TeamTomo

TeamTomo is a set of modular Python package for cryo-EM and cryo-ET for the modern scientific computing environment.

This unified repository contains the core TeamTomo data processing functionality under a single umbrella for better maintainability and cross-package development. File I/O packages are distributed separately and can be found under the organizations repositories.

Getting Started

Using TeamTomo packages is easy within the Python ecosystem. Simply install the latest release of packages from PyPI (e.g. pip install torch-grid-utils). A complete list of packages can be found on teamtomo.org.

If you're interested in contributing to TeamTomo, please look through the CONTRIBUTING guide for more info on adding, migrating, or updating packages. Source installation instructions for different use-cases are listed below. Note that the development workspace depends on the uv tool for Python environment/package management.

Basic source installation

git clone https://github.com/teamtomo/teamtomo.git
cd teamtomo
uv sync

For contributing developers

We strongly recommend making your own fork of the monorepo if you plan on contributing changes. Code should be edited in your repo (origin) and pull requests made into the TeamTomo repo (upstream).

First, fork the repository on GitHub (button near top-right of the repo home page), and then clone your fork locally:

git clone https://github.com/YOUR_USERNAME/teamtomo.git
cd teamtomo

Then, add the TeamTomo repository as an upstream remote to keep your fork up to date:

git remote add upstream https://github.com/teamtomo/teamtomo.git
git remote -v
# Verify remote setup looks like this
# origin        https://github.com/YOUR_USERNAME/teamtomo.git (fetch)
# origin        https://github.com/YOUR_USERNAME/teamtomo.git (push)
# upstream      https://github.com/teamtomo/teamtomo.git (fetch)
# upstream      https://github.com/teamtomo/teamtomo.git (push)

Package setting up via uv

Then, create and activate a new virtual environment:

uv venv
source .venv/bin/activate

And finally sync with the repository to install packages

uv sync --all-extras --all-packages

Note that the --all-extras and --all-packages flags install the development and testing requirements for all sub-packages. More granular install options are possible, if your system requires it.

Before opening a pull request

CI checks two things beyond the test suite, and a PR won't pass until both are satisfied:

• Formatting, linting, and type checks. These are defined in .pre-commit-config.yaml (ruff, ruff-format, mypy, validate-pyproject, typos). Run them locally with:

  uv run --group dev pre-commit run --all-files
  

  Or install them as a git hook so they run automatically on every commit:

  uv run --group dev pre-commit install
  

• A lockfile in sync with pyproject.toml. If you added, removed, or changed a dependency in any package's pyproject.toml, regenerate the lockfile before committing:

  uv lock
  

  CI runs uv sync --locked, which fails outright if uv.lock doesn't match what the pyproject.toml files declare.

Editable install for downstream development

For developing programs atop TeamTomo infrastructure, it's useful to have your program and TeamTomo both installed in editable mode in the same environment. Assuming you've cloned the teamtomo/teamtomo repo and your program uses uv for packaging, add the following to your packages pyproject.toml file:

[tool.uv.sources]
# (other lines for tool.uv.sources)
torch-grid-utils =          { path = "/path/to/teamtomo/packages/primitives/torch-grid-utils", editable = true }
torch-affine-utils =        { path = "/path/to/teamtomo/packages/primitives/torch-affine-utils", editable = true }
torch-image-interpolation = { path = "/path/to/teamtomo/packages/primitives/torch-image-interpolation", editable = true }
# ...
# Add other TeamTomo packages you want editable

# (continuation of pyproject.toml)

Then, in your project folder, run uv sync which will install those dependencies plus the listed teamtomo packages in editable mode. Changes made to TeamTomo packages will reflect in your project's environment.

List of Packages

🚧 Coming Soon 🚧