# AGENTS.md

## Environment

This project uses a conda environment named `longitudinal` (Python 3.14).

Activate with:

```bash
source /opt/conda/etc/profile.d/conda.sh && conda activate longitudinal
```

Key packages: torch 2.14 (+cu126), torchvision, monai 1.6 (pip, Pipeline C), numpy, scipy, pandas, scikit-learn, scikit-image, matplotlib, nibabel, SimpleITK.

## Project

Longitudinal (repeated-measures) analysis of medical imaging data. Repo is at an early stage — see README.md for any project notes.

## Conventions

- All Python commands must run inside the `longitudinal` conda environment.
- GPU is available (CUDA 12.6); use `torch.device('cuda')` when appropriate. Multi-GPU stages of Pipelines A and C run via `torchrun --standalone --nproc_per_node N` (rank = GPU).
- No lint/test tooling is configured yet; run scripts directly with `python <script>` from the repo root.