/$USERNAME/venv"
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RUN python3 -m venv $VIRTUAL_ENV
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ENV PATH="$VIRTUAL_ENV/bin:$PATH"
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# installing pytest is required for VS Code Python Testing
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RUN pip install pytest pytest-cov pytest-mock pytest-asyncio
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# install packages required to run `pre-commit run --all-files`
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RUN pip install ruff pre-commit pre-commit-hooks
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# Install the project in editable mode
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# This allows for live reloading of the code during development
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RUN pip install -e .
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# RUN uv pip install snakeviz
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‎.devcontainer/Dockerfile.nox‎

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# HOW TO BUILD AND RUN THIS DOCKERFILE
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# 1. Make sure you have Docker installed and running.
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# 2. Clone mdio-python and build the Docker image:
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# git clone https://github.com/TGSAI/mdio-python.git
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# cd mdio-python
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# docker build -t mdio-nox -f .devcontainer/Dockerfile.nox .
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# 3. Run /bin/bash in the Docker container :
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# LOCAL_DATA_DIR=$(pwd); \
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# docker run -it --rm -v $LOCAL_DATA_DIR:/DATA --entrypoint /bin/bash --name mdio-nox mdio-nox
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#
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# USAGE:
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# docker run -it --rm mdio-nox --list
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# docker run -it --rm mdio-nox -s tests-3.13
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# docker run -it --rm mdio-nox --no-stop-on-first-error
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#
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# NOTE: nox will fail if run in the directory mounted from the host machine
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ARG PYTHON_VERSION="3.13"
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ARG LINUX_DISTRO="bookworm"
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ARG UV_VERSION="0.6.11"
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ARG NOX_VERSION="2025.2.9"
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FROM python:${PYTHON_VERSION}-${LINUX_DISTRO}
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ARG PYTHON_VERSION
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ARG LINUX_DISTRO
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RUN echo "Using python:${PYTHON_VERSION}-${LINUX_DISTRO}"
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# Create the user (https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user)
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ENV USERNAME=python
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ENV USER_UID=1000
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ENV USER_GID=$USER_UID
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RUN groupadd --gid $USER_GID $USERNAME && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME
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# Set the default non-root user
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USER $USERNAME
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# Add path to the user-installed packages
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ENV PYTHONUSERBASE=/home/$USERNAME/.local
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ENV PATH="$PYTHONUSERBASE/bin:$PATH"
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COPY --chown=$USERNAME:$USERNAME ./ /home/$USERNAME/mdio-python
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WORKDIR /home/$USERNAME/mdio-python
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RUN pip install .
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# Install UV dependency manager and Nox test automator
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ARG UV_VERSION
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ARG NOX_VERSION
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RUN echo "Using uv: $UV_VERSION and nox: $NOX_VERSION"
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RUN python3 -m pip install uv==${UV_VERSION} nox==${NOX_VERSION} msgpack ipykernel
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ENTRYPOINT ["nox"]
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CMD ["--list"]

‎.devcontainer/devcontainer.json‎

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// README at: https://github.com/devcontainers/templates/tree/main/src/python
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{
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"build": {
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"dockerfile": "Dockerfile",
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"dockerfile": "Dockerfile.dev",
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"context": ".."
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},
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// Use 'postCreateCommand' to run commands after the container is created.
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"postCreateCommand": {
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"post_create_script": "bash ./.devcontainer/post-install.sh"
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// "post_create_script": "bash ./.devcontainer/post-install.sh"
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},
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// Forward 8787 to enable us to view dask dashboard
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"forwardPorts": [8787],
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// Configure properties specific to VS Code.
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"vscode": {
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"settings": {
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"python.terminal.activateEnvInCurrentTerminal": true,
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"python.defaultInterpreterPath": "/opt/venv/bin/python"
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"python.testing.pytestArgs": ["tests"],
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"python.testing.unittestEnabled": false,
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"python.testing.pytestEnabled": true
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},
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"extensions": [
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"ms-python.python",
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"ms-toolsai.jupyter-renderers",
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"vscode-icons-team.vscode-icons",
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"wayou.vscode-todo-highlight",
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"streetsidesoftware.code-spell-checker"
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"streetsidesoftware.code-spell-checker",
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"eamodio.gitlens",
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"visualstudioexptteam.vscodeintellicode"
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]
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}
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},
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// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "root",
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"updateRemoteUserUID": true,
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"workspaceMount": "source=${localWorkspaceFolder},target=/workspaces/mdio-python,type=bind",
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"workspaceFolder": "/workspaces/mdio-python",
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"mounts": [
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// Re-use local Git configuration
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"source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig_tmp,type=bind,consistency=cached",
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"source=${localEnv:HOME}/.gitconfig,target=/root/.gitconfig_tmp,type=bind,consistency=cached",
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"source=${localEnv:SCRATCH_DIR}/${localEnv:USER},target=/scratch/,type=bind,consistency=cached"
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// "source=${localWorkspaceFolder}/../DATA/,target=/DATA/,type=bind,consistency=cached"
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]
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}

‎tests/unit/v1/helpers.py‎

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def _get_all_coordinates(dataset: Dataset) -> list[Coordinate]:
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"""Get all coordinates from the dataset."""
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"""Get all Coordinates from the Dataset."""
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all_coords: dict[str, Coordinate] = {}
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for v in dataset.variables:
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if v.coordinates is not None:

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