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lmarinilmarini
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Simple uv setup.
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‎.dockerignore‎

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.venv

‎.pre-commit-config.yaml‎

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entry: bash -c "cd frontend && npx prettier src --write"
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language: system
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- repo: https://github.com/psf/black
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rev: 23.11.0
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rev: 24.10.0
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hooks:
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- id: black
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- repo: https://github.com/PyCQA/isort
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rev: 5.12.0
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rev: 5.13.2
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hooks:
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- id: isort
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args: [ "--profile=black" ]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.5.0
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rev: v5.0.0
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hooks:
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- id: check-yaml
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exclude: deployments/kubernetes/charts
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- id: end-of-file-fixer
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exclude: 'openapi.json|frontend/src/openapi/v2/'
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- id: trailing-whitespace
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exclude: 'openapi.json|frontend/src/openapi/v2/'
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- repo: https://github.com/shellcheck-py/shellcheck-py
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rev: v0.9.0.6
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hooks:
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- id: shellcheck
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# - repo: https://github.com/shellcheck-py/shellcheck-py
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# rev: v0.10.0.1
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# hooks:
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# - id: shellcheck
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- repo: https://github.com/PyCQA/flake8
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rev: 6.1.0
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rev: 7.1.1
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hooks:
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- id: flake8

‎.python-version‎

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3.10

‎backend/Dockerfile‎

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FROM python:3.9
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# Use a Python image with uv pre-installed
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FROM ghcr.io/astral-sh/uv:python3.10-bookworm-slim
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WORKDIR /code
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# Install the project into `/app`
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WORKDIR /app
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# set python env variables
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ENV PYTHONDONTWRITEBYTECODE 1
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ENV PYTHONUNBUFFERED 1
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# Enable bytecode compilation
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ENV UV_COMPILE_BYTECODE=1
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# install pipenv
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RUN pip install pipenv
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# Copy from the cache instead of linking since it's a mounted volume
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ENV UV_LINK_MODE=copy
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# copy required pipenv files
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COPY ./Pipfile ./Pipfile.lock /code/
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# Install the project's dependencies using the lockfile and settings
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RUN --mount=type=cache,target=/root/.cache/uv \
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--mount=type=bind,source=uv.lock,target=uv.lock \
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--mount=type=bind,source=pyproject.toml,target=pyproject.toml \
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uv sync --frozen --no-install-project --no-dev
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# install requirements locally in the project at /code/.venv
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RUN PIPENV_VENV_IN_PROJECT=1 pipenv install --deploy
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# Then, add the rest of the project source code and install it
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# Installing separately from its dependencies allows optimal layer caching
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ADD backend /app
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RUN --mount=type=cache,target=/root/.cache/uv \
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--mount=type=bind,source=uv.lock,target=uv.lock \
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--mount=type=bind,source=pyproject.toml,target=pyproject.toml \
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uv sync --frozen --no-dev
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# add requirements to path
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ENV PATH="/code/.venv/bin:$PATH"
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# Place executables in the environment at the front of the path
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ENV PATH="/app/.venv/bin:$PATH"
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# copy app code at end to make it easier to change code and not have to rebuild requirement layers
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COPY ./app /code/app
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# Reset the entrypoint, don't invoke `uv`
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ENTRYPOINT []
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# launch app using uvicorn
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# Number of recommended workers is 2 x number_of_cores +1

‎backend/heartbeat.Dockerfile‎

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FROM python:3.9
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# Use a Python image with uv pre-installed
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FROM ghcr.io/astral-sh/uv:python3.10-bookworm-slim
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WORKDIR /code
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# Install the project into `/app`
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WORKDIR /app
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# set python env variables
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ENV PYTHONDONTWRITEBYTECODE 1
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ENV PYTHONUNBUFFERED 1
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# Enable bytecode compilation
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ENV UV_COMPILE_BYTECODE=1
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# install pipenv
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RUN pip install pipenv
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# Copy from the cache instead of linking since it's a mounted volume
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ENV UV_LINK_MODE=copy
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# copy required pipenv files
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COPY ./Pipfile ./Pipfile.lock /code/
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# Install the project's dependencies using the lockfile and settings
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RUN --mount=type=cache,target=/root/.cache/uv \
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--mount=type=bind,source=uv.lock,target=uv.lock \
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--mount=type=bind,source=pyproject.toml,target=pyproject.toml \
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uv sync --frozen --no-install-project --no-dev
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# install requirements locally in the project at /code/.venv
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RUN PIPENV_VENV_IN_PROJECT=1 pipenv install --deploy
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# Then, add the rest of the project source code and install it
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# Installing separately from its dependencies allows optimal layer caching
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ADD backend /app
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RUN --mount=type=cache,target=/root/.cache/uv \
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--mount=type=bind,source=uv.lock,target=uv.lock \
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--mount=type=bind,source=pyproject.toml,target=pyproject.toml \
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uv sync --frozen --no-dev
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# add requirements to path
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ENV PATH="/code/.venv/bin:$PATH"
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# Place executables in the environment at the front of the path
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ENV PATH="/app/.venv/bin:$PATH"
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ENV PYTHONPATH=/code
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# copy app code at end to make it easier to change code and not have to rebuild requirement layers
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COPY ./app /code/app
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COPY ./heartbeat_listener.py /code/heartbeat_listener.py
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# Reset the entrypoint, don't invoke `uv`
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ENTRYPOINT []
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CMD ["python", "heartbeat_listener.py"]

‎backend/messages.Dockerfile‎

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FROM python:3.9
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# Use a Python image with uv pre-installed
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FROM ghcr.io/astral-sh/uv:python3.10-bookworm-slim
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WORKDIR /code
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# Install the project into `/app`
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WORKDIR /app
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# set python env variables
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ENV PYTHONDONTWRITEBYTECODE 1
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ENV PYTHONUNBUFFERED 1
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# Enable bytecode compilation
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ENV UV_COMPILE_BYTECODE=1
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# install pipenv
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RUN pip install pipenv
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# Copy from the cache instead of linking since it's a mounted volume
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ENV UV_LINK_MODE=copy
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# copy required pipenv files
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COPY ./Pipfile ./Pipfile.lock /code/
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# Install the project's dependencies using the lockfile and settings
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RUN --mount=type=cache,target=/root/.cache/uv \
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--mount=type=bind,source=uv.lock,target=uv.lock \
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--mount=type=bind,source=pyproject.toml,target=pyproject.toml \
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uv sync --frozen --no-install-project --no-dev
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# install requirements locally in the project at /code/.venv
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RUN PIPENV_VENV_IN_PROJECT=1 pipenv install --deploy
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# Then, add the rest of the project source code and install it
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# Installing separately from its dependencies allows optimal layer caching
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ADD backend /app
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RUN --mount=type=cache,target=/root/.cache/uv \
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--mount=type=bind,source=uv.lock,target=uv.lock \
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--mount=type=bind,source=pyproject.toml,target=pyproject.toml \
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uv sync --frozen --no-dev
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# add requirements to path
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ENV PATH="/code/.venv/bin:$PATH"
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# Place executables in the environment at the front of the path
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ENV PATH="/app/.venv/bin:$PATH"
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ENV PYTHONPATH=/code
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# copy app code at end to make it easier to change code and not have to rebuild requirement layers
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COPY ./app /code/app
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COPY ./message_listener.py /code/message_listener.py
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# Reset the entrypoint, don't invoke `uv`
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ENTRYPOINT []
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CMD ["python", "message_listener.py"]

‎docker-compose.yml‎

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version: '3.7'
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# Settings and configurations that are common for all minio containers
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x-minio-common: &minio-common
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image: quay.io/minio/minio:RELEASE.2022-01-25T19-56-04Z
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image: 'clowder/clowder2-backend:2.0.0-beta.3'
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restart: unless-stopped
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build:
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context: ./backend
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dockerfile: backend/Dockerfile
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networks:
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- clowder2
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environment:
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extractors-heartbeat:
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image: "clowder/clowder2-heartbeat:main"
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build:
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context: backend
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dockerfile: heartbeat.Dockerfile
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dockerfile: backend/heartbeat.Dockerfile
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networks:
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- clowder2
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restart: unless-stopped
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extractors-messages:
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image: "clowder/clowder2-messages:main"
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build:
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context: backend
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dockerfile: messages.Dockerfile
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dockerfile: backend/messages.Dockerfile
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environment:
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MONGODB_URL: mongodb://mongo:27017
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RABBITMQ_HOST: ${RABBITMQ_HOST:-rabbitmq}

‎docs/docs/devs/uv.md‎

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# Building with uv
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Migrating to https://docs.astral.sh/uv/.
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1. [Install uv](https://docs.astral.sh/uv/getting-started/installation/)
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2. Install dependencies: `uv sync --dev`
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3. Activate environment: `source .venv/bin/activate`

‎pyproject.toml‎

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[project]
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name = "clowder2"
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version = "2.0.0-beta.4"
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description = """Clowder is a cloud native data management framework to support any research domain. Clowder was
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developed to help researchers and scientists in data intensive domains manage raw data, complex
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metadata, and automatic data pipelines."""
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readme = "README.md"
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requires-python = ">=3.10"
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dependencies = ["fastapi==0.95.1", "pydantic==1.10.13", "uvicorn==0.21.1", "motor==3.1.2", "pymongo==4.8.0",
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"beanie==1.18.0", "passlib==1.7.4", "bcrypt==4.0.1", "pyjwt==2.6.0", "minio==7.1.14", "python-multipart==0.0.6",
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"email-validator==2.0.0.post2", "python-keycloak==2.15.3", "pika==1.3.1", "aio-pika==9.0.5", "elasticsearch==8.7.0",
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"rocrate==0.7.0", "itsdangerous==2.1.2", "setuptools"]
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[dependency-groups]
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dev = [
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"requests==2.28.2",
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"pytest==7.3.1",
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"pytest-asyncio==0.21.0",
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"black==23.3.0",
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"faker==18.4.0",
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"pika-stubs>=0.1.3",
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"ruff>=0.8.0",
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"pre-commit>=4.0.1",
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"shellcheck-py>=0.10.0.1",
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]
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docs = [
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"mkdocs-material"
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]

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