openmedaxis-init 0.1.2

Project scaffolder for OpenMedAxis

openmedaxis-init

A command-line scaffolder that creates ready-to-run OpenMedAxis projects with a fully configured Python environment, PyTorch stack, and all standard dependencies pre-installed.

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Requirements

• uv 0.5 or later

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Usage

uvx openmedaxis-init <project-name> [OPTIONS]

No installation needed. uvx runs the tool directly from PyPI in an isolated environment.

This single command will:

1. Create a new project directory named <project-name>
2. Generate a pyproject.toml with the correct uv/PyTorch index configuration
3. Create a virtual environment via uv sync
4. Install the full dependency stack
5. Run a smoke test to verify the environment

Options

Option	Choices	Default	Description
--template	modern	modern	Project template to use
--torch-backend	cu118, cpu	cu118	PyTorch backend (CUDA 11.8 or CPU-only)
--oma	any version string	latest	OpenMedAxis version to pin (e.g. 0.4.2)

Examples

GPU project (CUDA 11.8, latest OpenMedAxis):

uvx openmedaxis-init my-segmentation-project

CPU-only project:

uvx openmedaxis-init my-project --torch-backend cpu

Pin a specific OpenMedAxis version:

uvx openmedaxis-init my-project --oma 0.4.2

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What Gets Installed

Every modern template project installs the following packages:

Package	Version
torch	2.6.0
torchvision	0.21.0
torchaudio	2.6.0
openmedaxis	latest or pinned
lightning	2.5.2
einops	0.8.1
matplotlib	3.10.0
nibabel	5.4.0
numpy	2.1.2
pip	latest
scikit-image	0.25.2
scipy	1.16.0
torchmetrics	1.7.3
tqdm	4.67.1

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Generated Project Structure

my-project/
├── pyproject.toml          # Project config with uv/PyTorch index settings
├── .python-version         # Pins Python 3.11
├── .gitignore
├── README.md
└── src/
    └── my_project/
        ├── __init__.py
        └── train.py        # Entry point: uv run python -m my_project.train

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After Scaffolding

cd my-project
uv run python -m my_project.train

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Development

To work on openmedaxis-init itself:

git clone <repo-url>
cd openmedaxis_init
uv sync
uv run openmedaxis-init --help