Sometimes it is better to simply work through examples and see how it works in practice. We provide a repository were you can download examples including data, configuration files and notebooks. Below we also include a brief description of what you can find in there so you can direct yourself to whatever is most useful.

https://codebase.helmholtz.cloud/cosmos/neptoon_examples

Quick Start

If you want to try out the neptoon examples without setting things up locally, try out the MyBinder link below!

Setting Up Neptoon Examples

Here we'll explain how to set your environment up to work with the neptoon examples.

Quick Start

Here we show how to set up using the terminal. First, clone the examples repository and change into the downloaded repository with the following terminal command:

git clone https://codebase.helmholtz.cloud/cosmos/neptoon_examples.git
cd neptoon_examples

This will download the example data and scripts.

Next you want to create a python environment on your system to use neptoon. Below are some commands that will do just that for you, using the requirements.txt you've just downloaded from the examples repository.

pip + venv (Windows)pip + venv (Linux/macOS)condamamba

Create and activate a virtual environment using Python's built-in venv:

python -m venv neptoon-env
# Activate the environment:
neptoon-env\Scripts\activate     # Windows

# Install dependencies
pip install -r requirements.txt

Create and activate a virtual environment using Python's built-in venv:

python -m venv neptoon-env
# Activate the environment:
source neptoon-env/bin/activate  # Linux/macOS

# Install dependencies
pip install -r requirements.txt

Create and activate a Conda environment:

conda create -n neptoon_examples python=3.10
conda activate neptoon_examples

# Install dependencies
conda install --file requirements.txt

Create and activate a Mamba environment (faster than conda):

mamba create -n neptoon_examples python=3.10
mamba activate neptoon_examples

# Install dependencies
mamba install --file requirements.txt

Development Environments

VS Code Setup

Whilst your terminal is still in the example repository - launch VSCode

1. Open project in VS Code:

   code .
   

2. Install essential VS Code extensions:

   • Python (ms-python.python)
   • Jupyter (ms-toolsai.jupyter)

3. Configure Python interpreter:

pip + venvconda/mamba

1. Press `Ctrl+Shift+P` (Windows/Linux) or `Cmd+Shift+P` (Mac)
2. Type "Python: Select Interpreter"
3. Choose `./venv/bin/python` from the list

1. Press `Ctrl+Shift+P` (Windows/Linux) or `Cmd+Shift+P` (Mac)
2. Type "Python: Select Interpreter"
3. Look for `conda env:neptoon_examples` in the list

Environment Detection

If VS Code doesn't automatically detect your conda/mamba environment, try: 1. Closing and reopening VS Code 2. Running conda init in your terminal 3. Ensuring the Python extension is properly installed

1. Working with notebooks:
   • Open .ipynb files directly in VS Code
   • Select your configured kernel (neptoon_examples)

Jupyter Lab (Optional)

If installed, launch Jupyter Lab:

jupyter lab

Features:

• Browser-based interface at http://localhost:8888
• Multiple notebook support
• Integrated file browser

MyBinder (No Installation)

For quick exploration without local setup:

1. Visit Neptoon Examples on MyBinder
2. Wait for environment to build - it could be a minute or two if no one has been on in a while
3. Access notebooks directly in browser

Temporary

MyBinder sessions are temporary. All changes are lost after inactivity.