uv, part 1: running scripts and tools

This is part 1 of a series on uv. Other posts in this series:

1. This post

2. uv, part 2: building and publishing packages

3. uv, part 3: Python in R with reticulate

4. uv, part 4: uv with Jupyter

Lately I've heard a lot great things about uv, an extremely fast Python package and project manager, written in Rust. After the volume of praise I see about uv reached a critical level I decided to take a look at the docs myself and give it a try. After just a few minutes of use: uv is awesome, and I'm going to add to that praise here. It's probably going to replace pip, pipx, poetry, and most of conda for me. The "extremely fast" bit is no lie. Having used conda and pip for so many years, uv is unbelievably fast.

This is the first part in what will be a multi-part series on using the uv package manager. In this part I'll cover using uv (1) running scripts with inline metadata, and (2) running tools. I'll cover creating environments, projects, packages, managing python versions, using Jupyter in future posts.

You can read more about uv at docs.astral.sh/uv.

Running scripts

One of the most immediately useful things you can do with uv is running Python scripts. With no dependencies you can do this with: uv run example.py. This doesn't do anything more than running python example.py would do.

print("Hello world")

$ uv run example.py
Hello world

Add dependencies

But what if we have imports that aren't part of the standard library? Here's a script that uses Biopython to reverse complement a DNA sequence, and prints the original and the reverse complement.

from Bio.Seq import Seq

my_seq = Seq("GATTACA")
print(my_seq)

rc = my_seq.reverse_complement()
print(rc)

If we just try to run that with python example.py or uv run example.py, it will fail because we haven't installed Biopython.

$ uv run example.py
Traceback (most recent call last):
  File "/Users/turner/Downloads/uv/example.py", line 1, in <module>
    from Bio.Seq import Seq
ModuleNotFoundError: No module named 'Bio'

You could go through the trouble of setting up a new Conda environment or venv, the pip installing biopython, but this adds extra maintenance burden and time solving your Conda environment.

Running scripts with inline metadata

PEP 723 specifies a metadata format that can be embedded in single-file Python scripts to declare dependencies, and uv supports declaring dependencies inline according to PEP 723.

uv add --script example.py biopython

This modifies the script in place, adding the biopython dependency in this specialized form of a comment at the top of the script.

# /// script
# requires-python = ">=3.12"
# dependencies = [
#     "biopython",
# ]
# ///
from Bio.Seq import Seq

my_seq = Seq("AGTACACTGGT")
print(my_seq)

rc = my_seq.reverse_complement()
print(rc)

We can now run it with uv run, and when we do so, uv understands this inline metadata at the top and creates this temporary virtual environment on the fly, installs Biopython, and runs the code. It does this all in less than one second (package installation took only 10 milliseconds) 🔥.

$ time uv run example.py
Reading inline script metadata from `example.py`
Installed 2 packages in 10ms

GATTACA
TGTAATC

real	0m0.767s
user	0m0.223s
sys	0m0.231s

That on-demand environment is cached, so running it again takes milliseconds 🔥.

$ time uv run example.py
Reading inline script metadata from `example.py`

GATTACA
TGTAATC

real	0m0.080s
user	0m0.048s
sys	0m0.027s

Executable scripts with a uv shebang

You can add a shebang line to the top of your script that'll allow you to run it as an executable: #!/usr/bin/env -S uv run. I also added the --quiet flag so you don't get any additional output ("Reading inline script metadata…"). I learned about this on Simon Willison's blog.

#!/usr/bin/env -S uv run --quiet

# /// script
# requires-python = ">=3.12"
# dependencies = [
#     "biopython",
# ]
# ///

from Bio.Seq import Seq

my_seq = Seq("AGTACACTGGT")
print(my_seq)

rc = my_seq.reverse_complement()
print(rc)

You can chmod 755 your script and run it as an executable on any machine where uv is available, and if the dependencies you specify with inline metadata will automatically be installed and cached into a temporary isolated environment, using the correct version of Python as specified.

$ ./example.py 
AGTACACTGGT
ACCAGTGTACT

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Running tools

From PyPI

With uv you can also use tools that are part of Python packages. You can do this with uv tool run <toolname> or the shortcut, uvx <toolname> (uvx is meant to be a faster drop-in replacement for pipx). At my previous job we wrote a little Python package called vcferr (paper, PyPI, GitHub) that takes a VCF and changes some of the genotypes in ways you control. You could set up a virtual environment and pip install it, or a conda environment and conda install it. But you can avoid creating and managing these environments and just use uv to run the tool directly. Because vcferr is on PyPI, we can just use uv tool run vcferr, or shorter, uvx vcferr. You can see that installation of its dependencies into a temporary environment took only 5 milliseconds, and the entire process required only 3 seconds. Because this is now cached, running it again would only take milliseconds 🔥.

$ time uvx vcferr --help
Installed 3 packages in 5ms

Usage: vcferr [OPTIONS] <input_vcf>

Options:
  -s, --sample TEXT        ID of sample in VCF file 
                           to be simulated[required]
  -o, --output_vcf TEXT    Output VCF file containing simulated 
                           genotypes ex:example.sim.vcf.gz
  ...(truncated)...
  -a, --seed INTEGER       Random number seed
  --help                   Show this message and exit.

real	0m3.351s
user	0m0.280s
sys	0m0.184s

You could use this for little tools where you don't want to set up a full environment, such as running a code formatter/linter like black (uvx black) or ruff (uvx ruff). If you use the tool a lot, you could use uv tool install <toolname> to make the tool available in a special directory on your PATH.

From GitHub

We can also run a tool directly from GitHub. A few months ago I wrote about making a Python CLI using click, and making this a package using a cookiecutter template.

This tool, caffeinated (GitHub, PyPI), is a silly little command line tool to tell you how much caffeine remains in your system at bedtime based on how much you consume in the morning. It's on PyPI so you could just use uvx caffeinated to run it. However, what if it wasn't on PyPI? We can run the tool directly from GitHub by passing in the --from option and giving it the GitHub URL. You can see that it installed the two required dependencies in 1 millisecond, and runs the code in 1.6 seconds. The tool is cached so running it a second time takes only milliseconds 🔥.

$ time uvx --from \
  git+https://github.com/stephenturner/caffeinated \
  caffeinated -c 200 -s 0600 -b 2000

 Updated https://github.com/stephenturner/caffeinated (762d601)
   Built caffeinated @ git+https://github.com/stephenturner/caffeinated@762d60111ac84f4af5031141ea29232d26659f9f
Installed 2 packages in 1ms

You would have 39.7mg of caffeine in your system 
if you went to bed at 8:00pm (in 14.0 hours).
That's like having 44% of a cup of coffee before bed.

real	0m1.678s
user	0m0.611s
sys	0m1.481s

Tools with many dependencies

In the examples above the tools had a very lightweight dependency stack. What about a tool with more first and second order dependencies? The nf-core/tools Python package has a few dependencies, each of those has a few second-order and deeper dependencies. When we run it the first time with uvx nf-core it takes ~7.5 seconds to resolve the dependency stack of 95 packages, but less than one second to install those dependencies 🔥.

$ time uvx nf-core
Installed 95 packages in 255ms
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.1.1 - https://nf-co.re

 Usage: nf-core [OPTIONS] COMMAND [ARGS]...

(...truncated...)

real	0m7.501s
user	0m2.089s
sys	0m5.420s

Since the result is cached, running it a second time required less than one second 🔥.

$ time uvx nf-core
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.1.1 - https://nf-co.re

 Usage: nf-core [OPTIONS] COMMAND [ARGS]...

(...truncated...)

real	0m0.447s
user	0m0.390s
sys	0m0.106s

Tools requiring other packages in the environment

There's a tool on PyPI called voila (documentation) that turns Jupyter notebooks into standalone web applications. Let's take a look at this notebook that uses bqplot to create an interactive graphic. Here's what it looks like in Jupyter lab (I'll cover running Jupyter with uv in another post).

We can use voila to turn that notebook into an interactive web app. You may think of running something like uvx voila bqplot.ipynb. But this won't work — voila runs without an issue but it'll complain that you need a jupyter kernel, numpy, and bqplot installed to actually run the conversion. Because none of these are dependencies of voila itself, uv happily runs voila. But because the thing you're doing with voila requires additional packages available that aren't dependencies of voila itself, you'll have to add the --with option, specifying which additional packages you want installed in the on-demand environment you create when using uvx voila.

uvx --with jupyter,numpy,bqplot voila bqplot.ipynb

The result is below. The first run with a clean cache installs 105 packages from PyPI, and took ~6 seconds. Subsequent runs using uv's cache initialized in <1 second 🔥.

More Info

The best way to learn more is by going through the Getting started section and the Guides sections on the official docs at docs.astral.sh/uv.

I've recommended videos from ArjanCodes in the past. Arjan's video on uv provides a good overview of what you can do with uv.

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