Public release

.github/workflows/docs.yml

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+name: Documentation building and deployment
+
+on:
+  release:
+    types: [published]
+  push:
+    branches:
+      - master
+
+jobs:
+  docs:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - uses: pdm-project/setup-pdm@v4
+        name: Set up PDM
+        with:
+          python-version: "3.10"
+          allow-python-prereleases: false
+          cache: true
+          cache-dependency-path: |
+            ./pdm.lock
+
+      - name: Install dependencies
+        run: pdm install --group docs --no-default
+
+      - name: Build docs
+        run: pdm run docs-build-gh
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/_build

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+docker/.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+*.drawio.bkp
+*.drawio.dtmp
+*.pdf
+
+.idea/
+.vscode/
+
+# EOS config file
+/config.yml
+
+/user/*
+!/user/.gitkeep

LICENSE

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+Copyright 2024 The University of North Carolina at Chapel Hill
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+<p align="center">
+    <img src="docs/_static/img/eos-logo.png" alt="Alt Text" width="512">
+</p>
+
+<h1 align="center">The Experiment Orchestration System (EOS)</h1>
+
+![os](https://img.shields.io/badge/OS-win%7Cmac%7Clinux-9cf)
+![python](https://img.shields.io/badge/Python-3.10+-darkgreen)
+
+The Experiment Orchestration System (EOS) is a comprehensive software framework and runtime for laboratory automation, designed
+to serve as the foundation for one or more automated or self-driving labs (SDLs).
+
+EOS provides:
+
+* A common framework to implement laboratory automation
+* A plugin system for defining labs, devices, experiments, tasks, and optimizers
+* A package system for sharing and reusing code and resources across the community
+* Extensive static and dynamic validation of experiments, task parameters, and more
+* A runtime for executing tasks, experiments, and experiment campaigns
+* A central authoritative orchestrator that can communicate with and control multiple devices
+* Distributed task execution and optimization using the Ray framework
+* Built-in Bayesian experiment parameter optimization
+* Optimized task scheduling
+* Device and sample container allocation system to prevent conflicts
+* Result aggregation such as automatic output file storage
+
+## Installation
+
+### 1. Install PDM
+
+PDM is used as the project manager for EOS, making it easier to install dependencies and build it.
+
+#### Linux/Mac
+
+```shell
+curl -sSL https://pdm-project.org/install-pdm.py | python3 -
+```
+
+#### Windows
+
+```shell
+(Invoke-WebRequest -Uri https://pdm-project.org/install-pdm.py -UseBasicParsing).Content | py -
+```
+
+### 2. Clone the EOS Repository
+
+```shell
+git clone https://github.com/aangelos28/eos
+```
+
+### 3. Install Dependencies
+
+Navigate to the cloned repository and run:
+
+```shell
+pdm install
+```
+
+(Optional) If you wish to contribute to EOS development:
+
+```shell
+pdm install -G dev
+```
+
+(Optional) If you also wish to contribute to the EOS documentation:
+
+```shell
+pdm install -G docs
+```
+
+## Configuration
+
+After installation, you need to configure external services such as MongoDB and MinIO as well as EOS itself.
+
+### 1. Configure External Services
+
+We provide a Docker Compose file that can run all external services for you.
+
+Copy the example environment file:
+
+```shell
+cp docker/.env.example docker/.env
+```
+
+Edit `docker/.env` and provide values for all fields.
+
+### 2. Configure EOS
+
+EOS reads parameters from a YAML configuration file.
+
+Copy the example configuration file:
+
+```shell
+cp config.example.yml config.yml
+```
+
+Edit `config.yml`. Ensure that credentials are provided for the MongoDB and MinIO services.
+
+## Running
+### 1. Start External Services
+
+```shell
+cd docker
+docker compose up -d
+```
+
+### 2. Source the Virtual Environment
+
+```shell
+source env/bin/activate
+```
+
+### 3. Start the EOS Orchestrator
+
+```shell
+eos orchestrator
+```
+
+### 4. Start the EOS REST API
+
+```shell
+eos api
+```

config.example.yml

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+user_dir: ./user
+labs:
+  - lab1
+  - lab2
+experiments:
+  - experiment1
+  - experiment2
+log_level: INFO
+
+# EOS orchestrator's internal web API server configuration
+web_api:
+  host: localhost
+  port: 8070
+
+# EOS database configuration
+db:
+  host: localhost
+  port: 27017
+  username: ""
+  password: ""
+
+# EOS file database configuration
+file_db:
+  host: localhost
+  port: 9004
+  username: ""
+  password: ""