{Project name}

One or two sentences on what this project does and why it exists.

Status

{Early exploration | Active development | Stable | Archived}. {Anything a newcomer should know before relying on this: what works, what doesn't.}

Getting started

Requires Python >=3.12 and uv.

uv sync                 # create the virtualenv and install dependencies
uvx pre-commit install  # install the pre-commit hooks

Check the install works:

uv run python -m {package_name}.hello

Usage

{The shortest command that produces something useful, and the output it prints. Add one example per entry point.}

uv run python -m {package_name}.{entry_point} --help

Layout

Path	Contents
src/{package_name}/	Library code, importable as {package_name}.
src/{package_name}/data/	config.yaml — data paths and project settings.
tests/	Test suite, run with uv run pytest.
containers/	Apptainer definition and entrypoint.
{scripts, notebooks, …}	{Fill in the folders this project actually adds.}

Data paths live in config.yaml and are read through config.py — never hardcode them in scripts.

Data

{Where the inputs come from, where they live on the lab storage, and how to get them. Say if anything is restricted or must not be committed.}

Results

LOGBOOK.md records each iteration in antichronological order (hypothesis, method, key results, next steps). RESULTS.md compiles the comparable results across iterations, and is the place to look first.

{Link the reports here as they are produced.}

Containers

Build and run the Apptainer image, binding your working directory:

apptainer build --build-arg PROJECT_NAME={project-name} project.sif containers/apptainer.def
apptainer run --bind /path/to/workdir:/mnt/{project-name} project.sif

See the header of containers/apptainer.def for the available build arguments.

Development

GUIDELINES.md covers the lab-wide toolchain (uv, ruff, ty, pre-commit); AGENTS.md covers the coding style and research workflow, and is what coding agents read. Both apply to this project — document only the deviations here.

uv run pytest              # run the tests
uvx pre-commit run --all-files  # run every hook, as CI does

.github/workflows/ci.yml runs those same two checks on every push.

Contact

{Maintainer name and how to reach them.}