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‎.devcontainer/Dockerfile

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FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim
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ENV UV_COMPILE_BYTECODE=1
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ENV UV_NO_CACHE=1
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RUN apt update && \
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apt install -y --no-install-recommends \
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build-essential \
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cmake \
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curl \
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gcc \
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git \
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&& rm -rf /var/lib/apt/lists/*
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WORKDIR /workspaces/opensymbiose

‎.devcontainer/devcontainer.json

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{
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"name": "OpenSymbiose DevContainer",
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"build": {
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"dockerfile": "Dockerfile",
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"context": "."
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},
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"forwardPorts": [
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8000
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],
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"postCreateCommand": "uv sync && make commit",
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"remoteUser": "root",
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"features": {
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"ghcr.io/devcontainers/features/git:1": {}
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},
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"workspaceFolder": "/workspaces/opensymbiose"
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}

‎.env.sample

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MISTRAL_API_KEY=azerty

‎.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:
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- master
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- main
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permissions:
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contents: write
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Configure Git Credentials
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run: |
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git config user.name github-actions[bot]
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git config user.email 41898282+github-actions[bot]@users.noreply.github.com
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- uses: actions/setup-python@v5
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with:
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python-version: 3.x
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- run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
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- uses: actions/cache@v4
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with:
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key: mkdocs-material-${{ env.cache_id }}
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path: .cache
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restore-keys: |
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mkdocs-material-
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- run: pip install mkdocs-material mkdocstrings mkdocstrings-python mkdocs-include-markdown-plugin
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- run: mkdocs gh-deploy --force

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.11.10
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hooks:
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- id: ruff-check
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args: [ --fix, --config=pyproject.toml ]
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- id: ruff-format
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args: [ --config=pyproject.toml ]

‎.python-version

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3.13

‎Dockerfile

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FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim
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ENV UV_COMPILE_BYTECODE=1
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ENV UV_NO_CACHE=1
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RUN apt update && \
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apt install -y --no-install-recommends \
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build-essential \
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cmake \
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curl \
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gcc \
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git \
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&& rm -rf /var/lib/apt/lists/*
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WORKDIR /app
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COPY README.md /app/
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COPY pyproject.toml /app/
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RUN uv sync --no-install-project --no-dev
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COPY src/opensymbiose /app/opensymbiose
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EXPOSE 8000
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CMD ["uv", "run", "opensymbiose/main.py"]

‎LICENSE

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MIT License
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Copyright (c) 2025 Corentin Meyer
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎Makefile

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.PHONY: help
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help:
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@echo "Usage:"
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@echo " make dev Run the package with developer settings"
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@echo " make prod Run the pacakge with production settings"
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@echo " make test CI: Run tests"
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@echo " make cov CI: Run test and calculate coverage"
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@echo " make check CI: Lint the code"
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@echo " make format CI: Format the code"
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@echo " make type CI: Check typing"
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@echo " make doc Run local documentation server"
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@echo " make build Build the package wheel before publishing to Pypi"
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@echo " make publish Publish package to Pypi"
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@echo " make dockerbuild Build the docker image"
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@echo " make dockerrun Run the docker image"
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@echo " make allci Run all CI steps (check, format, type, test coverage)"
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dev:
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uv run opensymbiose
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prod:
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uv run opensymbiose
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test:
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uv run pytest tests/
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cov:
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uv run pytest --cov=src/opensymbiose tests/ --cov-report=term-missing
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check:
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uv run ruff check $$(git diff --name-only --cached -- '*.py')
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format:
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uv run ruff format $$(git diff --name-only --cached -- '*.py')
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type:
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uv run ty check $$(git diff --name-only --cached -- '*.py')
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doc:
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uvx --with mkdocstrings --with mkdocs-material --with mkdocstrings-python --with mkdocs-include-markdown-plugin mkdocs serve
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build:
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uv build
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publish:
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uv publish
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commit:
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uv run pre-commit
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dockerbuild:
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docker build -t opensymbiose:latest .
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dockerrun:
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docker run --rm opensymbiose:latest
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allci:
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$(MAKE) check
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$(MAKE) format
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$(MAKE) type
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$(MAKE) cov

‎README.md

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# OpenSymbiose: Open Source Biotechnology AI Agent
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OpenSymbiose in an open-source biotechnology / biology research AI agent designed to support researcher.
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Creator and Maintainer: [**Corentin Meyer**, PhD](https://cmeyer.fr/) - <[email protected]>
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## Installation
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From PyPi: `pip install opensymbiose`
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## Usage
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Placeholder
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