linkinpy

A Python package to bring uv-managed workflows to common image analysis tools.

Quick Start

uv sync
uv run pytest

Run these commands from the LinkinPy/ folder.

This package pins its local development interpreter in .python-version and keeps package metadata in pyproject.toml.

Common Commands

uv sync                  # create/update the local environment
uv run pytest            # run the test suite
uv run ruff check .      # lint the codebase
uv run ruff format .     # format the codebase
uv run python -m build   # build the source and wheel distributions
uv run pre-commit install

If you prefer shorter aliases, the same workflow is available through make:

make sync
make test
make lint
make format
make build

LinkinPy Spec Workflow

LinkinPy reads YAML spec files such as ../Library/nanopyx.yaml. Each spec file owns exactly one isolated uv virtual environment at ~/.linkinpy/<spec-file-name>/, and all runs for that spec execute inside that environment. LinkinPy checks whether uv is installed, bootstraps it when missing, and installs the core package into every spec-owned environment automatically.

uv run linkinpy list ../Library/nanopyx.yaml
uv run linkinpy install ../Library/nanopyx.yaml --interface cli
uv run linkinpy run ../Library/nanopyx.yaml eSRRF image=input.tif --output result.tif

The run command accepts callable arguments as name=value. Image arguments declared as np.ndarray can be passed as image file paths for the CLI path. The core also exposes Python APIs for spec parsing, environment management, image transport, direct callable execution, and magicgui widget construction.

Project Layout

src/linkinpy/
tests/
pyproject.toml
.python-version
GETTING_STARTED.md
CONTRIBUTING.md

Documentation

• Start with GETTING_STARTED.md for first-time setup
• See CONTRIBUTING.md for the contributor workflow
• Track user-facing changes in CHANGELOG.md

For the multi-project repository overview, see the repository root README.