JUPyTER: JWST Unified Pipeline Toolkit for Exoplanet Reduction

JUPyTER is an automated, unified wrapper designed to run raw JWST time-series data through three pipelines simultaneously: Eureka!, exoTEDRF, and SPARTA.

Because this wrapper interfaces with three distinct, heavy-duty astrophysics pipelines, you must install the backend pipelines and their Conda environments on your machine before running JUPyTER.

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🛠️ Phase 1: Environment Setup

You will need three separate Conda environments. JUPyTER uses these names to automatically switch environments during the reduction process.

1. Eureka!

The official Eureka! Installation Instructions.

Use Eureka! v1.3

# Create the Eureka! environment
conda create -n eureka python==3.13.0
conda activate eureka

# Clone repo
git clone -b v1.3 https://github.com/kevin218/Eureka.git
cd Eureka

# Install from source
pip install -e '.[jwst]'

2. exoTEDRF

Follow the official exoTEDRF Installation Instructions.

Use ExoTEDRF v2.4.1

# Create the ! environment
conda create -n exotedrf python<3.14
conda activate exotedrf

# Clone repo
git clone https://github.com/radicamc/exoTEDRF.git
cd exoTEDRF

# Install 
python setup.py install

Also intall some dependencies (if not installed with the above commands)

pip install exouprf==1.1.1 exotic_ld h5py
pip install webbpsf

3. SPARTA

Unlike the other two pipelines, SPARTA is executed via direct script calls. You must clone the SPARTA repository directly into your JUPyTER folder and build its environment.

# Clone JUPyTER first
git clone [https://github.com/CodeSythe/JUPyTER.git](https://github.com/CodeSythe/JUPyTER.git)
cd JUPyTER

# Clone SPARTA directly inside the JUPyTER directory
git clone [https://github.com/ideasrule/sparta.git](https://github.com/ideasrule/sparta.git)

# Create the SPARTA environment
conda create -n sparta python=3.11
conda activate sparta
pip install numpy scipy astropy matplotlib pyyaml emcee
conda deactivate

🚀 Phase 2: How to Use JUPyTER

1. Add your Raw Data

Download your uncalibrated JWST .fits files from MAST and place them into the inputs directory.

2. Set up your CRDS Cache

JWST requires calibration reference files. Create a folder on your machine to act as the cache

mkdir crds_cache

3. Configure the Run

Open configs/master_run_config.yaml

• Update the top_dir and crds_cache paths to match your machine's absolute paths.
• Set your planetary priors, target name, and instrument parameters.
• Toggle which pipelines you want to run (run: True or False).

4. Execute

python master_run.py

💡 Tips & Best Practices

• Pipeline Roles: I highly recommend using Eureka! exclusively to perform your broad White Light Curve (WLC) fits to derive and lock in your precise orbital parameters. Use Eureka!/exoTEDRF for your spectroscopic reduction and final transmission spectrum.
• SPARTA Status: ⚠️ Put SPARTA on hold for now. The current SPARTA source code contains several bugs related to MIRI rotation and optimal extraction. Keep run: False for SPARTA in the master config until patched.
• Advanced Configuration: If you need to deeply customize pipeline parameters beyond what is available in the master config, you can edit the underlying pipeline template files directly inside the configs/ folder.
• Documentation & Parameters: * For questions about detector-level parameters (like jump detection or ramp fitting), consult the Official JWST Pipeline ReadTheDocs.
  • More information about the instruments consult JWST User Documentation
  • For step specific logic, consult Eureka! Docs and exoTEDRF Docs