\[ \newcommand{\figleft}{{\em (Left)}} \newcommand{\figcenter}{{\em (Center)}} \newcommand{\figright}{{\em (Right)}} \newcommand{\figtop}{{\em (Top)}} \newcommand{\figbottom}{{\em (Bottom)}} \newcommand{\captiona}{{\em (a)}} \newcommand{\captionb}{{\em (b)}} \newcommand{\captionc}{{\em (c)}} \newcommand{\captiond}{{\em (d)}} \newcommand{\newterm}[1]{{\bf #1}} \def\figref#1{figure~\ref{#1}} \def\Figref#1{Figure~\ref{#1}} \def\twofigref#1#2{figures \ref{#1} and \ref{#2}} \def\quadfigref#1#2#3#4{figures \ref{#1}, \ref{#2}, \ref{#3} and \ref{#4}} \def\secref#1{section~\ref{#1}} \def\Secref#1{Section~\ref{#1}} \def\twosecrefs#1#2{sections \ref{#1} and \ref{#2}} \def\secrefs#1#2#3{sections \ref{#1}, \ref{#2} and \ref{#3}} \def\eqref#1{equation~\ref{#1}} \def\Eqref#1{Equation~\ref{#1}} \def\plaineqref#1{\ref{#1}} \def\chapref#1{chapter~\ref{#1}} \def\Chapref#1{Chapter~\ref{#1}} \def\rangechapref#1#2{chapters\ref{#1}--\ref{#2}} \def\algref#1{algorithm~\ref{#1}} 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\def\rmR{{\mathbf{R}}} \def\rmS{{\mathbf{S}}} \def\rmT{{\mathbf{T}}} \def\rmU{{\mathbf{U}}} \def\rmV{{\mathbf{V}}} \def\rmW{{\mathbf{W}}} \def\rmX{{\mathbf{X}}} \def\rmY{{\mathbf{Y}}} \def\rmZ{{\mathbf{Z}}} \def\ermA{{\textnormal{A}}} \def\ermB{{\textnormal{B}}} \def\ermC{{\textnormal{C}}} \def\ermD{{\textnormal{D}}} \def\ermE{{\textnormal{E}}} \def\ermF{{\textnormal{F}}} \def\ermG{{\textnormal{G}}} \def\ermH{{\textnormal{H}}} \def\ermI{{\textnormal{I}}} \def\ermJ{{\textnormal{J}}} \def\ermK{{\textnormal{K}}} \def\ermL{{\textnormal{L}}} \def\ermM{{\textnormal{M}}} \def\ermN{{\textnormal{N}}} \def\ermO{{\textnormal{O}}} \def\ermP{{\textnormal{P}}} \def\ermQ{{\textnormal{Q}}} \def\ermR{{\textnormal{R}}} \def\ermS{{\textnormal{S}}} \def\ermT{{\textnormal{T}}} \def\ermU{{\textnormal{U}}} \def\ermV{{\textnormal{V}}} \def\ermW{{\textnormal{W}}} \def\ermX{{\textnormal{X}}} \def\ermY{{\textnormal{Y}}} \def\ermZ{{\textnormal{Z}}} \def\vzero{{\bm{0}}} \def\vone{{\bm{1}}} \def\vmu{{\bm{\mu}}} \def\vtheta{{\bm{\theta}}} \def\va{{\bm{a}}} \def\vb{{\bm{b}}} \def\vc{{\bm{c}}} \def\vd{{\bm{d}}} \def\ve{{\bm{e}}} \def\vf{{\bm{f}}} \def\vg{{\bm{g}}} \def\vh{{\bm{h}}} \def\vi{{\bm{i}}} \def\vj{{\bm{j}}} \def\vk{{\bm{k}}} \def\vl{{\bm{l}}} \def\vm{{\bm{m}}} \def\vn{{\bm{n}}} \def\vo{{\bm{o}}} \def\vp{{\bm{p}}} \def\vq{{\bm{q}}} \def\vr{{\bm{r}}} \def\vs{{\bm{s}}} \def\vt{{\bm{t}}} \def\vu{{\bm{u}}} \def\vv{{\bm{v}}} \def\vw{{\bm{w}}} \def\vx{{\bm{x}}} \def\vy{{\bm{y}}} \def\vz{{\bm{z}}} \def\evalpha{{\alpha}} \def\evbeta{{\beta}} \def\evepsilon{{\epsilon}} \def\evlambda{{\lambda}} \def\evomega{{\omega}} \def\evmu{{\mu}} \def\evpsi{{\psi}} \def\evsigma{{\sigma}} \def\evtheta{{\theta}} \def\eva{{a}} \def\evb{{b}} \def\evc{{c}} \def\evd{{d}} \def\eve{{e}} \def\evf{{f}} \def\evg{{g}} \def\evh{{h}} \def\evi{{i}} \def\evj{{j}} \def\evk{{k}} \def\evl{{l}} \def\evm{{m}} \def\evn{{n}} \def\evo{{o}} \def\evp{{p}} \def\evq{{q}} \def\evr{{r}} \def\evs{{s}} \def\evt{{t}} \def\evu{{u}} \def\evv{{v}} \def\evw{{w}} \def\evx{{x}} \def\evy{{y}} \def\evz{{z}} \def\mA{{\bm{A}}} \def\mB{{\bm{B}}} \def\mC{{\bm{C}}} \def\mD{{\bm{D}}} \def\mE{{\bm{E}}} \def\mF{{\bm{F}}} \def\mG{{\bm{G}}} \def\mH{{\bm{H}}} \def\mI{{\bm{I}}} \def\mJ{{\bm{J}}} \def\mK{{\bm{K}}} \def\mL{{\bm{L}}} \def\mM{{\bm{M}}} \def\mN{{\bm{N}}} \def\mO{{\bm{O}}} \def\mP{{\bm{P}}} \def\mQ{{\bm{Q}}} \def\mR{{\bm{R}}} \def\mS{{\bm{S}}} \def\mT{{\bm{T}}} \def\mU{{\bm{U}}} \def\mV{{\bm{V}}} \def\mW{{\bm{W}}} \def\mX{{\bm{X}}} \def\mY{{\bm{Y}}} \def\mZ{{\bm{Z}}} \def\mBeta{{\bm{\beta}}} \def\mPhi{{\bm{\Phi}}} \def\mLambda{{\bm{\Lambda}}} \def\mSigma{{\bm{\Sigma}}} \newcommand{\tens}[1]{\bm{\mathsfit{#1}}} \def\tA{{\tens{A}}} \def\tB{{\tens{B}}} \def\tC{{\tens{C}}} \def\tD{{\tens{D}}} \def\tE{{\tens{E}}} \def\tF{{\tens{F}}} \def\tG{{\tens{G}}} \def\tH{{\tens{H}}} \def\tI{{\tens{I}}} \def\tJ{{\tens{J}}} \def\tK{{\tens{K}}} \def\tL{{\tens{L}}} \def\tM{{\tens{M}}} \def\tN{{\tens{N}}} \def\tO{{\tens{O}}} \def\tP{{\tens{P}}} \def\tQ{{\tens{Q}}} \def\tR{{\tens{R}}} \def\tS{{\tens{S}}} \def\tT{{\tens{T}}} \def\tU{{\tens{U}}} \def\tV{{\tens{V}}} \def\tW{{\tens{W}}} \def\tX{{\tens{X}}} \def\tY{{\tens{Y}}} \def\tZ{{\tens{Z}}} \def\gA{{\mathcal{A}}} \def\gB{{\mathcal{B}}} \def\gC{{\mathcal{C}}} \def\gD{{\mathcal{D}}} \def\gE{{\mathcal{E}}} \def\gF{{\mathcal{F}}} \def\gG{{\mathcal{G}}} \def\gH{{\mathcal{H}}} \def\gI{{\mathcal{I}}} \def\gJ{{\mathcal{J}}} \def\gK{{\mathcal{K}}} \def\gL{{\mathcal{L}}} \def\gM{{\mathcal{M}}} \def\gN{{\mathcal{N}}} \def\gO{{\mathcal{O}}} \def\gP{{\mathcal{P}}} \def\gQ{{\mathcal{Q}}} \def\gR{{\mathcal{R}}} \def\gS{{\mathcal{S}}} \def\gT{{\mathcal{T}}} \def\gU{{\mathcal{U}}} \def\gV{{\mathcal{V}}} \def\gW{{\mathcal{W}}} \def\gX{{\mathcal{X}}} \def\gY{{\mathcal{Y}}} \def\gZ{{\mathcal{Z}}} \def\sA{{\mathbb{A}}} \def\sB{{\mathbb{B}}} \def\sC{{\mathbb{C}}} \def\sD{{\mathbb{D}}} \def\sF{{\mathbb{F}}} \def\sG{{\mathbb{G}}} \def\sH{{\mathbb{H}}} \def\sI{{\mathbb{I}}} \def\sJ{{\mathbb{J}}} \def\sK{{\mathbb{K}}} \def\sL{{\mathbb{L}}} \def\sM{{\mathbb{M}}} \def\sN{{\mathbb{N}}} \def\sO{{\mathbb{O}}} \def\sP{{\mathbb{P}}} \def\sQ{{\mathbb{Q}}} \def\sR{{\mathbb{R}}} \def\sS{{\mathbb{S}}} \def\sT{{\mathbb{T}}} \def\sU{{\mathbb{U}}} \def\sV{{\mathbb{V}}} \def\sW{{\mathbb{W}}} \def\sX{{\mathbb{X}}} \def\sY{{\mathbb{Y}}} \def\sZ{{\mathbb{Z}}} \def\emLambda{{\Lambda}} \def\emA{{A}} \def\emB{{B}} \def\emC{{C}} \def\emD{{D}} \def\emE{{E}} \def\emF{{F}} \def\emG{{G}} \def\emH{{H}} \def\emI{{I}} \def\emJ{{J}} \def\emK{{K}} \def\emL{{L}} \def\emM{{M}} \def\emN{{N}} \def\emO{{O}} \def\emP{{P}} \def\emQ{{Q}} \def\emR{{R}} \def\emS{{S}} \def\emT{{T}} \def\emU{{U}} \def\emV{{V}} \def\emW{{W}} \def\emX{{X}} \def\emY{{Y}} \def\emZ{{Z}} \def\emSigma{{\Sigma}} \newcommand{\etens}[1]{\mathsfit{#1}} \def\etLambda{{\etens{\Lambda}}} \def\etA{{\etens{A}}} \def\etB{{\etens{B}}} \def\etC{{\etens{C}}} \def\etD{{\etens{D}}} \def\etE{{\etens{E}}} \def\etF{{\etens{F}}} \def\etG{{\etens{G}}} \def\etH{{\etens{H}}} \def\etI{{\etens{I}}} \def\etJ{{\etens{J}}} \def\etK{{\etens{K}}} \def\etL{{\etens{L}}} \def\etM{{\etens{M}}} \def\etN{{\etens{N}}} \def\etO{{\etens{O}}} \def\etP{{\etens{P}}} \def\etQ{{\etens{Q}}} \def\etR{{\etens{R}}} \def\etS{{\etens{S}}} \def\etT{{\etens{T}}} \def\etU{{\etens{U}}} \def\etV{{\etens{V}}} \def\etW{{\etens{W}}} \def\etX{{\etens{X}}} \def\etY{{\etens{Y}}} \def\etZ{{\etens{Z}}} \newcommand{\pdata}{p_{\rm{data}}} \newcommand{\ptrain}{\hat{p}_{\rm{data}}} \newcommand{\Ptrain}{\hat{P}_{\rm{data}}} \newcommand{\pmodel}{p_{\rm{model}}} \newcommand{\Pmodel}{P_{\rm{model}}} \newcommand{\ptildemodel}{\tilde{p}_{\rm{model}}} \newcommand{\pencode}{p_{\rm{encoder}}} \newcommand{\pdecode}{p_{\rm{decoder}}} \newcommand{\precons}{p_{\rm{reconstruct}}} \newcommand{\E}{\mathbb{E}} \newcommand{\Ls}{\mathcal{L}} \newcommand{\R}{\mathbb{R}} \newcommand{\emp}{\tilde{p}} \newcommand{\lr}{\alpha} \newcommand{\reg}{\lambda} \newcommand{\rect}{\mathrm{rectifier}} \newcommand{\softmax}{\mathrm{softmax}} \newcommand{\sigmoid}{\sigma} \newcommand{\softplus}{\zeta} \newcommand{\KL}{D_{\mathrm{KL}}} \newcommand{\Var}{\mathrm{Var}} \newcommand{\standarderror}{\mathrm{SE}} \newcommand{\Cov}{\mathrm{Cov}} \newcommand{\normlzero}{L^0} \newcommand{\normlone}{L^1} \newcommand{\normltwo}{L^2} \newcommand{\normlp}{L^p} \newcommand{\normmax}{L^\infty} \newcommand{\parents}{Pa} % See usage in notation.tex. 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Managing dependencies with pixi and uv

2025-09-04
pixi (1) venv (2) python (6) uv (1)

What is uv/pixi?

pixi is a relatively new dependency management tool for python (version 0.54.1 as of writing this article). If you are familiar with uv, you will notice that this feels like uv, except now with conda backend. You can think of it as a management for conda environments, but now with a different way of thinking. The commands for these are quite similar, and the main difference we want to keep in mind is that pixi uses conda as a backend, while uv uses venv and pypi.

Why use uv?

uv is basically an executable command that takes care of creating and managing virtual environments at the project level (i.e. directory). The nice thing about uv is that it is tighly coupled with pyproject.toml. If you have used node.js, you will be familiar with this concept (npm is the manager and package.json is the project file). This means you can run things like uv add <package-name> to add a package to your peojct, and you can also run any command that assumes the venv is activated by running uv run <command> where <command> can be anything (e.g. python my_script.py, pytest, etc.). uv is also able to change the python version used in the venv by simply changing the pyproject.toml file, which is definitely an improvement over the traditional venv that was bound to parent python executable.

Why use pixi?

Conda is a great tool with a very robust ecosystem. However, the solver can be slow at times, and it can be a struggle to figure out how to set up a conda environment for a project -- will it be shared? how do I run jobs with the environment using a job scheduler? etc. Of course, these are all solvable problems. But sometimes you just don't want to bother.

For example, if I have a project that uses conda, I will have to make sure to activate that environment before running anything. Pixi addresses this by looking for the closest pixi.toml or pyproject.toml file in the current directory to automatically resolve and activate the environment. This is similar to how uv works, and it is very convenient.

So if you had to do this:

conda create -n MYENV python=3.10 -y;
conda activate MYENV;
pip install -r requirements.txt;

# now to run stuff later
conda activate MYENV;
python my_script.py

Now you can do this:

pixi init MYPROJ
pixi add XYZ
pixi add --pypi XXX # if you do not need a conda package (i.e. pure python packages)
# and to run stuff
pixi run python my_script.py

So instead of runnig a python command directly, you let pixi do the running for you. There are other benefits as well. For example, both uv and pixi maintain a lockfile that records the versions of all packages installed, as well as a reproducible instructions for environment (through pyproject.toml or pixi.toml). If you have used npm before, this should feel very familiar. This means that you now don't have to write down every major package you install -- it will be recorded automatically. The backends for this hasn't changed. It's still conda and pip under the hood, but now we are approaching this from a project-based view.

Why not UV?

Like I noted, this feels quite similar to uv. So why not just use uv? The main reason is that uv only knows about pypi packages -- i.e. stuff you can get from pip. This is fine for most cases, but in scientific computing, you often need packages that have compiled binaries (numpy, torch, pandas, etc) -- this is the same reason people use conda instead of venv. Pixi on the other hand uses conda as the default backend -- meaning you can install from pypi using --pypi flag, but you can also install stuff from conda repositories.

Starting commands

Starting a project

if already created, run pixi init . inside. Or run pixi init <project-name> to create a new directory.

Running code

instead of just python <file>, run pixi run <file> to ensure all dependencies are installed.

Entering a shell

Run pixi shell to enter a shell with all dependencies installed. This is equivalent to using conda activate <env>. (so the venv stuff is prepended to your PATH, meaning we will look there first for python and pip). So that means once you do this, you can do the python XXX stuff. Of course, do not do pip install XXX here, as this will not be recorded in the lockfile.

Adding dependencies

Best practice

Managing a python package

Removing dependencies

My thoughts so far

Pixi has a lot more features than I have shared here. But my use is pretty limited and this is good enough. It feels pretty portable, and I especially like the automatic dependency file management.

No more conda?

Probably not. pixi doesn't support PowerPC architectures and is still a very young project. Conda will still be a good tool, but when applicable, pixi is a good alternative. In addition, it's easier to install global binaries using conda. You can also do this with --global flag in pixi, but I haven't dug too deep into it.


![tip/Installing user-level software using conda]

  1. First create ~/.local/bin if it doesn't exist.
  2. in your ~/.bashrc or ~/.zshrc, add export PATH="$HOME/.local/bin:$PATH" to the end of the file.
    • If you don't know what this does, we are telling the shell to look for binaries in ~/.local/bin first before looking anywhere else.
  3. Now install the package you want using conda, for example conda install -n base git -y.
  4. Now create a symlink to the binary in ~/.local/bin, for example ln -sf {YOUR_CONDA_PATH}/bin/git $HOME/.local/bin.
  5. Now you should be able to run git without any issues, and it will use the conda-installed version. (you can check this by running which git. it should say something like ~/.local/bin/git)

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