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This page contains basic and advanced examples for using mach-nix inside a nix expression

Import mach-nix

every mach-nix expression should begin like this:

let
  mach-nix = import (builtins.fetchGit {
    url = "https://github.com/DavHau/mach-nix";
    ref = "refs/tags/3.5.0";
  }) {
    # optionally bring your own nixpkgs
    # pkgs = import <nixpkgs> {};

    # optionally specify the python version
    # python = "python38";

    # optionally update pypi data revision from https://github.com/DavHau/pypi-deps-db
    # pypiDataRev = "some_revision";
    # pypiDataSha256 = "some_sha256";
  };
in
...

Use mach-nix from a Flake

{
  inputs = {
    mach-nix.url = "mach-nix/3.5.0";
  };

  outputs = {self, nixpkgs, mach-nix }@inp:
    let
      l = nixpkgs.lib // builtins;
      supportedSystems = [ "x86_64-linux" "aarch64-darwin" ];
      forAllSystems = f: l.genAttrs supportedSystems
        (system: f system (import nixpkgs {inherit system;}));
    in
    {
      # enter this python environment by executing `nix shell .`
      defaultPackage = forAllSystems (system: pkgs: mach-nix.lib."${system}".mkPython {
        requirements = ''
          pillow
          numpy
          requests
        '';
      });
    };
}

mkPython / mkPythonShell

From a list of requirements

mach-nix.mkPython {  # replace with mkPythonShell if shell is wanted
  requirements = builtins.readFile ./requirements.txt;
}

Include extra packages.

packagesExtra accepts:

  • python packages built via mach-nix.buildPythonPackage.
  • R Packages from nixpkgs.rPackages (see R example further down)
  • python package source trees as paths or derivations
  • URLs pointing to a tarball archives containing a python source tree
...
mach-nix.mkPython {
  requirements = builtins.readFile ./requirements.txt;
  packagesExtra = [
    "https://github.com/psf/requests/tarball/2a7832b5b06d"   # from tarball url
    ./some/local/project                                     # from local path
    mach-nix.buildPythonPackage { ... };                     # from package
  ];
}

Alternatively, if requirements are not needed, packagesExtra can be passed directly to mkPython

...
mach-nix.mkPython [
  "https://github.com/psf/requests/tarball/2a7832b5b06d"   # from tarball url
  ./some/local/project                                     # from local path
  mach-nix.buildPythonPackage { ... };                     # from package
]

buildPythonPackage / buildPythonApplication

These functions can be used to manually build individual python modules or applications. Those can either be used directly, or fed as packagesExtra of mkPython. Whenever requirements are not explicitly specified, they will be extracted automatically from the packages setup.py/setup.cfg. The same goes for the name and version.

Build python package from its source code

...
mach-nix.buildPythonPackage /python-project-path

buildPythonPackage from GitHub

...
mach-nix.buildPythonPackage "https://github.com/psf/requests/tarball/2a7832b5b06d"

buildPythonPackage from GitHub with extras

...
mach-nix.buildPythonPackage {
  src = "https://github.com/psf/requests/tarball/2a7832b5b06d";
  extras = "socks";
}

buildPythonPackage from GitHub and add requirements

Use requirementsExtra in case the auto detected requirements are incomplete

...
mach-nix.buildPythonPackage {
  src = "https://github.com/psf/requests/tarball/2a7832b5b06d";
  requirementsExtra = "pytest";
}

buildPythonPackage from GitHub (reproducible source)

...
mach-nix.buildPythonPackage {
  src = builtins.fetchGit{
    url = "https://github.com/user/projectname";
    ref = "master";
    # rev = "put_commit_hash_here";
  };
}

buildPythonPackage from GitHub (manual requirements)

Use this if automatic requirements extraction doesn't work at all.

...
mach-nix.buildPythonPackage {
  src = "https://github.com/psf/requests/tarball/2a7832b5b06d";
  requirements = ''
    # list of requirements
  '';
}

Simplified overrides ('_' argument)

General usage

with mach-nix.nixpkgs;
mach-nix.mkPython {

  requirements = "some requirements";

  _.{package}.buildInputs = [...];             # replace buildInputs
  _.{package}.buildInputs.add = [...];         # add buildInputs
  _.{package}.buildInputs.mod =                # modify buildInputs
      oldInputs: filter (inp: ...) oldInputs;

  _.{package}.patches = [...];                 # replace patches
  _.{package}.patches.add = [...];             # add patches
  ...
}

Example: add missing build inputs

For example the package web2ldap depends on another python package ldap0 which fails to build because of missing dependencies.

...
with mach-nix.nixpkgs;
mach-nix.mkPython {

  requirements = "web2ldap";

  # add missing dependencies to ldap0
  _.ldap0.buildInputs.add = [ openldap.dev cyrus_sasl.dev ];
}

Example: add missing .so shared object library for instance you are getting a Pyside on nixos ImportError: libgssapi_krb5.so.2 error

If you have nix-index package installed you should be able to find the package that should provide the lib fast with

nix-locate -1 -w libgssapi_krb5.so.2  | grep -v \(
libkrb5.out
krb5.out
hyperion-ng.out

Once you have decided on the lib in this case libkrb5 for pyside2

...
with mach-nix.nixpkgs;
mach-nix.mkPython {

  requirements = "web2ldap";

  # add missing os library to libkrb5
  _.pyside2.buildInputs.add = with pkgs; [ libkrb5 ];  # LINE ADDED
}

Overrides (overridesPre / overridesPost)

Include poetry2nix overrides

imagecodecs is available via wheel, but if one wants to build it from source, dependencies will be missing since there is no nixpkgs candidate available. poetry2nix luckily maintains overrides for this package. They can be included into the mach-nix build like this.

...
mach-nix.mkPython rec {

  requirements = ''
    # bunch of other requirements
    imagecodecs
  '';

  providers = {
    _default = "sdist";
  };

  # Import overrides from poetry2nix
  # Caution! Use poetry2nix overrides only in `overridesPost`, not `overridesPre`.
  overridesPost = [
    (
      import (builtins.fetchurl {
        url = "https://raw.githubusercontent.com/nix-community/poetry2nix/1cfaa4084d651d73af137866622e3d0699851008/overrides.nix";
      }) { pkgs = mach-nix.nixpkgs; }
    )
  ];
}

Tensorflow

Tensorflow with SSE/AVX/FMA support

Tensorflow from pypi does not provide any hardware optimization support. To get a SSE/AVX/FMA enabled version, set the provider for tensorflow to nixpkgs.

...
mach-nix.mkPython {

  requirements = ''
    # bunch of other requirements
    tensorflow
  '';

  # force tensorflow to be taken from nixpkgs
  providers.tensorflow = "nixpkgs";
}

This only works if the restrictions in requirements.txt allow for the tensorflow version from nixpkgs.

Tensorflow via wheel (newer versions, quicker builds)

Install recent tensorflow via wheel

...
mach-nix.mkPython {

  requirements = ''
    # bunch of other requirements
    tensorflow == 2.2.0rc4
  '';
  # no need to specify provider settings since wheel is the default anyways
}

PyTorch

Recent PyTorch with nixpkgs dependencies, and custom python

Recent pytorch version, Build dependencies from source

...
mach-nix.mkPython rec {

  requirements = ''
    # bunch of other requirements
    torch == 1.5.0
  '';

  providers = {
    # disallow wheels by default
    _default = "nixpkgs,sdist";
    # allow wheels only for torch
    torch = "wheel";
  };
}

Jupyter

...using jupyterWith + mach-nix

In this example, mach-nix is used to resolve our python dependencies and provide them to jupyterWith which is a Nix-based framework for the definition of declarative and reproducible Jupyter environments.

let
  mach-nix = import (builtins.fetchGit {
    url = "https://github.com/DavHau/mach-nix";
    ref = "refs/tags/3.5.0";  # update this version
  }) {
    python = "python37";
  };

  # load your requirements
  machNix = mach-nix.mkPython rec {
    requirements = builtins.readFile ./requirements.txt;
  };

  jupyter = import (builtins.fetchGit {
    url = https://github.com/tweag/jupyterWith;
    ref = "master";
    #rev = "some_revision";
  }) {};

  iPython = jupyter.kernels.iPythonWith {
    name = "mach-nix-jupyter";
    python3 = machNix.python;
    packages = machNix.python.pkgs.selectPkgs;
  };

  jupyterEnvironment = jupyter.jupyterlabWith {
    kernels = [ iPython ];
  };
in
  jupyterEnvironment.env

...using mach-nix only

...
let
  pyEnv = mach-nix.mkPython rec {

    requirements =  ''
        jupyterlab
        geopandas
        pyproj
        pygeos
        shapely>=1.7.0
      '';

    providers.shapely = "sdist,nixpkgs";
  };
in
mach-nix.nixpkgs.mkShell {

  buildInputs = [
    pyEnv
  ] ;

  shellHook = ''
    jupyter lab --notebook-dir=~/
  '';
}

For more information regarding Jupyter Lab extensions see an other example.

Docker

Docker images can be built by using mkDockerImage instead of mkPython. It accepts the same arguments.

JupyterLab Docker Image

Assuming the following expression under ./jupyter-docker.nix:

...
let
  image = mach-nix.mkDockerImage {
    requirements =  ''
      jupyterlab
      # add more packages here
    '';
  };
in
# The following overrides a call to nixpkgs.dockerTools.buildImage.
# Find more buildImage examples here: https://github.com/NixOS/nixpkgs/blob/master/pkgs/build-support/docker/examples.nix
image.override (oldAttrs: {
  name = "jupyterlab";
  config.Cmd = [ "jupyter" "lab" "--notebook-dir=/mnt" "--allow-root" "--ip=0.0.0.0" ];
})

Execute the build like:

nix-build ./jupyter-docker.nix -o ./docker-image

Afterwards, load the docker image:

docker load < ./docker-image

Start the jupyterlab container:

docker run --rm -it -p 8888:8888 -v $HOME:/mnt jupyterlab

R and Python

The following is an example for a Python environment mixed with R packages. R packages can be added via packagesExtra. If mach-nix finds R packages inside packagesExtra, it will automatically include rpy2 and add the selected R packages to its buildInputs. To get a list of available R packages, execute: echo "builtins.attrNames(import <nixpkgs> {}).rPackages" | nix repl

...
mach-nix.mkPython {
  requirements =  ''
    # some python requirements
  '';
  packagesExtra = with mach-nix.rPackages; [
    data_table
  ];
}

Raspberry PI / aarch64 SD Image

This example builds an aarch64 sd image via emulator. For this to work, binfmt support for aarch64 must be installed first. (On NixOS simply set boot.binfmt.emulatedSystems = [ "aarch64-linux" ]) For the SD-image, create a configuration.nix file which adds the mach-nix tool and some default python packages to the system environment. configuration.nix:

{ config, lib, pkgs, ... }:

let
  machNix = import (builtins.fetchGit {
    url = "https://github.com/DavHau/mach-nix";
    ref = "refs/tags/put_version_here";
  }) { inherit pkgs; };

  defaultPythonEnv = machNix.mkPython {
    requirements = ''
      cryptography
    '';
    providers.cffi = "nixpkgs";
  };

in {
  imports = [
    <nixpkgs/nixos/modules/installer/cd-dvd/sd-image-aarch64.nix>
  ];
  environment.systemPackages = [ defaultPythonEnv machNix.mach-nix ];
  sdImage.compressImage = false;  # speeds up the build
}

with the following default.nix:

with import <nixpkgs/nixos> {
  system = "aarch64-linux";
};
config.system.build.sdImage

Execute:

NIXOS_CONFIG=$PWD/configuration.nix nix build -f default.nix

Or to select a specific channel:

NIXOS_CONFIG=$PWD/configuration.nix nix build -f default.nix -I nixpkgs=channel:nixos-20.03

Troubleshooting

collision between /nix/store/X and /nix/store/Y

In general, there can be two different reasons for this error:

1. Environment contains different versions of same package.

This is the case, if both store paths, mentioned by the error message, contain the same package name. For example:

collision between
/nix/store/p3cwaa05gsbssgxfabisaw350yz8gd8i-python3.7-apscheduler-3.6.3/lib/python3.7/site-packages/apscheduler/executors/__pycache__/__init__.cpython-37.pyc
and
/nix/store/v1k9fi7vq9cmp3vjrl6pk2gq9cnjayv6-python3.7-apscheduler-3.6.3/lib/python3.7/site-packages/apscheduler/executors/pycache/init.cpython-37.pyc

Python environments are never allowed to contain two versions of the same package. Therefore, if something like this happens, it is most likely a bug in mach-nix. Please open an issue with the error message and nix expression attached causing the error.

2. Different packages contain same named file

This is the case, if both store paths, mentioned by the error message, contain different package names. For example:

collision between
/nix/store/zn4ksalrynlx3iwd4d0ldq7aiqn84ysv-python3.8-opencensus-context-0.1.2/lib/python3.8/site-packages/opencensus/common/__pycache__/__init__.cpython-38.pyc
and
/nix/store/2cfyjnic605mjr5j7zck88gk7bkqwpim-python3.8-opencensus-0.7.12/lib/python3.8/site-packages/opencensus/common/__pycache__/__init__.cpython-38.pyc

In this example, both packages opencensus-context and opencensus contain a file with the exact same import path [...]/opencensus/common/__pycache__/__init__.cpython-38.pyc. Would you be installing these two packages via pip, then the later installed package would overwrite the file of the earlier installed package. This leads to undefined behavior, since the outcome dependes on the order of installation which is not necessarily the same across different installations. Still, those collisions are common among some python packages, since pip does not raise an error when this happens, and just blindly overwrites files, leaving package maintainers in the dark about the problem. It should be in the best interest of the packages maintainers to remove these collisions and get rid of undeclared behavior. Therefore it might be a good idea to report the collision issue upstream. To fix the immediate error with your current mach-nix environment, you have two options:

  1. (recommended) Fix the collision manually by removing the problematic file for one of the packages. Example 
    mach-nix.mkPython {

  requirements = "...";

  _.{package1}.postInstall = ''
    rm $out/lib/python*/site-packages/colliding/file.pyc
  '';

}
  2. (not recommended) Ignore collisions in general 
    mach-nix.mkPython {

  requirements = "...";

  ignoreCollisions = true;

}