Python: Difference between revisions

Revision as of 08:55, 18 August 2024

Python development environments with Nix

Nix supports a number of approaches to creating "development environments" for Python programming. These provide functionality analogous to virtualenv or conda: a shell environment with access to pinned versions of the python executable and Python packages.

Using the Nixpkgs Python infrastructure via `shell.nix` (recommended)

Nixpkgs has the few last Python versions packaged, as well as a consequent set of Python packages packaged that you can use to quickly create a Python environment.

Create a file shell.nix in the project directory, with the following template:

# shell.nix
let
  # We pin to a specific nixpkgs commit for reproducibility.
  # Last updated: 2024-04-29. Check for new commits at https://status.nixos.org.
  pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/cf8cc1201be8bc71b7cbbbdaf349b22f4f99c7ae.tar.gz") {};
in pkgs.mkShell {
  packages = [
    (pkgs.python3.withPackages (python-pkgs: [
      # select Python packages here
      python-pkgs.pandas
      python-pkgs.requests
    ]))
  ];
}

In this example, we create a Python environment with packages pandas and requests.

You can find Python packages that are available in Nixpkgs using search.nixos.org. For instance, type a Python package name like numpy in the search bar and click on the search button on the right. You can narrow down results by clicking on eg. "python311Packages" in the "Package sets" section on the left. Note that in the snippet above, on lines 8 and 9, each package is listed in the form python-pkgs.<name> where <name> corresponds to the one found in search.nixos.org . See Nix language basics for more information on the python-pkgs attribute set.

Once you have picked the Python packages you want, run nix-shell (or nix develop -f shell.nix) to build the Python environment and enter it. Once in the environment Python will be available in your PATH, so you can run eg. python --version.

Using a Python package not in Nixpkgs

Python packages in Nixpkgs are created and updated by Nixpkgs maintainers. Although the community invests a great effort to keep a complete and up-to-date package set, some packages you want may be missing, out of date, or broken. To use your own packages in a Nix environment, you may package it yourself.

The following is a high-level overview. For a complete explanation, see Developing with Python in the Nixpkgs Manual.

Generally, you may create a file that looks like this:

# toolz.nix
{ lib
, buildPythonPackage
, fetchPypi
, setuptools
, wheel
}:

buildPythonPackage rec {
  pname = "toolz";
  version = "0.10.0";

  src = fetchPypi {
    inherit pname version;
    hash = "sha256-CP3V73yWSArRHBLUct4hrNMjWZlvaaUlkpm1QP66RWA=";
  };

  # do not run tests
  doCheck = false;

  # specific to buildPythonPackage, see its reference
  pyproject = true;
  build-system = [
    setuptools
    wheel
  ];
}

Given the file above is named toolz.nix and is the same directory as the previous shell.nix , you can edit shell.nix to use the package toolz above like so:

# shell.nix
let
  pkgs = import <nixpkgs> {};

  python = pkgs.python3.override {
    self = python;
    packageOverrides = pyfinal: pyprev: {
      toolz = pyfinal.callPackage ./toolz.nix { };
    };
  };

in pkgs.mkShell {
  packages = [
    (python.withPackages (python-pkgs: [
      # select Python packages here
      python-pkgs.pandas
      python-pkgs.requests
      python-pkgs.toolz
    ]))
  ];
}

Next time you enter the shell specified by this file, Nix will build and include the Python package you have written.

Running compiled libraries

If you want to run some compiled libraries as for example grpcio^[1], you may encounter the following error :

$ python -c 'import grpc'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/.../grpc/__init__.py", line 22, in <module>
    from grpc import _compression
  File "/.../grpc/_compression.py", line 20, in <module>
    from grpc._cython import cygrpc
ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory

This means that the library use compiled dynamically linked binaries that your NixOs environment fail to resolve.

On NixOS, installing packages that need to compile code or use C libraries from outside of the nix package manager may fail if dependencies are not found in the expected locations. There are multiple ways to make it work:

Use fix-python, this is most suited for beginners.

Create a FHS user env with buildFHSUserEnv.
Setup nix-ld^[2] in your NixOS configuration.

Setup nix-ld

nix-ld^[2] allow you to Run unpatched dynamic binaries on NixOS.

The following configuration automatically fix the dependencies :

let
  python = pkgs.python311;
  # https://github.com/NixOS/nixpkgs/blob/c339c066b893e5683830ba870b1ccd3bbea88ece/nixos/modules/programs/nix-ld.nix#L44
  # > We currently take all libraries from systemd and nix as the default.
  pythonldlibpath = lib.makeLibraryPath (with pkgs; [
    zlib
    zstd
    stdenv.cc.cc
    curl
    openssl
    attr
    libssh
    bzip2
    libxml2
    acl
    libsodium
    util-linux
    xz
    systemd
  ]);
  patchedpython = (python.overrideAttrs (
    previousAttrs: {
      # Add the nix-ld libraries to the LD_LIBRARY_PATH.
      # creating a new library path from all desired libraries
      postInstall = previousAttrs.postInstall + ''
        mv  "$out/bin/python3.11" "$out/bin/unpatched_python3.11"
        cat << EOF >> "$out/bin/python3.11"
        #!/run/current-system/sw/bin/bash
        export LD_LIBRARY_PATH="${pythonldlibpath}"
        exec "$out/bin/unpatched_python3.11" "\$@"
        EOF
        chmod +x "$out/bin/python3.11"
      '';
    }
  ));
  # if you want poetry
  patchedpoetry =  ((pkgs.poetry.override { python3 = patchedpython; }).overrideAttrs (
    previousAttrs: {
      # same as above, but for poetry
      # not that if you dont keep the blank line bellow, it crashes :(
      postInstall = previousAttrs.postInstall + ''

        mv "$out/bin/poetry" "$out/bin/unpatched_poetry"
        cat << EOF >> "$out/bin/poetry"
        #!/run/current-system/sw/bin/bash
        export LD_LIBRARY_PATH="${pythonldlibpath}"
        exec "$out/bin/unpatched_poetry" "\$@"
        EOF
        chmod +x "$out/bin/poetry"
      '';
    }
  ));
in
{
  # Some other config...
  
  environment.systemPackages = with pkgs; [
    patchedpython

    # if you want poetry
    patchedpoetry
  ];
}

This configuration set the LD_LIBRARY_PATH environment variable before running python using the overrideAttrs^[3] function to override the postInstall script of cpython mkDerivation^[4].

After this step, you should be able to install compiled libraries using venv, poetry, conda or other packages managers...

Using `venv`

To create a Python virtual environment with venv:

$ nix-shell -p python3 --command "python -m venv .venv --copies"

You can then activate and use the Python virtual environment as usual and install dependencies with pip and similar.

Using poetry

# shell.nix
let
  pkgs = import <nixpkgs> {};
in pkgs.mkShell {
  packages = with pkgs; [
    python310
    (poetry.override { python3 = python310; })
  ];
}

Using micromamba

Install the micromamba package to create environments and install packages as documented by micromamba.

To activate an environment you will need a FHS environment e.g.:

$ nix-shell -E 'with import <nixpkgs> {}; (pkgs.buildFHSUserEnv { name = "fhs"; }).env'
$ eval "$(micromamba shell hook -s bash)"
$ micromamba activate my-environment
$ python
>>> import numpy as np

Eventually you'll probably want to put this in a shell.nix so you won't have to type all that stuff every time e.g.:

{ pkgs ? import <nixpkgs> {}}:
let
  fhs = pkgs.buildFHSUserEnv {
    name = "my-fhs-environment";

    targetPkgs = _: [
      pkgs.micromamba
    ];

    profile = ''
      set -e
      eval "$(micromamba shell hook --shell=posix)"
      export MAMBA_ROOT_PREFIX=${builtins.getEnv "PWD"}/.mamba
      if ! test -d $MAMBA_ROOT_PREFIX/envs/my-mamba-environment; then
          micromamba create --yes -q -n my-mamba-environment
      fi
      micromamba activate my-mamba-environment
      micromamba install --yes -f conda-requirements.txt -c conda-forge
      set +e
    '';
  };
in fhs.env

Using conda

Install the package conda and run

$ conda-shell
$ conda-install
$ conda env update --file environment.yml

Imperative use

It is also possible to use conda-install directly. On first use, run:

$ conda-shell
$ conda-install

to set up conda in ~/.conda

Package a Python application

With `setup.py`

To package a Python application that uses setup.py you can use buildPythonApplication. More details about this and similar functions can be found in the nixpkgs manual.

For example, we can package this simple flask server main.py:

#!/usr/bin/env python

from flask import Flask

app = Flask(__name__)

@app.route('/')
def hello_world():
    return 'Hello, World!'

if __name__ == '__main__':
    app.run(host="0.0.0.0", port=8080)

We also need a setup.py file, like this:

from setuptools import setup, find_packages

setup(name='myFlaskServer',
      version='1.0',
      # Modules to import from other scripts:
      packages=find_packages(),
      # Executables
      scripts=["main.py"],
     )

Then, we use the buildPythonApplication in the default.nix:

{ pkgs ? import <nixpkgs> {} }:

pkgs.python3Packages.buildPythonApplication {
  pname = "myFlaskApp";
  version = "0.1.0";

  propagatedBuildInputs = with pkgs.python3Packages; [
    flask
  ];

  src = ./.;
}

Finally, build your project using nix-build. The result will be executable in ./result/bin/app.py.

With `pyproject.toml`

When your project is using pyproject.tomlyou can use pyproject.nix to package your application.

First, a simple file structure could look like this:

├── app/
    └── main.py
├── flake.nix
├── pyproject.toml
└── README.md

To reuse the example from above, we use the same flask application:

from flask import Flask

app = Flask(__name__)

@app.route('/')
def hello_world():
    return 'Hello, World!'

if __name__ == '__main__':
    app.run(host="0.0.0.0", port=8080)

Also, you need to define the pyproject.toml. Here, we only show some of the important parts. Please refer to pyproject.nix documentation for a full example.

[project]
name = "my-app"
version = "0.1.0"
description = "Simple app"

# define any Python dependencies
dependencies = [
  "flask>3",
]

# define the CLI executable
# Here, we define the entry point to be the 'main()' function in the module 'app/main.py'
[project.scripts]
cli = "app.main:main"

We package the application by calling the loadPyproject function from pyproject.nix. Again, we only show a minimal example. More information can be found in the documentation.

{
  description = "A basic flake using pyproject.toml project metadata";

  inputs = {
    pyproject-nix = {
      url = "github:nix-community/pyproject.nix";
      inputs.nixpkgs.follows = "nixpkgs";
    };
  };

  outputs = { nixpkgs, pyproject-nix, ... }:
    let
      inherit (nixpkgs) lib;

      project = pyproject-nix.lib.project.loadPyproject {
        # Read & unmarshal pyproject.toml relative to this project root.
        # projectRoot is also used to set `src` for renderers such as buildPythonPackage.
        projectRoot = ./.;
      };

      # This example is only using x86_64-linux
      pkgs = nixpkgs.legacyPackages.x86_64-linux;

      python = pkgs.python3;

    in
    {
      # Build our package using `buildPythonPackage
      packages.x86_64-linux.default =
        let
          # Returns an attribute set that can be passed to `buildPythonPackage`.
          attrs = project.renderers.buildPythonPackage { inherit python; };
        in
        # Pass attributes to buildPythonPackage.
        # Here is a good spot to add on any missing or custom attributes.
        python.pkgs.buildPythonPackage (attrs // {
          env.CUSTOM_ENVVAR = "hello";
        });
    };
}

To run the application, call nix run.

Nixpkgs Python contribution guidelines

Libraries

According to the official guidelines for Python, new package expressions for libraries should be placed in pkgs/development/python-modules/<name>/default.nix.

Those expressions are then referenced from pkgs/top-level/python-packages.nix as in

  aenum = callPackage ../development/python-modules/aenum { };

Applications

Applications meant to be executed should be referenced directly from pkgs/top-level/all-packages.nix.

Other Python packages used in the Python package of the application should be taken from the callPackage argument pythonPackages , which guarantees that they belong to the same "pythonPackage" set. For example:

{ lib
, pythonPackages
}:
buildPythonApplication {
  propagatedBuildInputs = [ pythonPackages.numpy ];
  # ...
}

Special Modules

GNOME

gobject-introspection based python modules need some environment variables to work correctly. For standalone applications, wrapGAppsHook (see the relevant documentation) wraps the executable with the necessary variables. But this is not fit for development. In this case use a nix-shell with gobject-introspection and all the libraries you are using (gtk and so on) as buildInputs. For example:

$ nix-shell -p gobjectIntrospection gtk3 'python2.withPackages (ps: with ps; [ pygobject3 ])' --run "python -c \"import pygtkcompat; pygtkcompat.enable_gtk(version='3.0')\""

Or, if you want to use matplotlib interactively:

$ nix-shell -p gobject-introspection gtk3 'python36.withPackages(ps : with ps; [ matplotlib pygobject3 ipython ])'
$ ipython

In [1]: import matplotlib
In [2]: matplotlib.use('gtk3agg')
In [3]: import matplotlib.pyplot as plt
In [4]: plt.ion()
In [5]: plt.plot([1,3,2,4])

You can also set backend : GTK3Agg in your ~/.config/matplotlib/matplotlibrc file to avoid having to call matplotlib.use('gtk3agg').

Performance

The derivation of CPython that is available via nixpkgs only contains optimizations that do not harm reproducibility. Link-Time-Optimization (LTO) is only enabled on 64-bit Linux systems, while Profile Guided Optimization (PGO) is currently disabled. See Configuring Python 3.1.3. Performance options Additionally, when compiling something within nix-shell or a derivation security hardening flags are passed to the compiler by default which may have a small performance impact.

At the time of writing certain optimizations cause Python wheels to be non-reproducible and increase install times. For a detailed overview of the trials and tribulations of discovering such performance regressions see Why is the nix-compiled Python slower?.

Regression

With the nixpkgs version of Python you can expect anywhere from a 30-40% regression on synthetic benchmarks. For example:

## Ubuntu's Python 3.8
username:dir$ python3.8 -c "import timeit; print(timeit.Timer('for i in range(100): oct(i)', 'gc.enable()').repeat(5))"
[7.831622750498354, 7.82998560462147, 7.830805554986, 7.823807033710182, 7.84282516874373]

## nix-shell's Python 3.8
[nix-shell:~/src]$ python3.8 -c "import timeit; print(timeit.Timer('for i in range(100): oct(i)', 'gc.enable()').repeat(5))"
[10.431915327906609, 10.435049421153963, 10.449542525224388, 10.440207410603762, 10.431304694153368]

However, synthetic benchmarks are not necessarily reflective of real-world performance. In common real-world situations, the performance difference between optimized and non-optimized interpreters is minimal. For example, using pylint with a significant number of custom linters to scan a very large Python codebase (>6000 files) resulted in only a 5.5% difference. Other workflows that were not performance sensitive saw no impact to their run times.

Possible Optimizations

If you run code that heavily depends on Python performance, and you desire the most performant Python interpreter possible, here are some possible things you can do:

Enable the enableOptimizations flag for your Python derivation. See Example. Do note that this will cause you to compile Python the first time that you run it which will take a few minutes.
Switch to a newer version of Python. In the example above, going from 3.8 to 3.10 yielded an average 7.5% performance improvement, but this is only a single benchmark. Switching versions most likely won't make all your code 7.5% faster.
Disable hardening. Beware this only yields a small performance boost and it has impacts beyond Python code. See Hardening in Nixpkgs.

Ultimately, it is up to your use case to determine if you need an optimized version of the Python interpreter. We encourage you to benchmark and test your code to determine if this is something that would benefit you.

Troubleshooting

My module cannot be imported

If you are unable to do `import yourmodule` there are a number of reasons that could explain that.

First, make sure that you installed/added your module to python. Typically you would use something like (python3.withPackages (ps: with ps; [ yourmodule ])) in the list of installed applications.

It is also still possible (e.g. when using nix-shell) that you aren't using the python interpreter you want because another package provides its own python3.withPackages in buildInputs, for example, yosys. In this case, you should either include that package (or all needed packages) in your withPackages list to only have a single Python interpreter. Or you can change the order of your packages, such that the python3.withPackages comes first, and becomes the Python interpreter that you get.

If you packaged yourself your application, make sure to use buildPythonPackage and **not** buildPythonApplication or stdenv.mkDerivation. The reason is that python3.withPackages filters the packages to check that they are built using the appropriate python interpreter: this is done by verifying that the derivation has a pythonModule attribute and only buildPythonPackage sets this value (passthru here) thanks to, notably passthru = { pythonModule = python; }. If you used stdenv.mkDerivation then you can maybe set this value manually, but it's safer to simply use buildPythonPackage {format = "other"; … your derivation …} instead of mkDerivation.