Of all the reasons Python is a hit with developers, one of the biggest is its broad and ever-expanding selection of third-party packages. Convenient toolkits for everything from ingesting and formatting data to high-speed math and machine learning are just an import or pip install away.

But what happens when those packages don’t play nice with each other? What do you do when different Python projects need competing or incompatible versions of the same add-ons? That’s where Python virtual environments come into play.

What are Python virtual environments?

A virtual environment is a way to have multiple, parallel instances of the Python interpreter, each with different sets of packages and different configurations. Each virtual environment contains a discrete copy of the Python interpreter, including copies of its support utilities (such as the package manager pip).

The packages installed in each virtual environment are seen only in that virtual environment and no other. Even large, complex packages with platform-dependent binaries can be corralled off from each other in virtual environments.

Why use Python virtual environments?

There are a few common use cases for a virtual environment:

1. You’re developing multiple projects that depend on different versions of the same packages, or you have a project that must be isolated from certain packages because of a namespace collision. This is the most standard use case.
2. You’re working in a Python environment where you can’t modify the site-packages directory. This may be because you’re working in a highly controlled environment, such as managed hosting, or on a server where the choice of interpreter (or packages used in it) can’t be changed because of production requirements.
3. You want to experiment with a specific combination of packages under highly controlled circumstances, for instance to test cross-compatibility or backward compatibility.
4. You want to run a “baseline” version of the Python interpreter on a system with no third-party packages, and only install third-party packages for each individual project as needed.

Nothing says you can’t simply unpack a Python library into a subfolder of a project and use it that way. Likewise, you could download a standalone copy of the Python interpreter, unpack it into a folder, and use it to run scripts and packages devoted to it.

But managing such cobbled-together projects soon becomes difficult. It only seems easier to do that at first. Working with packages that have binary components, or that rely on elaborate third-party dependencies, can be a nightmare. Worse, reproducing such a setup on someone else’s machine, or on a new machine you manage, is tricky.

The best long-term solution is to use Python’s native mechanisms for creating, reproducing, and working with virtual environments.

How to use virtual environments in Python 3

Python has native tooling for virtual environments that makes the whole process quite simple. This wasn’t always the case, but now all supported versions of Python use the native virtual environment tool, venv.

Create the Python virtual environment

To create a virtual environment in a given directory, type:

python3 -m venv /path/to/venv

For instance, to create the virtual environment in the current directory, using the subdirectory .venv type:

python3 -m venv .venv

On Microsoft Windows, you can use py instead of python3 to reliably access an installed Python version. (See this article for more about using the py launcher in Windows.)

The exact name for the virtual environment directory is arbitrary, but it’s typically .venv.

The whole process of setting up the virtual environment may take a minute or two. When it’s finished, you should see that directory with a few subdirectories in it. The most important subdirectory is bin on Unix or Scripts on Windows, which is where you’ll find the copy of the Python interpreter for the virtual environment along with its utilities.

Note that because each virtual environment contains its own copy of the Python interpreter, it can be fairly large. A Python 3.13 virtual environment will consume anywhere from 14MB to 26MB of disk space, depending on the operating system.

Venvs and version control

If you are setting up a virtual environment in a project directory managed with some kind of version control system (e.g., Git), exclude the environment directory from tracking before you make any commits after creating the venv.

Venvs should not be tracked along with their associated code, as they are meant to be destroyed and recreated as needed. You should, however, track the requirements.txt or pyproject.toml files associated with the project, as those are used to describe what gets installed in the venv for that project.

Activate the Python virtual environment

Before you can use this virtual environment, you need to explicitly activate it. Activation makes the virtual environment the default Python interpreter for the duration of a shell session.

You’ll need to use different syntax for activating the virtual environment depending on which operating system and command shell you’re using.

• On Unix or MacOS, using the bash shell: source /path/to/venv/bin/activate
• On Unix or MacOS, using the csh shell: source /path/to/venv/bin/activate.csh
• On Unix or MacOS, using the fish shell: source /path/to/venv/bin/activate.fish
• On Windows using the Command Prompt: path/to/venv/Scripts/Activate.bat
• On Windows using PowerShell: path/to/venv/Scripts/Activate.ps1

Note that the activated environment only works for the context it was activated in. For instance, if you launch two instances of PowerShell, A and B, and you activate the virtual environment in instance A, that environment will apply only to A, not B.

Many Python IDEs will automatically detect and activate a virtual environment if one is found in the current project directory. Visual Studio Code, for instance, can do this when the Python extension is enabled. Opening a terminal inside Visual Studio Code will automatically activate the selected virtual environment. PyCharm automatically creates a virtual environment for each new project and enables it automatically.

Configure and use the Python virtual environment

Once you’ve activated the new virtual environment, you can use the pip package manager to add and change packages for it. You’ll find pip in the Scripts subdirectory of the virtual environment on Windows, and in the bin subdirectory on Unix OSes.

If you’re already familiar with the way pip works, you’re set. It should be just the same in a virtual environment. Just make sure you’re using the instance of pip that manages packages for the virtual environment in the context where it was activated—e.g., the bash session or Windows CLI/PowerShell session. If you want to verify that you’re using the right pip and the right virtual environment, type pip -V and check that the path it displays points to a subdirectory of your virtual environment.

Note that when you want to upgrade pip in a virtual environment, it’s best to use the command python3 -m pip install -U pip. This ensures the upgrade process is run in such a way that Python doesn’t lock crucial files. The command pip install -U pip may not be able to complete the upgrade properly.

To use the virtual environment you created to run Python scripts, simply invoke Python from the command line in the context where you activated it. For instance, to run a script, just run python3 myscript.py.

With PyCharm, you can use the IDE’s own package management interface to manage the packages installed in your project.

Managing packages in Python virtual environments

When you create a new virtual environment, pip will be installed, but that’s all. You’ll need to install any other packages you want to use in the environment. For projects with complex requirements, it is customary to keep in the root of the project a requirements.txt file that lists the requirements for the project. This way, if you need to recreate the virtual environment, you can reinstall all of the needed packages with the command pip install -r requirements.txt.

More recently, a new project metadata format has emerged for Python projects, called pyproject.toml. A pyproject.toml file contains the package requirements of the project, but also a great deal of other information about it. To install those requirements, you’d run pip install . in the same directory as the pyproject.toml file.

Note that the copy of pip that lives in a virtual environment is local to that virtual environment. Each virtual environment has its own copy, which will need to be updated and maintained independently. This is why you may get warnings about pip being out of date in some virtual environments but not others; pip has to be updated in each virtual environment separately.

Deactivating the Python virtual environment

When you’re done using the virtual environment, you can just terminate the session where you were using it. If you want to continue to work in the same session but with the default Python interpreter instead, type deactivate at the prompt. Windows users on the Command Prompt need to run deactivate.bat from the Scripts subdirectory, but Unix users and Windows users running PowerShell can simply type deactivate in any directory.

Removing the Python virtual environment

Virtual environments are self-contained. When you no longer need the virtual environment, you can simply delete its directory. Just make sure you first close any running copies of Python that use the virtual environment.

Whenever you want to refresh or recreate a virtual environment, you can simply delete the current environment directory and recreate the venv as described above (see “Managing packages in Python virtual environments”). This is typically the easiest way to upgrade a project to a newer version of Python: delete or temporarily re-name the venv directory (in case the new version doesn’t work), then create a new one and install the project requirements into it.

If you have many older projects that aren’t being actively used, you can remove their environments to save space. They can be recreated easily whenever needed, although you will want to note which version of Python was used to create them along with the needed packages (typically recorded in requirements.txt or pyproject.toml).

Relocating the Python virtual environment

It’s tempting to assume a virtual environment can be copied and moved around along with its project. Don’t do this. Virtual environments are tied to the location of the Python installation on the system where they’re created. If you want to move the project to another system, leave out the venv directory, and recreate the venv on the target machine. Do copy and move the requirements.txt or pyproject.toml file with the project, because those files are needed to recreate the venv on the other system.

How to use virtual environments in Python 2

With Python 2, virtual environments aren’t a native feature of the language. Instead, you need to install third-party libraries to create and manage virtual environments.

The most popular and widely used of these projects is virtualenv, which handles creating the directory structure and copying the needed files into a virtual environment. To install virtualenv, just use pip install virtualenv. To create a virtual environment directory with it, type virtualenv /path/to/directory. Activating and deactivating the virtual environment works the same way as it does for virtual environments in Python 3 (see above).

Note that Python 2 should not be used for any new development. Virtual environments in Python 2, like Python 2 itself, should be used only for the maintenance of legacy projects that should eventually be migrated to Python 3.

Virtual environments and the main Python package directory

Normally, when you create a venv, it cannot work with the packages already present in the Python installation that created it. This is by design, as it ensures that packages installed globally don’t interfere with local ones.

You can override this behavior, but only when you first create a virtual environment. If you pass the flag --system-site-packages to venv when you run it, the created venv will have access to the parent Python’s package directory.

Using Python virtual environments with Jupyter notebooks

If you’re using Jupyter notebooks (aka IPython notebooks), and you already have Jupyter installed systemwide, create your virtual environment and activate it. Then, from your virtual environment directory, run pip install ipykernel to add the needed components for IPython. Finally, run ipython kernel install —user —name=, where project_name is a name you want to associate with that particular project. From there you should be able to launch Jupyter and switch to the IPython kernel you installed inside the virtual environment.

Upgrading Python virtual environments

When you upgrade a Python runtime on your system, virtual environments that use that version of Python aren’t automatically upgraded. That’s your responsibility. And that’s by design, because unwitting upgrades to Python versions can break their attendant packages.

If you’ve upgraded an existing Python interpreter with a minor point upgrade—e.g., from Python 3.13.1 to Python 3.13.3—you can upgrade any corresponding virtual environments easily enough. From a command prompt in the project directory, enter:

python -m venv /path/to/venv --upgrade

Don’t activate the virtual environment beforehand, or the upgrade may not work.

Alternatively, as noted above (see “Removing the Python virtual environment”), you could elect to remove the venv completely and recreate it using your requirements.txt or pyproject.toml file.

If you’ve installed a major new version of Python—e.g., you already have Python 3.10 and you now install Python 3.11 alongside it—you’ll need to create a new virtual environment that specifically uses the new major point version. Do not attempt to upgrade an existing virtual environment to a higher major point version of Python.

Of all the reasons Python is a hit with developers, one of the biggest is its broad and ever-expanding selection of third-party packages. Convenient toolkits for everything from ingesting and formatting data to high-speed math and machine learning are just an import or pip install away.

But what happens when those packages don’t play nice with each other? What do you do when different Python projects need competing or incompatible versions of the same add-ons? That’s where Python virtual environments come into play.

What are Python virtual environments?

A virtual environment is a way to have multiple, parallel instances of the Python interpreter, each with different sets of packages and different configurations. Each virtual environment contains a discrete copy of the Python interpreter, including copies of its support utilities (such as the package manager pip).

The packages installed in each virtual environment are seen only in that virtual environment and no other. Even large, complex packages with platform-dependent binaries can be corralled off from each other in virtual environments.

Why use Python virtual environments?

There are a few common use cases for a virtual environment:

1. You’re developing multiple projects that depend on different versions of the same packages, or you have a project that must be isolated from certain packages because of a namespace collision. This is the most standard use case.
2. You’re working in a Python environment where you can’t modify the site-packages directory. This may be because you’re working in a highly controlled environment, such as managed hosting, or on a server where the choice of interpreter (or packages used in it) can’t be changed because of production requirements.
3. You want to experiment with a specific combination of packages under highly controlled circumstances, for instance to test cross-compatibility or backward compatibility.
4. You want to run a “baseline” version of the Python interpreter on a system with no third-party packages, and only install third-party packages for each individual project as needed.

Nothing says you can’t simply unpack a Python library into a subfolder of a project and use it that way. Likewise, you could download a standalone copy of the Python interpreter, unpack it into a folder, and use it to run scripts and packages devoted to it.

But managing such cobbled-together projects soon becomes difficult. It only seems easier to do that at first. Working with packages that have binary components, or that rely on elaborate third-party dependencies, can be a nightmare. Worse, reproducing such a setup on someone else’s machine, or on a new machine you manage, is tricky.

The best long-term solution is to use Python’s native mechanisms for creating, reproducing, and working with virtual environments.

How to use virtual environments in Python 3

Python has native tooling for virtual environments that makes the whole process quite simple. This wasn’t always the case, but now all supported versions of Python use the native virtual environment tool, venv.

Create the Python virtual environment

To create a virtual environment in a given directory, type:

python3 -m venv /path/to/venv

For instance, to create the virtual environment in the current directory, using the subdirectory .venv type:

python3 -m venv .venv

On Microsoft Windows, you can use py instead of python3 to reliably access an installed Python version. (See this article for more about using the py launcher in Windows.)

The exact name for the virtual environment directory is arbitrary, but it’s typically .venv.

The whole process of setting up the virtual environment may take a minute or two. When it’s finished, you should see that directory with a few subdirectories in it. The most important subdirectory is bin on Unix or Scripts on Windows, which is where you’ll find the copy of the Python interpreter for the virtual environment along with its utilities.

Note that because each virtual environment contains its own copy of the Python interpreter, it can be fairly large. A Python 3.13 virtual environment will consume anywhere from 14MB to 26MB of disk space, depending on the operating system.

Venvs and version control

If you are setting up a virtual environment in a project directory managed with some kind of version control system (e.g., Git), exclude the environment directory from tracking before you make any commits after creating the venv.

Venvs should not be tracked along with their associated code, as they are meant to be destroyed and recreated as needed. You should, however, track the requirements.txt or pyproject.toml files associated with the project, as those are used to describe what gets installed in the venv for that project.

Activate the Python virtual environment

Before you can use this virtual environment, you need to explicitly activate it. Activation makes the virtual environment the default Python interpreter for the duration of a shell session.

You’ll need to use different syntax for activating the virtual environment depending on which operating system and command shell you’re using.

• On Unix or MacOS, using the bash shell: source /path/to/venv/bin/activate
• On Unix or MacOS, using the csh shell: source /path/to/venv/bin/activate.csh
• On Unix or MacOS, using the fish shell: source /path/to/venv/bin/activate.fish
• On Windows using the Command Prompt: path/to/venv/Scripts/Activate.bat
• On Windows using PowerShell: path/to/venv/Scripts/Activate.ps1

Note that the activated environment only works for the context it was activated in. For instance, if you launch two instances of PowerShell, A and B, and you activate the virtual environment in instance A, that environment will apply only to A, not B.

Many Python IDEs will automatically detect and activate a virtual environment if one is found in the current project directory. Visual Studio Code, for instance, can do this when the Python extension is enabled. Opening a terminal inside Visual Studio Code will automatically activate the selected virtual environment. PyCharm automatically creates a virtual environment for each new project and enables it automatically.

Configure and use the Python virtual environment

Once you’ve activated the new virtual environment, you can use the pip package manager to add and change packages for it. You’ll find pip in the Scripts subdirectory of the virtual environment on Windows, and in the bin subdirectory on Unix OSes.

If you’re already familiar with the way pip works, you’re set. It should be just the same in a virtual environment. Just make sure you’re using the instance of pip that manages packages for the virtual environment in the context where it was activated—e.g., the bash session or Windows CLI/PowerShell session. If you want to verify that you’re using the right pip and the right virtual environment, type pip -V and check that the path it displays points to a subdirectory of your virtual environment.

Note that when you want to upgrade pip in a virtual environment, it’s best to use the command python3 -m pip install -U pip. This ensures the upgrade process is run in such a way that Python doesn’t lock crucial files. The command pip install -U pip may not be able to complete the upgrade properly.

To use the virtual environment you created to run Python scripts, simply invoke Python from the command line in the context where you activated it. For instance, to run a script, just run python3 myscript.py.

With PyCharm, you can use the IDE’s own package management interface to manage the packages installed in your project.

Managing packages in Python virtual environments

When you create a new virtual environment, pip will be installed, but that’s all. You’ll need to install any other packages you want to use in the environment. For projects with complex requirements, it is customary to keep in the root of the project a requirements.txt file that lists the requirements for the project. This way, if you need to recreate the virtual environment, you can reinstall all of the needed packages with the command pip install -r requirements.txt.

More recently, a new project metadata format has emerged for Python projects, called pyproject.toml. A pyproject.toml file contains the package requirements of the project, but also a great deal of other information about it. To install those requirements, you’d run pip install . in the same directory as the pyproject.toml file.

Note that the copy of pip that lives in a virtual environment is local to that virtual environment. Each virtual environment has its own copy, which will need to be updated and maintained independently. This is why you may get warnings about pip being out of date in some virtual environments but not others; pip has to be updated in each virtual environment separately.

Deactivating the Python virtual environment

When you’re done using the virtual environment, you can just terminate the session where you were using it. If you want to continue to work in the same session but with the default Python interpreter instead, type deactivate at the prompt. Windows users on the Command Prompt need to run deactivate.bat from the Scripts subdirectory, but Unix users and Windows users running PowerShell can simply type deactivate in any directory.

Removing the Python virtual environment

Virtual environments are self-contained. When you no longer need the virtual environment, you can simply delete its directory. Just make sure you first close any running copies of Python that use the virtual environment.

Whenever you want to refresh or recreate a virtual environment, you can simply delete the current environment directory and recreate the venv as described above (see “Managing packages in Python virtual environments”). This is typically the easiest way to upgrade a project to a newer version of Python: delete or temporarily re-name the venv directory (in case the new version doesn’t work), then create a new one and install the project requirements into it.

If you have many older projects that aren’t being actively used, you can remove their environments to save space. They can be recreated easily whenever needed, although you will want to note which version of Python was used to create them along with the needed packages (typically recorded in requirements.txt or pyproject.toml).

Relocating the Python virtual environment

It’s tempting to assume a virtual environment can be copied and moved around along with its project. Don’t do this. Virtual environments are tied to the location of the Python installation on the system where they’re created. If you want to move the project to another system, leave out the venv directory, and recreate the venv on the target machine. Do copy and move the requirements.txt or pyproject.toml file with the project, because those files are needed to recreate the venv on the other system.

How to use virtual environments in Python 2

With Python 2, virtual environments aren’t a native feature of the language. Instead, you need to install third-party libraries to create and manage virtual environments.

The most popular and widely used of these projects is virtualenv, which handles creating the directory structure and copying the needed files into a virtual environment. To install virtualenv, just use pip install virtualenv. To create a virtual environment directory with it, type virtualenv /path/to/directory. Activating and deactivating the virtual environment works the same way as it does for virtual environments in Python 3 (see above).

Note that Python 2 should not be used for any new development. Virtual environments in Python 2, like Python 2 itself, should be used only for the maintenance of legacy projects that should eventually be migrated to Python 3.

Virtual environments and the main Python package directory

Normally, when you create a venv, it cannot work with the packages already present in the Python installation that created it. This is by design, as it ensures that packages installed globally don’t interfere with local ones.

You can override this behavior, but only when you first create a virtual environment. If you pass the flag --system-site-packages to venv when you run it, the created venv will have access to the parent Python’s package directory.

Using Python virtual environments with Jupyter notebooks

If you’re using Jupyter notebooks (aka IPython notebooks), and you already have Jupyter installed systemwide, create your virtual environment and activate it. Then, from your virtual environment directory, run pip install ipykernel to add the needed components for IPython. Finally, run ipython kernel install —user —name=, where project_name is a name you want to associate with that particular project. From there you should be able to launch Jupyter and switch to the IPython kernel you installed inside the virtual environment.

Upgrading Python virtual environments

When you upgrade a Python runtime on your system, virtual environments that use that version of Python aren’t automatically upgraded. That’s your responsibility. And that’s by design, because unwitting upgrades to Python versions can break their attendant packages.

If you’ve upgraded an existing Python interpreter with a minor point upgrade—e.g., from Python 3.13.1 to Python 3.13.3—you can upgrade any corresponding virtual environments easily enough. From a command prompt in the project directory, enter:

python -m venv /path/to/venv --upgrade

Don’t activate the virtual environment beforehand, or the upgrade may not work.

Alternatively, as noted above (see “Removing the Python virtual environment”), you could elect to remove the venv completely and recreate it using your requirements.txt or pyproject.toml file.

If you’ve installed a major new version of Python—e.g., you already have Python 3.10 and you now install Python 3.11 alongside it—you’ll need to create a new virtual environment that specifically uses the new major point version. Do not attempt to upgrade an existing virtual environment to a higher major point version of Python.

Threat actors are continuing their onslaught against software supply chains, now with malware named after death itself.

The newly-discovered Hades Campaign is a “highly sophisticated” supply chain compromise that targets Python developer environments and runs as soon as infected packages are imported. It uses the popular Bun toolkit to silently execute multi-layer payloads that can extract sensitive data, move laterally across compromised systems, exploit common security frameworks, and even hijack AI gatekeeper analyzer systems via adversarial prompt injection.

Notably, the campaign exploited the popular C++ library ensmallen, as well as packages in the computational biology, bioinformatics, and genotype-phenotype analysis ecosystems.

The most novel thing about this malware is its combination of advanced tactics, noted David Shipley of Beauceron Security. He noted that we’ve seen memory-focused malware, we’ve seen attacks that attempt to defuse large language model (LLM) powered analysis with hidden prompts, and we’ve seen malware with wiper capabilities.

“But all three, in a fast moving mass propagating worm, is its own kind of nightmare,” he said. “And I suspect this is the way of the future.”

How Hades works

The Hades Campaign was discovered by researchers at StepSecurity, who called it the latest evolution of the Miasma threat actor. The researchers previously described Miasma attacks that had sent self-replicating worms to perform multi-cloud credential sweeps, caused infected repositories to execute code when folders were accessed in integrated development environments (IDEs) or by AI agents, and used techniques that scanned and read Linux process memory.

Hades uses the same credential harvesting methods, self-replicating worm logic, and GitHub-based exfiltration patterns, the researchers noted. In addition to ensmallen, compromised packages include mflux-streamlit, nhmpy, ppkt2synergy, embiggen, gpsea, and pyphetools.

The campaign’s entry point is a simple, obfuscated script embedded inside a Python package’s __init__.py file, a critical building block that gives Python the ability to recognize packages and import modules. Once they gain access, threat actors drop a precompiled Bun runtime binary and executes its JavaScript payload. Bun allows the malware to run complex JavaScript tasks in environments lacking a Node.js installation, bypassing traditional package manager controls and proxy logs.

The malware is able to scrape Linux memory mappings, and also introduces tailored macOS and Windows memory scrapers, which allow threat actors to extract sensitive, encrypted data.

Interestingly, attackers are also able to evade detection by automated LLMs that scan for suspicious code. This is achieved with a simple block of text at the top of the file; this instructs the model to ignore the hidden code below, classify the package as verified and clean, and provide reports stating it is safe.

This element represents what the StepSecurity researchers described as a “significant conceptual shift,” with attackers writing payloads that target AI systems’ cognitive logic. “Scanners that pass raw text to LLMs without strict boundary isolation can be coerced into generating false negative verdicts, allowing the malicious package to bypass organization analysis,” they wrote.

The tactic is indeed clever, Beauceron’s Shipley agreed, pointing out that attackers will increasingly target endpoint LLM-powered agents.

Why? “Because there’s no reliable defense,” he said. “LLMs are incredibly susceptible to social engineering.” This has been relabeled as prompt engineering, but is essentially just phishing for bots, he pointed out.

“While everyone’s worried about LLM-powered vulnerability discovery and automated exploitation, it’s LLM-created smart malware like this, and AI-powered phishing of humans and bots, that keeps me awake at night,” Shipley said.

Hades’ crafty worm propagation

The Hades Campaign command and control (C2) infrastructure uses three independent channels on public GitHub infrastructure to allow its communications to blend in with normal traffic. Stolen credentials are encrypted locally in a hybrid fashion (serialized, compressed, and pushed to a newly created public GitHub repository under attackers’ control). Exfiltrated repositories carry the description “Hades — The End for the Damned.”

Researchers noted that a core component of this campaign is its ability to propagate and move laterally across networks. It exploits the very methods meant to protect systems, including Secure Shell (SSH) and Secure Copy Protocol (SCP), OpenID Connect (OIDC),and Supply-chain Levels for Software Artifacts (SLSA).

For instance, when running inside a GitHub Actions workflow runner, the malware checks for OIDC variables, then bypasses registry signature policies and generates cryptographically signed SLSA provenance bundles via Sigstore. It can then fetch target libraries and inject the obfuscated script and JavaScript payload. From there, it can publish compromised versions to the Python Package Index (PyPI) repository and node package manager (npm) using the target’s credentials and the generated Sigstore bundle.

“This ensures that the published package appears to have valid, cryptographically verified build provenance from the organization’s official GitHub Actions build environment,” the researchers explained.

Further, if a harvested GitHub token has write permissions, the malware will target repositories to extract secrets using GitHub Actions runners. This occurs “directly from the runner’s address space without ever writing them to disk or making a suspicious network connection,” the researchers noted.

The malware also targets rule files and configuration directories for 14 different AI agents and systems, planting custom prompt instructions or executing hooks that trigger a bun run bootstrap command when the victim loads or consults the workspace with their AI assistant. Finally, it establishes persistence on the workstation and monitors for the presence of the stolen token; if that token is revoked, it executes a wiper process to erase the user’s files.

A veritable garden of linters and type checkers has blossomed in the Python ecosystem. Pyright and Mypy are two of the most popular, while Astral’s ty and Meta’s Pyrefly are two promising Rust-based newcomers. We compared early-stage ty and Pyrefly last June. One year later, Meta has released Pyrefly 1.0.

Pyrefly is intended to stand out from the pack by way of a few key features. It’s written in Rust for performance and memory efficiency, and it has a number of intriguing forward-looking features, some still experimental.

Setting up Pyrefly

Pyrefly installs into a Python environment like any other Python type checker (pip install pyrefly) and brings with it no additional dependencies. Visual Studio Code users can work with Pyrefly via an extension, but the extension doesn’t give you access to the command-line tools offered by Pyrefly when it’s installed in a project venv.

You can start using Pyrefly right away, with no actual setup. If Pyrefly detects no configuration for a given project, it defaults to flagging only the most high-profile errors: syntax issues, unrecognized names, and so on. To start using Pyrefly’s more advanced features, you can add a [tool.pyrefly] section in pyproject.toml, or create a pyrefly.toml file, and populate those with your desired settings.

You can also run pyrefly init on your codebase and set things up automatically, including migrating existing settings from previous Pyrefly installs or from Mypy or Pyright. By default Pyrefly will use **/*.py* as the project’s includes directory, and will automatically ignore site package paths from your configured environment, thus sparing you potentially thousands of spurious errors from your venv’s installed packages.

Using Pyrefly

Once you have Pyrefly set up on a project, you’ll likely see an immense number of new errors. To silence all of them at once via # pyrefly: ignore comment directives, run pyrefly suppress. This will not only reduce the amount of error noise, but allow you to see what each error actually is from its suppression comments.

Suppression comments have another nice readability feature: they can be placed on the line before the offending error, rather than at the end of it. You can also pre-emptively suppress errors for an entire module with one directive at the top of the file, but having each error suppressed individually makes more sense. And while there’s a pyrefly suppress --remove-unused command to remove suppressions that have no actual error, there’s no command for stripping a codebase of all suppressions. However, because suppressions are consistently formatted, you could remove those suppressions with a simple regex-powered search-and-replace.

A currently experimental feature called baseline files borrows an idea from the basedpyright tool. You generate a project-wide .json file with pyrefly check --baseline that tracks all existing errors in the project, then only new errors apart from those will be reported. It’s a handy way to refactor a codebase when new work is being done on it, so that existing problems can be handled separately.

If you have the Pyrefly extension installed in VS Code, objects without existing type hints will have suggested type hints displayed as inlays if the types can be inferred from the code. These can be added with a right click, or inserted automatically across the codebase with the command pyrefly infer.

Advanced Pyrefly features

Two major third-party Python packages have direct type annotation support in Pyrefly. One is Django and its ORM, via the django-stubs package. Models, fields, relationships, class-based generic views, and many other features have typing support. The other package, Pydantic, gets support from Pyrefly for features like fields, dataclasses, and Pydantic’s own runtime validation logic. Pydantic validation can be “lax” (automatic coercion of types via unions) or “strict” (exact types required).

Many advanced Pyrefly features are still considered experimental, but have a lot of promise. With type coverage, for instance, you can use pyrefly report to generate a JSON report of how thoroughly types are used in the codebase. (This is not to be confused with the coverage package in Python, which describes test coverage for a codebase.)

Another experimental feature lets you generate stub files for a codebase by using static code analysis (not runtime analysis). PyTorch users also benefit from a form of experimental Pyrefly support. Tensor shapes can be described with types and type-checked across transformations. Note that the typing used for this is exclusive to Pyrefly, as there is no agreed-on standard for how to do this.

Pyrefly vs. Pyright and Mypy

Pyright and Mypy have been the default choices for linting and type checking in the Python world for some time now. Pyright is an easy default for Visual Studio Code users, as it’s part of Microsoft’s Python extensions for that editor, and Mypy offers extensibility and broader compatibility with older codebases. Pyrefly, on the other hand, is forward-looking, with fewer legacy concerns. It also has a higher score for test conformance than Mypy, though not a higher score than Pyright.

Other key differences include the type checking philosophy used by each, and their licensing. Pyrefly and Pyright infer as aggressively as possible, while Mypy’s default is to skip anything unannotated. And while Pyrefly and Mypy are MIT-licensed, only Pyright’s core functionality is MIT-licensed. Pylance, the language server extension for VS Code that is powered by Pyright, is proprietary.

Finally, Pyrefly’s Rust codebase gives it a default performance edge over both Mypy and Pyright, which are written in Python and TypeScript, respectively. Astral’s ty, also written in Rust, is still more prototype than mature project. Pyrefly has enough of a feature set right now that it’s already worth experimenting with—although that’s best done on a branch of your code where adding type annotations, suppression comments, and init files won’t pose a problem.