Installing Python Packages

In reticulate: Interface to 'Python'

Declaring Python Requirements with py_require()

py_require() is the recommended way to declare Python dependencies. A py_require() call is similar to a library() call for Python packages.

py_require():

• Should appear near the beginning of an R script.
• Declares the Python dependencies needed for the script.
• Applies only to the current R session.
• Has no effect if called multiple times with the same arguments.

R packages can also call py_require() when loaded, and their declared dependencies are combined with those declared by the user and other loaded R packages.

Calling py_require("pkg") updates the Python requirements manifest that reticulate maintains for the current R session. This manifest is used only if no manually managed Python environment is found earlier in the Python Order of Discovery. The manifest is not consulted and requirements are not resolved until reticulate needs to initialize Python, typically at the first import() call. Requirements are resolved into a cached ephemeral environment specific to the unique set of dependencies declared.

While not required, it is generally recommended to declare all Python dependencies before reticulate initializes Python. The simplest approach is to place all py_require() calls at the start of the script, alongside library() calls.

Usage example:

library(reticulate)
py_require("jax")    # Declare jax is a requirement

jax <- import("jax") # <-- initialize Python with declared requirements

Unsatisfiable requirements.

It's possible to inadvertently declare an unsatisfiable set of Python requirements. This can happen for a variety of reasons, most often due to:

• Incompatible requirements declared by different R packages.
• A recently published Python package version that introduces conflicts.

To troubleshoot:

1. Figure out what the conflicting requirements are and where they are coming from.
2. Update the requirements to resolve conflicts.

To help with step 1, calling py_require() with no arguments will print out a manifest of the current requirements, as well as a table showing what requirements were declared by different R packages.

Additionally, attempting to initialize Python will print out a detailed error message.

For example:

library(reticulate)
py_require("numpy>2")
py_require("numpy<2")
import("numpy")

  × No solution found when resolving `--with` dependencies:
  ╰─▶ Because you require numpy>2 and numpy<2, we can conclude that your
      requirements are unsatisfiable.
uv error code: 1
-- Current requirements -------------------------------------------------
 Python:   3.11.11 (reticulate default)
 Packages: numpy, numpy>2, numpy<2
-------------------------------------------------------------------------
Error in uv_get_or_create_env() :
  Call `py_require()` to remove or replace conflicting requirements.

You can call py_require() again to update the requirements and make them satisfiable. Options for resolving issues include:

1. Rolling Back to a Known Working State

   If your requirements were previously satisfiable but recently broke, it is likely due to a newly published package version. You can roll back to a known working state by specifying a date with exclude_newer.

   ``` r

   Roll back to a known working state.

   py_require(exclude_newer = "2025-01-19") ```

2. Removing Conflicting Requirements

   If your requirements cannot be satisfied due to conflicts, you can use action = "remove" or action = "set" to update or remove specific packages.

   r py_require("numpy<2", action = "remove")

   You can also retrieve and modify the full set of current requirements if needed. For example, given a larger set of conflicting tensorflow requirements:

   ``` r

   Declare conflicting requirements.

   py_require(c("tensorflow==2.17.*", "tensorflow<=2.16", "tensorflow[and-cuda]", "tensorflow-cpu", "tensorflow<=2.18")) ```

   You can use action = "remove" to remove all TensorFlow-related requirements:

   ``` r

   Remove all TensorFlow requirements.

   all_py_pkgs <- py_require()$packages tf_pkgs <- grep("tensorflow", all_py_pkgs, value = TRUE) py_require(tf_pkgs, action = "remove") ```

   Or you can use action = "set" to replace all declared requirements:

   ``` r

   Replace all package requirements except TensorFlow.

   all_py_pkgs <- py_require()$packages all_py_pkgs_sans_tf <- grep("tensorflow", all_py_pkgs, value = TRUE, invert = TRUE) py_require(all_py_pkgs_sans_tf, action = "set") ```

3. Installing a Development Version

   If a development version of a package has fixed the issue but has not yet been published to PyPi, you can install it directly from GitHub or the local filesystem.

   ``` r

   Install the 'markitdown' package from GitHub.

   py_require("markitdown@git+https://github.com/microsoft/markitdown.git@main#subdirectory=packages/markitdown")

   Install it from the local filesystem.

   py_require("markitdown@/Users/tomasz/github/microsoft/markitdown/packages/markitdown/") ```

   See py_require() for more examples.

Manually managing Python installations

::: {.alert .alert-info}

⚠ Updated Guidance

The remainder of this vignette describes how to manually manage Python installations. Manually managing Python installations is no longer necessary nor recommended.

It is instead recommended to use py_require() to specify Python dependencies. Note that py_require() has no effect if using a self-managed Python installation. :::

Overview

Python packages are typically installed from one of two package repositories:

1) PyPI; or

2) Conda

Any Python package you install from PyPI or Conda can be used from R with reticulate.

Each installation of Python on your system has its own set of packages. How reticulate selects a Python installation, and how you can configure the behavior, is described in the version vignette.

Python environments

When installing Python packages it's best practice to isolate them within a Python environment (a named Python installation that exists for a specific project or purpose). This provides a measure of isolation, so that updating a Python package for one project doesn't impact other projects. The risk for package incompatibilities is significantly higher with Python packages than it is with R packages, because unlike CRAN, PyPI does not enforce, or even check, if the current versions of packages currently available are compatible.

The reticulate package includes functions for creating Python environments (either virtualenvs or conda envs) and installing packages within them. Both virtual environments and conda environments are supported on all platforms (Linux, macOS, and Windows).

Note that facilities to create and manage virtual environments (commonly refereed to as a "venv") come with the Python standard library, and are the recommended way to create isolated python installations. Conda environments are supported as well, but be aware that there is the potential for binary incompatibilities between packages built by conda and packages built outside of conda (e.g., CRAN, or PPM).

Simple Installation

The reticulate package includes a py_install() function that can be used to install one or more Python packages. The packages will be by default be installed within a virtualenv or Conda environment named "r-reticulate". For example:

library(reticulate)
py_install("pandas")

This provides a straightforward high-level interface to package installation and helps encourage the use of a common default environment ("r-reticulate") across the installation of distinct Python packages.

There are also functions available for directly managing both Conda and virtualenvs for situations where you want more control over how packages are installed. These functions are covered in the sections below.

Virtualenv installation

The following functions are available for managing Python virtualenvs:

| Function | Description | |------------------------|----------------------------------------------------| | virtualenv_list() | List all available virtualenvs | | virtualenv_create() | Create a new virtualenv | | virtualenv_install() | Install a package within a virtualenv | | virtualenv_remove() | Remove individual packages or an entire virtualenv |

Virtual environments are by default located at ~/.virtualenvs. You can change this behavior by defining the WORKON_HOME environment variable.

Here's an example of using these functions to create an environment, install packages within it, then use the environment from R:

library(reticulate)

# create a new environment
virtualenv_create("r-reticulate")

# install SciPy
virtualenv_install("r-reticulate", "scipy")

# import SciPy (it will be automatically discovered in "r-reticulate")
scipy <- import("scipy")

Note that you may have a given Python package installed in multiple environments, in that case you may want to call the use_virtualenv() function to ensure that a specific virtualenv is utilized by reticulate:

library(reticulate)

# indicate that we want to use a specific virtualenv
use_virtualenv("r-reticulate")

# import SciPy (will use "r-reticulate" as per call to use_virtualenv)
scipy <- import("scipy")

Virtual environments are typically derived from (created using) a "starter" python installation. That is, there must be a python installation already installed on the system before you can create virtual environments. You can install a "venv starter" python in a variety of ways, however is most convenient:

• On macOS and Windows, visit https://www.python.org/downloads/ and install a suitable version for your system.
• On Linux, you can use prebuilt python binaries from https://github.com/rstudio/python-builds
• On all platforms, you can use reticulate::install_python(). Note that on macOS and Linux, this will build Python from source on your system, which may take up to a few minutes.

There can be multiple versions of Python installed along-side each other on a system (for example, Python versions 3.9, 3.10, and 3.11). By default, reticulate will use the latest version installed on the system for creating the virtualenv. If you have specific version constraints on the version of Python required, you can supply those to the version argument--for example: virtualenv_create(version = ">=3.9")

At anytime, you can see all the available virtualenv starters on your system by calling virtualenv_starter(all = TRUE). If you have Python venv starters installed in non-standard locations, you can inform reticulate where to look by setting the environment variable RETICULATE_VIRTUALENV_STARTER.

Conda installation

The following functions are available for managing Conda environments:

| Function | Description | |-------------------|-----------------------------------------------------------| | conda_list() | List all available conda environments | | conda_create() | Create a new conda environment | | conda_install() | Install a package within a conda environment | | conda_remove() | Remove individual packages or an entire conda environment |

Here's an example of using these functions to create an environment, install packages within it, then use the environment from R:

library(reticulate)

# create a new environment
conda_create("r-reticulate")

# install SciPy
conda_install("r-reticulate", "scipy")

# import SciPy (it will be automatically discovered in "r-reticulate")
scipy <- import("scipy")

Note that you may have a given Python package installed in multiple Conda environments, in that case you may want to call the use_condaenv() function to ensure that a specific Conda environment is utilized by reticulate:

library(reticulate)

# indicate that we want to use a specific condaenv
use_condaenv("r-reticulate")

# import SciPy (will use "r-reticulate" as per call to use_condaenv)
scipy <- import("scipy")

Shell installation

You can also use standard shell installation utilities (pip or conda) to install Python packages:

# install into system level Python
$ sudo pip install SciPy

# install into active Conda environment
$ conda install SciPy

When doing this, be sure to make note of which version of Python your package has been installed within, and call use_python() functions as appropriate to ensure that this version is used by reticulate.

Alternatively, within repl_python(), you can prefix ! to send a shell command, and the version of pip or conda used will already be configured for the Python installation reticulate is currently using.

!pip install scipy

reticulate documentation built on April 3, 2025, 10:38 p.m.