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UV setup (#5)
* Enhance documentation and setup instructions in README and CONTRIBUTING files; add .gitignore and pyproject.toml for project configuration and dependency management. * Notebook for BAIS2 (#4) * readme and contrib initial commit. * Add attribution section to NDCI cyanobacteria detection notebook * Specifies how to install virtual environment * Adds files to ignore * Processes BAIS2 evalscript with openEO * Adds requirement file * Removes unused libraries * Removes UDP print * Updates text-based math formulae with latex --------- Co-authored-by: Emmanuel Mathot <[email protected]> * Enhance documentation and setup instructions in README and CONTRIBUTING files; add .gitignore and pyproject.toml for project configuration and dependency management. * Update .gitignore to include additional environment and temporary file exclusions --------- Co-authored-by: Firza Riany <[email protected]>
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‎CONTRIBUTING.md‎

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Thank you for your interest in contributing to the Sentinel Hub evalscript to openEO conversion project! This guide will help you understand our conversion process and standards so your contributions can be integrated smoothly.
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## Getting Started
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### Development Environment Setup
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Before you begin converting evalscripts, set up your development environment properly:
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#### Prerequisites
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- Python 3.11 or later
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- [uv](https://docs.astral.sh/uv/) for dependency management
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- Git for version control
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- Access to an openEO backend for testing
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#### Environment Setup
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1. **Install uv** if you haven't already:
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```bash
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# On macOS and Linux
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curl -LsSf https://astral.sh/uv/install.sh | sh
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# On Windows
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powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
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```
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2. **Fork and clone the repository**:
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```bash
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git clone https://github.com/your-username/openeo-udp.git
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cd openeo-udp
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```
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3. **Set up the development environment**:
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```bash
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# Create virtual environment and install all dependencies
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uv sync
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# Install development dependencies (for linting, testing)
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uv sync --group dev
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# Install as Jupyter kernel for notebook development
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uv run python -m ipykernel install --user --name openeo-udp-dev --display-name "openEO UDP (Dev)"
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```
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#### Jupyter Kernel Management
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After installation, you should have the "openEO UDP (Dev)" kernel available in Jupyter. When creating or opening notebooks:
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- Ensure you select the correct kernel
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- Verify the kernel has access to all required packages
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- Test the openEO connection in the first cell
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### Working with the Development Environment
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- **Starting Jupyter**: Use `uv run jupyter lab` or `uv run jupyter notebook`
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- **Running tests**: Use `uv run pytest`
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- **Code formatting**: Use `uv run black .`
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- **Linting**: Use `uv run ruff check .`
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- **Installing new packages**: Use `uv add package-name`
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- **Running any Python script**: Use `uv run python script.py`
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#### Verifying Your Environment
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Before starting development, verify your environment is set up correctly:
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1. **Test Python and package availability**:
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```bash
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uv run python -c "
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import openeo
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import matplotlib.pyplot as plt
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import numpy as np
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from PIL import Image
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print('All packages imported successfully!')
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"
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```
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2. **Test openEO connection** (optional, requires backend access):
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```bash
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uv run python -c "
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import openeo
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connection = openeo.connect('https://openeo.ds.io/')
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print('OpenEO connection successful!')
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"
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```
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3. **Check Jupyter kernel**:
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- Launch Jupyter: `uv run jupyter lab`
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- Create a new notebook
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- Ensure "openEO UDP (Dev)" kernel is available and selected
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- Run the import test from step 1
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## Understanding the Conversion Process
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Converting a Sentinel Hub evalscript to an openEO User-Defined Process involves more than simple translation. You need to understand both what the algorithm does scientifically and how to express that logic using openEO's process graph structure.

‎README.md‎

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To run these notebooks, you need:
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- Python 3.11 or later
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- Jupyter Notebook or JupyterLab
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- [uv](https://docs.astral.sh/uv/) for fast and reliable dependency management
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- Access to an openEO backend (we recommend https://openeo.ds.io/ for testing)
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- Basic understanding of remote sensing concepts and Python programming
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### Installation
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### Environment Setup
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Clone the repository and install the required dependencies:
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This project uses [uv](https://docs.astral.sh/uv/) for fast and reliable dependency management.
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```bash
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git clone https://github.com/developmentseed/openeo-udp.git
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cd openeo-udp
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1. **Install uv** if you haven't already:
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# Create a virtual environment
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python -m venv .venv
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```bash
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# On macOS and Linux
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curl -LsSf https://astral.sh/uv/install.sh | sh
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# Activate the virtual environment
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source .venv/bin/activate
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# On Windows
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powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
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```
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# Install requirements
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pip install -r requirements.txt
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```
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2. **Clone the repository and set up the environment**:
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```bash
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git clone https://github.com/developmentseed/openeo-udp.git
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cd openeo-udp
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# Create virtual environment and install all dependencies
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uv sync
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```
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The requirements file includes the openEO Python client library, visualization tools like matplotlib and Pillow, and any specialized processing libraries needed for specific algorithms.
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3. **Install as Jupyter kernel** (recommended for running notebooks):
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```bash
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# Install the environment as a Jupyter kernel
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uv run python -m ipykernel install --user --name openeo-udp --display-name "openEO UDP"
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```
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The environment includes the openEO Python client library, visualization tools like matplotlib and Pillow, Jupyter, and all other dependencies needed to run the notebooks.
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### Running a Notebook
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Start Jupyter and open any notebook. For example, the [NDCI cyanobacteria notebook](notebooks/sentinel/sentinel-2/marine_and_water_bodies/ndci_cyanobacteria.ipynb):
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```bash
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jupyter notebook notebooks/sentinel/sentinel-2/marine_and_water_bodies/ndci_cyanobacteria.ipynb
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# Start Jupyter using uv
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uv run jupyter lab
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# Or start Jupyter Notebook
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uv run jupyter notebook
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```
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Execute the cells sequentially to see the conversion process, validate results, and export the UDP definition. Most notebooks are designed to run completely from top to bottom without modification, though you may want to adjust spatial extents or temporal ranges to explore different areas.
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When creating or opening a notebook:
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1. Make sure the "openEO UDP" kernel is selected (if you installed it as a kernel)
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2. Open the [NDCI cyanobacteria notebook](notebooks/sentinel/sentinel-2/marine_and_water_bodies/ndci_cyanobacteria.ipynb)
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3. Execute the cells sequentially to see the conversion process, validate results, and export the UDP definition
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Most notebooks are designed to run completely from top to bottom without modification, though you may want to adjust spatial extents or temporal ranges to explore different areas.
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## Using the Exported UDPs
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‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=45", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "openeo-udp"
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description = "openEO User-Defined Processes converted from Sentinel Hub evalscripts"
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readme = "README.md"
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license = {text = "Apache-2.0"}
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authors = [
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{name = "Development Seed", email = "[email protected]"},
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]
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classifiers = [
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"Development Status :: 4 - Beta",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering :: GIS",
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]
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requires-python = ">=3.11"
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dependencies = [
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"openeo>=0.24.0",
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"matplotlib>=3.7.0",
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"Pillow>=10.0.0",
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"numpy>=1.24.0",
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"jupyter>=1.0.0",
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"ipykernel>=6.25.0",
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"requests>=2.28.0",
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]
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[project.optional-dependencies]
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dev = [
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"pytest>=7.0.0",
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"pytest-cov>=4.0.0",
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"black>=23.0.0",
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"ruff>=0.0.290",
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"pre-commit>=3.0.0",
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]
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docs = [
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"mkdocs>=1.5.0",
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"mkdocs-material>=9.0.0",
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"mkdocstrings[python]>=0.23.0",
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]
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[project.urls]
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Homepage = "https://github.com/developmentseed/openeo-udp"
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Documentation = "https://github.com/developmentseed/openeo-udp"
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Repository = "https://github.com/developmentseed/openeo-udp"
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"Bug Tracker" = "https://github.com/developmentseed/openeo-udp/issues"
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[tool.setuptools.packages.find]
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where = ["src"]
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[tool.setuptools.package-dir]
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"" = "src"
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[tool.black]
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line-length = 88
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target-version = ['py311']
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include = '\.pyi?$'
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extend-exclude = '''
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/(
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# directories
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\.eggs
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| \.git
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| \.hg
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| \.mypy_cache
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| \.tox
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| \.venv
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| _build
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| buck-out
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| build
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| dist
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)/
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'''
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[tool.ruff]
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target-version = "py311"
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line-length = 88
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select = [
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"E", # pycodestyle errors
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"W", # pycodestyle warnings
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"F", # pyflakes
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"I", # isort
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"C", # flake8-comprehensions
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"B", # flake8-bugbear
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]
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ignore = [
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"E501", # line too long, handled by black
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"B008", # do not perform function calls in argument defaults
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"C901", # too complex
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]
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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python_files = ["test_*.py"]
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python_functions = ["test_*"]
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addopts = "-v --tb=short --strict-markers"
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markers = [
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"slow: marks tests as slow (deselect with '-m \"not slow\"')",
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"integration: marks tests as integration tests",
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]

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