pyre

A framework for building scientific applications in Python. Visit the project homepage for more info

Getting started

If you are reading this from within pyre, you should be able to skip to the launching instructions at the end of this section.

Similarly, if you are lucky enough to work on a machine that is managed professionally, pyre may already be installed. Please contact the system administrators for instructions about how to access it, and skip to the end of this section.

If you are comfortable with jupyter notebooks, the current release tarball contains a notebook that can walk you through the installation procedure with minimal tweaking. It is located in etc/mamba/pyre.ipynb. Please report any difficulties you encounter.

The same tarball has instructions on how to build a docker instance with a pyre installation. You will find support for many recent ubuntu distributions in etc/docker.

If none of these options work for you, read on to the next section for a walk through of how to build pyre from source.

Dependencies

The easiest way to install the pyre dependencies is using micromamba and conda-forge. The following configuration file will install everything pyre needs in an environment named pyre. Feel free to add these packages to an existing environment, rather than building one from scratch, although it might be easier at first if you avoid any potential conflicts with your existing environment.

# -*- yaml -*-

name: pyre

channels:
  - conda-forge

dependencies:
  # python and runtime packages
  - python
  - pyyaml
  - ruamel.yaml
  # optional: external libraries
  - gsl
  - hdf5
  - libpq
  # optional: building from source
  - git
  - gcc
  - gxx
  # GNU make 4.4 or later, which mm needs
  - make >=4.4
  - nodejs
  - pybind11

# end of file

Save this as pyre.yaml, then create the environment from it and activate it:

~> micromamba create --file pyre.yaml
~> micromamba activate pyre

On macOS, you will want to use clang instead of gcc. Keeping this environment active as you proceed is important: it is what puts the conda-forge compilers on your PATH, and mm reads the install prefix and dependency locations from it. If you open a new shell at any point, re-activate it with micromamba activate pyre before running mm.

It is also possible to use other package managers to install these dependencies. pyre has been tested on both ubuntu and macOS using their native environments, as well as macports, homebrew, and spack. Please keep in mind that most enterprise systems provide compilers and packages that are too old to build this code, so you will have to lean on something else to satisfy the dependencies. Further, you may have to adjust your PATH, LD_LIBRARY_PATH, PYTHONPATH, and perhaps other environment variables that control access to binaries, shared objects, and python packages on your machine.

Cloning the repositories

We will need a place to clone the necessary source repositories. For the sake of concreteness, let's pick ~/dv as the source directory.

~> mkdir ~/dv
~> cd ~/dv

GitHub allows access through ssh or https, with slightly different syntax. If you already have your ssh key installed on your GitHub account, you can clone the two repositories using

~/dv> git clone git@github.com:aivazis/mm
~/dv> git clone git@github.com:pyre/pyre

Alternatively, you can use the https protocol for anonymous access:

~> mkdir ~/dv
~> cd ~/dv
~/dv> git clone https://github.com/aivazis/mm
~/dv> git clone https://github.com/pyre/pyre

You can probably get away with installing pyre from conda-forge, but pyre is currently evolving rather quickly. Being tied to a slower release cycle may delay access to the latest features. Generally speaking, the HEAD of the two repositories is a safe place to pull from, as they are thoroughly tested.

Setting up the build system

Recent versions of mm interrogate the active conda environment and configure the build automatically. The two key settings are:

• mode: conda tells mm to resolve the installation prefix and the python site-packages location directly from the active environment (via $CONDA_DEFAULT_ENV), so you don't have to specify these locations by hand.
• pkgdb: conda tells mm to discover the external dependencies by reading the environment's conda-meta database, so you no longer need to hand-write a package database of versions and install locations.

We will place them in a small ~/.config/pyre/mm.yaml configuration file that also records your preferred compilers and build targets:

~/dv> cd ~
~> mkdir -p .config/pyre

# -*- yaml -*-

# mm configuration
mm:

  # resolve locations and externals from the active conda environment
  pkgdb: conda
  # install the build assets back into the active conda environment
  mode: conda

  # compilers
  compilers: "gcc, python/python3"
  # build target: turn optimizations on, and build shared libraries
  target: "opt, shared"

  # misc
  # the name of GNU make; may be 'gmake' on your machine
  make: make
  # local makefiles with build hooks; you can ignore this
  local: Make.mmm

# end of file

You may need to replace gcc with whatever is available in your environment; on macOS use clang. Incidentally, the directory ~/.config/pyre is the home for configuration files for all pyre applications, including yours, so we will be adding more files here later on.

Building

The next step is to build pyre. We will invoke mm a few times, so you may find it convenient to create an alias for it.

~/dv> alias mm='python3 ${HOME}/dv/mm/mm'

You might want to make this more permanent by also adding it to your shell startup file, e.g. your ~/.bash_profile.

First, build the external package database from the active environment. This is a one-time step; re-run it whenever you add or update the environment's dependencies:

~/dv> cd pyre
~/dv/pyre> mm --setup

The first time you run this, the package database is empty and make issues many warnings about undefined variables; this is normal and can be safely ignored.

Now let's verify that everything is ok so far by asking mm to show details about the build. This should generate a few lines of output similar to the following, with the prefix pointing at your active conda environment:

~/dv/pyre> mm builder.info

    mm 5.4.1
    Michael Aïvázis <michael.aivazis@para-sim.com>
    copyright 1998-2026 all rights reserved

builder directory layout:
  staging layout:
           tmp = /Users/mga/dv/pyre/builds/pyre/clang/opt-shared-darwin-arm64/
  install layout:
        prefix = /Users/mga/.local/envs/pyre
           bin = /Users/mga/.local/envs/pyre/bin/
           doc = /Users/mga/.local/envs/pyre/doc/
           inc = /Users/mga/.local/envs/pyre/include/
           lib = /Users/mga/.local/envs/pyre/lib/
         share = /Users/mga/.local/envs/pyre/share/
           pyc = /Users/mga/.local/envs/pyre/lib/python3.13/site-packages/
~/dv/pyre>

The prefix shown here is the root of your active conda environment. Depending on how micromamba (or mamba/conda) was configured when it was installed, the home of its environments may differ slightly from what is shown above — common locations include ~/.local/envs, ~/micromamba/envs, or ~/miniconda3/envs. Whatever the location, mm discovers it from the active environment, so the paths in your output will reflect your own setup.

You may see mm download a pyre archive from github to bootstrap the process. This is normal, as mm is itself a pyre application.

If anything goes wrong at this stage that cannot be resolved by retracing your steps looking for typos, please file an issue at the pyre repository, and attach a log file or a screenshot to help diagnose the problem.

If everything looks ok, let's build and install pyre. If you are on a linux system, mm will automatically discover the number of cores on your machine and launch a parallel build:

~/dv/pyre> mm

On macOS, it needs some help until pyre is built, so use something like:

~/dv/pyre> mm --slots=20

Don't worry if you don't have twenty cores on your machine. Most modern machines will be able to handle this load. Feel free to up the count if you are on a machine with more cores. If all goes well, you will have a functional pyre in the site-packages directory of your python installation. Let's verify:

~/dv/pyre> python3
>>> import pyre
>>> pyre.__file__

Both statements should succeed, and the latter should print out the pyre installation location.