Installation

sparrow runs on Python 3.7+ and includes compiled (Cython) extensions. The sections below cover setting up an isolated environment and installing sparrow with either pip or uv, from PyPI or directly from GitHub.

1. Create a virtual environment (recommended)

Installing into an isolated environment keeps sparrow and its dependencies from interfering with other projects. Use either the built-in venv (with pip) or uv (a fast drop-in replacement).

With `venv` + `pip`

# create the environment
python -m venv sparrow-env

# activate it
source sparrow-env/bin/activate        # macOS / Linux
# sparrow-env\Scripts\activate         # Windows (PowerShell/cmd)

# make sure pip is current
python -m pip install --upgrade pip

With `uv`

# create and activate
uv venv sparrow-env
source sparrow-env/bin/activate        # macOS / Linux
# sparrow-env\Scripts\activate         # Windows

uv can also manage the environment for you transparently; in that case use uv pip install ... in place of pip install ... below.

2. Install sparrow 

Install from PyPI (stable)

# with pip
pip install idptools-sparrow

# with uv
uv pip install idptools-sparrow

Install from GitHub (latest)

To get the most recent development version straight from the repository:

# with pip
pip install git+https://github.com/idptools/sparrow.git

# with uv
uv pip install git+https://github.com/idptools/sparrow.git

Note

Installing from GitHub builds the Cython extensions locally, so you need a working C compiler (Xcode command-line tools on macOS, build-essential on Debian/Ubuntu, or MSVC build tools on Windows). NumPy is required at build time and is installed automatically.

3. Verify the installation 

python -c "import sparrow; print(sparrow.__version__)"

from sparrow import Protein

p = Protein("MEEEKKKKSSSTTTDDD")
print(p.FCR, p.NCPR, p.kappa)

If those run without error, sparrow is installed correctly.

Dependencies 

Core sequence analysis works out of the box. The deep-learning predictors (reached via Protein.predictor) rely on PyTorch through the parrot dependency, which is installed automatically; the first call to a given predictor loads its network lazily.

Next steps 

New to sparrow? See Worked Examples for worked, runnable walkthroughs.
Looking for a specific call? Everything you can do with a protein is in The Protein Object.