Python Environments

> Dependency hell is real. Virtual environments are the cure.

Type: Build
Languages: Shell
Prerequisites: Phase 0, Lesson 01
Time: ~30 minutes

Learning Objectives

• Create isolated virtual environments using uv, venv, or conda
• Write a pyproject.toml with optional dependency groups and generate lockfiles for reproducibility
• Diagnose and fix common pitfalls: global installs, pip/conda mixing, CUDA version mismatches
• Implement a per-phase environment strategy for projects with conflicting dependencies

The Problem

You install PyTorch 2.4 for a fine-tuning project. Next week, a different project needs PyTorch 2.1 because its CUDA build is pinned. You upgrade globally, and the first project breaks. You downgrade, and the second one breaks.

This is dependency hell. It happens constantly in AI/ML work because:

• PyTorch, JAX, and TensorFlow each ship their own CUDA bindings
• Model libraries pin specific framework versions
• A global pip install overwrites whatever was there before
• CUDA 11.8 builds don’t work with CUDA 12.x drivers (and vice versa)

The fix: every project gets its own isolated environment with its own packages.

The Concept

graph TD
    subgraph without["Without virtual environments"]
        SP[System Python] --> T24["torch 2.4.0 (CUDA 12.4)nProject A needs this"]
        SP --> T21["torch 2.1.0 (CUDA 11.8)nProject B needs this"]
        SP --> CONFLICT["CONFLICT: only onentorch version can exist"]
    end
    subgraph with["With virtual environments"]
        PA["Project A (.venv/)"] --> PA1["torch 2.4.0 (CUDA 12.4)"]
        PA --> PA2["transformers 4.44"]
        PB["Project B (.venv/)"] --> PB1["torch 2.1.0 (CUDA 11.8)"]
        PB --> PB2["diffusers 0.28"]
    end

s0-env-isolation

Build It

Option 1: uv venv (Recommended)

uv is the fastest Python package manager (10-100x faster than pip). It handles virtual environments, Python versions, and dependency resolution in one tool.

curl -LsSf https://astral.sh/uv/install.sh | sh
uv python install 3.12
cd your-project
uv venv
source .venv/bin/activate

Install packages:

uv pip install torch numpy

Create a project with pyproject.toml in one step:

uv init my-ai-project
cd my-ai-project
uv add torch numpy matplotlib

Option 2: venv (Built-in)

If you can’t install uv, Python ships with venv:

python3 -m venv .venv
source .venv/bin/activate  # Linux/macOS
.venvScriptsactivate     # Windows
pip install torch numpy

Slower than uv, but works everywhere Python is installed.

Option 3: conda (When You Need It)

Conda manages non-Python dependencies like CUDA toolkits, cuDNN, and C libraries. Use it when:

• You need a specific CUDA toolkit version without installing it system-wide
• You’re on a shared cluster where you can’t install system packages
• A library’s install instructions say “use conda”

Install miniconda (not the full Anaconda)
curl -LsSf https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
bash miniconda.sh -b
conda create -n myproject python=3.12
conda activate myproject
conda install pytorch torchvision torchaudio pytorch-cuda=12.4 -c pytorch -c nvidia

One rule: if you use conda for an environment, use conda for all packages in that environment. Mixing pip install into a conda env causes dependency conflicts that are painful to debug.

For This Course: Per-Phase Strategy

You could create one environment for the whole course. Don’t. Different phases need different (sometimes conflicting) dependencies.

Strategy:

ai-engineering-from-scratch/
├── .venv/                    <-- shared lightweight env for phases 0-3
├── phases/
│   ├── 04-neural-networks/
│   │   └── .venv/            <-- PyTorch env
│   ├── 05-cnns/
│   │   └── .venv/            <-- same PyTorch env (symlink or shared)
│   ├── 08-transformers/
│   │   └── .venv/            <-- might need different transformer versions
│   └── 11-llm-apis/
│       └── .venv/            <-- API SDKs, no torch needed

The script in code/env_setup.sh creates the base environment for this course.

pyproject.toml Basics

Every Python project should have a pyproject.toml. It replaces setup.py, setup.cfg, and requirements.txt in one file.

[project]
name = "ai-engineering-from-scratch"
version = "0.1.0"
requires-python = ">=3.11"
dependencies = [
    "numpy>=1.26",
    "matplotlib>=3.8",
    "jupyter>=1.0",
    "scikit-learn>=1.4",
]
[project.optional-dependencies]
torch = ["torch>=2.3", "torchvision>=0.18"]
llm = ["anthropic>=0.39", "openai>=1.50"]

Then install:

uv pip install -e ".[torch]"    # base + PyTorch
uv pip install -e ".[llm]"     # base + LLM SDKs
uv pip install -e ".[torch,llm]" # everything

Lockfiles

A lockfile pins every dependency (including transitive ones) to exact versions. This guarantees reproducibility: anyone who installs from the lockfile gets exactly the same packages.

uv generates uv.lock automatically when using uv add
uv add numpy
pip-tools approach
uv pip compile pyproject.toml -o requirements.lock
uv pip install -r requirements.lock

Commit your lockfile to git. When someone clones the repo, they install from the lockfile and get identical versions.

Common Mistakes

1. Installing globally

pip install torch  # BAD: installs to system Python
source .venv/bin/activate
pip install torch  # GOOD: installs to virtual environment

Check where your packages go:

which python       # should show .venv/bin/python, not /usr/bin/python
which pip           # should show .venv/bin/pip

2. Mixing pip and conda

conda create -n myenv python=3.12
conda activate myenv
conda install pytorch -c pytorch
pip install some-other-package   # BAD: can break conda's dependency tracking
conda install some-other-package # GOOD: let conda manage everything

If you must use pip inside conda (some packages are pip-only), install all conda packages first, then pip packages last.

3. Forgetting to activate

python train.py           # uses system Python, missing packages
source .venv/bin/activate
python train.py           # uses project Python, packages found

Your shell prompt should show the environment name:

(.venv) $ python train.py

4. Committing .venv to git

echo ".venv/" >> .gitignore

Virtual environments are 200MB-2GB. They're local, not portable between machines. Commit pyproject.toml and the lockfile instead.

5. CUDA version mismatch

nvidia-smi                # shows driver CUDA version (e.g., 12.4)
python -c "import torch; print(torch.version.cuda)"  # shows PyTorch CUDA version
These must be compatible.
PyTorch CUDA version must be <= driver CUDA version.

Use It

Run the setup script to create your course environment:

bash phases/00-setup-and-tooling/06-python-environments/code/env_setup.sh

This creates a .venv at the repo root with core dependencies installed and verified.

Exercises

1. Run env_setup.sh and verify all checks pass
2. Create a second virtual environment, install a different version of numpy in it, and confirm the two environments are isolated
3. Write a pyproject.toml for a project that needs both PyTorch and the Anthropic SDK
4. Deliberately install a package globally (without activating a venv), notice where it goes, then uninstall it

Hints

Exercise 1. Run bash phases/00-setup-and-tooling/06-python-environments/code/env_setup.sh from the repository root. Read each line of output; when a check fails, fix that one item and run the script again until no check fails.

Exercise 2. Make the second environment in a new folder with uv venv, activate it, and install an older numpy with a version pin such as numpy==1.26.4. Run python -c "import numpy; print(numpy.__version__)" in each environment; the two versions must be different.

Exercise 3. Start from the example in pyproject.toml Basics and list torch and anthropic under dependencies. Run uv pip install -e . or uv sync in a new environment; the file is correct when both packages import without an error.

Exercise 4. Deactivate every environment, run pip install --user , then run pip show and read the Location line. Uninstall it with pip uninstall and run pip show again to confirm that it is gone.

Key Terms

| Term | What people say | What it actually means |
|------|----------------|----------------------|
| Virtual environment | "A venv" | An isolated directory containing a Python interpreter and packages, separate from the system Python |
| Lockfile | "Pinned dependencies" | A file listing every package and its exact version, guaranteeing identical installs across machines |
| pyproject.toml | "The new setup.py" | The standard Python project configuration file, replacing setup.py/setup.cfg/requirements.txt |
| Transitive dependency | "A dependency of a dependency" | Package B depends on C; if you install A which depends on B, C is a transitive dependency of A |
| CUDA mismatch | "My GPU isn't working" | PyTorch was compiled for a different CUDA version than what your GPU driver supports |

Code for this lesson

https://github.com/rohitg00/ai-engineering-from-scratch/tree/main/phases/00-setup-and-tooling/06-python-environments

Course content adapted from AI Engineering from Scratch by Rohit Ghumare (MIT License)