Frederik Rietdijk 8d491ec6c6 Python docs: Python 2.x namespace packages may collide when using .withPackages

2017-04-18 09:05:00 +02:00

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Python

User Guide

Several versions of Python are available on Nix as well as a high amount of packages. The default interpreter is CPython 2.7.

Using Python

Installing Python and packages

It is important to make a distinction between Python packages that are used as libraries, and applications that are written in Python.

Applications on Nix are installed typically into your user profile imperatively using nix-env -i, and on NixOS declaratively by adding the package name to environment.systemPackages in /etc/nixos/configuration.nix. Dependencies such as libraries are automatically installed and should not be installed explicitly.

The same goes for Python applications and libraries. Python applications can be installed in your profile, but Python libraries you would like to use to develop cannot. If you do install libraries in your profile, then you will end up with import errors.

Python environments using `nix-shell`

The recommended method for creating Python environments for development is with nix-shell. Executing

$ nix-shell -p python35Packages.numpy python35Packages.toolz

opens a Nix shell which has available the requested packages and dependencies. Now you can launch the Python interpreter (which is itself a dependency)

[nix-shell:~] python3

If the packages were not available yet in the Nix store, Nix would download or build them automatically. A convenient option with nix-shell is the --run option, with which you can execute a command in the nix-shell. Let's say we want the above environment and directly run the Python interpreter

$ nix-shell -p python35Packages.numpy python35Packages.toolz --run "python3"

This way you can use the --run option also to directly run a script

$ nix-shell -p python35Packages.numpy python35Packages.toolz --run "python3 myscript.py"

In fact, for this specific use case there is a more convenient method. You can add a shebang to your script specifying which dependencies Nix shell needs. With the following shebang, you can use nix-shell myscript.py and it will make available all dependencies and run the script in the python3 shell.

#! /usr/bin/env nix-shell
#! nix-shell -i python3 -p python3Packages.numpy

import numpy

print(numpy.__version__)

Likely you do not want to type your dependencies each and every time. What you can do is write a simple Nix expression which sets up an environment for you, requiring you only to type nix-shell. Say we want to have Python 3.5, numpy and toolz, like before, in an environment. With a shell.nix file containing

with import <nixpkgs> {};

(pkgs.python35.withPackages (ps: [ps.numpy ps.toolz])).env

executing nix-shell gives you again a Nix shell from which you can run Python.

What's happening here?

We begin with importing the Nix Packages collections. import <nixpkgs> import the <nixpkgs> function, {} calls it and the with statement brings all attributes of nixpkgs in the local scope. Therefore we can now use pkgs.
Then we create a Python 3.5 environment with the withPackages function.
The withPackages function expects us to provide a function as an argument that takes the set of all python packages and returns a list of packages to include in the environment. Here, we select the packages numpy and toolz from the package set.
And finally, for in interactive use we return the environment by using the env attribute.

Developing with Python

Now that you know how to get a working Python environment on Nix, it is time to go forward and start actually developing with Python. We will first have a look at how Python packages are packaged on Nix. Then, we will look how you can use development mode with your code.

Python packaging on Nix

On Nix all packages are built by functions. The main function in Nix for building Python packages is buildPythonPackage. Let's see how we would build the toolz package. According to python-packages.nix toolz is build using

{ # ...

  toolz = buildPythonPackage rec {
    name = "toolz-${version}";
    version = "0.7.4";

    src = pkgs.fetchurl {
      url = "mirror://pypi/t/toolz/toolz-${version}.tar.gz";
      sha256 = "43c2c9e5e7a16b6c88ba3088a9bfc82f7db8e13378be7c78d6c14a5f8ed05afd";
    };

    meta = {
      homepage = "http://github.com/pytoolz/toolz/";
      description = "List processing tools and functional utilities";
      license = licenses.bsd3;
      maintainers = with maintainers; [ fridh ];
    };
  };
}

What happens here? The function buildPythonPackage is called and as argument it accepts a set. In this case the set is a recursive set (rec). One of the arguments is the name of the package, which consists of a basename (generally following the name on PyPi) and a version. Another argument, src specifies the source, which in this case is fetched from an url. fetchurl not only downloads the target file, but also validates its hash. Furthermore, we specify some (optional) meta information.

The output of the function is a derivation, which is an attribute with the name toolz of the set pythonPackages. Actually, sets are created for all interpreter versions, so e.g. python27Packages, python35Packages and pypyPackages.

The above example works when you're directly working on pkgs/top-level/python-packages.nix in the Nixpkgs repository. Often though, you will want to test a Nix expression outside of the Nixpkgs tree. If you create a shell.nix file with the following contents

with import <nixpkgs> {};

pkgs.python35Packages.buildPythonPackage rec {
  name = "toolz-${version}";
  version = "0.8.0";

  src = pkgs.fetchurl {
    url = "mirror://pypi/t/toolz/toolz-${version}.tar.gz";
    sha256 = "e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479";
  };

  doCheck = false;

  meta = {
    homepage = "http://github.com/pytoolz/toolz/";
    description = "List processing tools and functional utilities";
    license = licenses.bsd3;
    maintainers = with maintainers; [ fridh ];
  };
}

and then execute nix-shell will result in an environment in which you can use Python 3.5 and the toolz package. As you can see we had to explicitly mention for which Python version we want to build a package.

The above example considered only a single package. Generally you will want to use multiple packages. If we create a shell.nix file with the following contents

with import <nixpkgs> {};

( let
    toolz = pkgs.python35Packages.buildPythonPackage rec {
      name = "toolz-${version}";
      version = "0.8.0";

      src = pkgs.fetchurl {
        url = "mirror://pypi/t/toolz/toolz-${version}.tar.gz";
        sha256 = "e8451af61face57b7c5d09e71c0d27b8005f001ead56e9fdf470417e5cc6d479";
      };

      doCheck = false;

      meta = {
        homepage = "http://github.com/pytoolz/toolz/";
        description = "List processing tools and functional utilities";
      };
    };

  in pkgs.python35.withPackages (ps: [ps.numpy toolz])
).env

and again execute nix-shell, then we get a Python 3.5 environment with our locally defined package as well as numpy which is build according to the definition in Nixpkgs. What did we do here? Well, we took the Nix expression that we used earlier to build a Python environment, and said that we wanted to include our own version of toolz. To introduce our own package in the scope of withPackages we used a let expression. You can see that we used ps.numpy to select numpy from the nixpkgs package set (ps). But we do not take toolz from the nixpkgs package set this time. Instead, toolz will resolve to our local definition that we introduced with let.

Handling dependencies

Our example, toolz, doesn't have any dependencies on other Python packages or system libraries. According to the manual, buildPythonPackage uses the arguments buildInputs and propagatedBuildInputs to specify dependencies. If something is exclusively a build-time dependency, then the dependency should be included as a buildInput, but if it is (also) a runtime dependency, then it should be added to propagatedBuildInputs. Test dependencies are considered build-time dependencies.

The following example shows which arguments are given to buildPythonPackage in order to build datashape.

{ # ...

  datashape = buildPythonPackage rec {
    name = "datashape-${version}";
    version = "0.4.7";

    src = pkgs.fetchurl {
      url = "mirror://pypi/D/DataShape/${name}.tar.gz";
      sha256 = "14b2ef766d4c9652ab813182e866f493475e65e558bed0822e38bf07bba1a278";
    };

    buildInputs = with self; [ pytest ];
    propagatedBuildInputs = with self; [ numpy multipledispatch dateutil ];

    meta = {
      homepage = https://github.com/ContinuumIO/datashape;
      description = "A data description language";
      license = licenses.bsd2;
      maintainers = with maintainers; [ fridh ];
    };
  };
}

We can see several runtime dependencies, numpy, multipledispatch, and dateutil. Furthermore, we have one buildInput, i.e. pytest. pytest is a test runner and is only used during the checkPhase and is therefore not added to propagatedBuildInputs.

In the previous case we had only dependencies on other Python packages to consider. Occasionally you have also system libraries to consider. E.g., lxml provides Python bindings to libxml2 and libxslt. These libraries are only required when building the bindings and are therefore added as buildInputs.

{ # ...

  lxml = buildPythonPackage rec {
    name = "lxml-3.4.4";

    src = pkgs.fetchurl {
      url = "mirror://pypi/l/lxml/${name}.tar.gz";
      sha256 = "16a0fa97hym9ysdk3rmqz32xdjqmy4w34ld3rm3jf5viqjx65lxk";
    };

    buildInputs = with self; [ pkgs.libxml2 pkgs.libxslt ];

    meta = {
      description = "Pythonic binding for the libxml2 and libxslt libraries";
      homepage = http://lxml.de;
      license = licenses.bsd3;
      maintainers = with maintainers; [ sjourdois ];
    };
  };
}

In this example lxml and Nix are able to work out exactly where the relevant files of the dependencies are. This is not always the case.

The example below shows bindings to The Fastest Fourier Transform in the West, commonly known as FFTW. On Nix we have separate packages of FFTW for the different types of floats ("single", "double", "long-double"). The bindings need all three types, and therefore we add all three as buildInputs. The bindings don't expect to find each of them in a different folder, and therefore we have to set LDFLAGS and CFLAGS.

{ # ...

  pyfftw = buildPythonPackage rec {
    name = "pyfftw-${version}";
    version = "0.9.2";

    src = pkgs.fetchurl {
      url = "mirror://pypi/p/pyFFTW/pyFFTW-${version}.tar.gz";
      sha256 = "f6bbb6afa93085409ab24885a1a3cdb8909f095a142f4d49e346f2bd1b789074";
    };

    buildInputs = [ pkgs.fftw pkgs.fftwFloat pkgs.fftwLongDouble];

    propagatedBuildInputs = with self; [ numpy scipy ];

    # Tests cannot import pyfftw. pyfftw works fine though.
    doCheck = false;

    preConfigure = ''
      export LDFLAGS="-L${pkgs.fftw.dev}/lib -L${pkgs.fftwFloat.out}/lib -L${pkgs.fftwLongDouble.out}/lib"
      export CFLAGS="-I${pkgs.fftw.dev}/include -I${pkgs.fftwFloat.dev}/include -I${pkgs.fftwLongDouble.dev}/include"
    '';

    meta = {
      description = "A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms";
      homepage = http://hgomersall.github.com/pyFFTW/;
      license = with licenses; [ bsd2 bsd3 ];
      maintainer = with maintainers; [ fridh ];
    };
  };
}

Note also the line doCheck = false;, we explicitly disabled running the test-suite.

Develop local package

As a Python developer you're likely aware of development mode (python setup.py develop); instead of installing the package this command creates a special link to the project code. That way, you can run updated code without having to reinstall after each and every change you make. Development mode is also available. Let's see how you can use it.

In the previous Nix expression the source was fetched from an url. We can also refer to a local source instead using src = ./path/to/source/tree;

If we create a shell.nix file which calls buildPythonPackage, and if src is a local source, and if the local source has a setup.py, then development mode is activated.

In the following example we create a simple environment that has a Python 3.5 version of our package in it, as well as its dependencies and other packages we like to have in the environment, all specified with propagatedBuildInputs. Indeed, we can just add any package we like to have in our environment to propagatedBuildInputs.

with import <nixpkgs>;
with pkgs.python35Packages;

buildPythonPackage rec {
  name = "mypackage";
  src = ./path/to/package/source;
  propagatedBuildInputs = [ pytest numpy pkgs.libsndfile ];
}

It is important to note that due to how development mode is implemented on Nix it is not possible to have multiple packages simultaneously in development mode.

Organising your packages

So far we discussed how you can use Python on Nix, and how you can develop with it. We've looked at how you write expressions to package Python packages, and we looked at how you can create environments in which specified packages are available.

At some point you'll likely have multiple packages which you would like to be able to use in different projects. In order to minimise unnecessary duplication we now look at how you can maintain yourself a repository with your own packages. The important functions here are import and callPackage.

Including a derivation using `callPackage`

Earlier we created a Python environment using withPackages, and included the toolz package via a let expression. Let's split the package definition from the environment definition.

We first create a function that builds toolz in ~/path/to/toolz/release.nix

{ pkgs, buildPythonPackage }:

buildPythonPackage rec {
  name = "toolz-${version}";
  version = "0.7.4";

  src = pkgs.fetchurl {
    url = "mirror://pypi/t/toolz/toolz-${version}.tar.gz";
    sha256 = "43c2c9e5e7a16b6c88ba3088a9bfc82f7db8e13378be7c78d6c14a5f8ed05afd";
  };

  meta = {
    homepage = "http://github.com/pytoolz/toolz/";
    description = "List processing tools and functional utilities";
    license = licenses.bsd3;
    maintainers = with maintainers; [ fridh ];
  };
}

It takes two arguments, pkgs and buildPythonPackage. We now call this function using callPackage in the definition of our environment

with import <nixpkgs> {};

( let
    toolz = pkgs.callPackage /path/to/toolz/release.nix {
      pkgs = pkgs;
      buildPythonPackage = pkgs.python35Packages.buildPythonPackage;
    };
  in pkgs.python35.withPackages (ps: [ ps.numpy toolz ])
).env

Important to remember is that the Python version for which the package is made depends on the python derivation that is passed to buildPythonPackage. Nix tries to automatically pass arguments when possible, which is why generally you don't explicitly define which python derivation should be used. In the above example we use buildPythonPackage that is part of the set python35Packages, and in this case the python35 interpreter is automatically used.

Reference

Interpreters

Versions 2.7, 3.3, 3.4, 3.5 and 3.6 of the CPython interpreter are available as respectively python27, python33, python34, python35 and python36. The PyPy interpreter is available as pypy. The aliases python2 and python3 correspond to respectively python27 and python35. The default interpreter, python, maps to python2. The Nix expressions for the interpreters can be found in pkgs/development/interpreters/python.

All packages depending on any Python interpreter get appended out/{python.sitePackages} to $PYTHONPATH if such directory exists.

Missing `tkinter` module standard library

To reduce closure size the Tkinter/tkinter is available as a separate package, pythonPackages.tkinter.

Attributes on interpreters packages

Each interpreter has the following attributes:

libPrefix. Name of the folder in ${python}/lib/ for corresponding interpreter.
interpreter. Alias for ${python}/bin/${executable}.
buildEnv. Function to build python interpreter environments with extra packages bundled together. See section python.buildEnv function for usage and documentation.
withPackages. Simpler interface to buildEnv. See section python.withPackages function for usage and documentation.
sitePackages. Alias for lib/${libPrefix}/site-packages.
executable. Name of the interpreter executable, e.g. python3.4.
pkgs. Set of Python packages for that specific interpreter. The package set can be modified by overriding the interpreter and passing packageOverrides.

Building packages and applications

Python libraries and applications that use setuptools or distutils are typically build with respectively the buildPythonPackage and buildPythonApplication functions. These two functions also support installing a wheel.

All Python packages reside in pkgs/top-level/python-packages.nix and all applications elsewhere. In case a package is used as both a library and an application, then the package should be in pkgs/top-level/python-packages.nix since only those packages are made available for all interpreter versions. The preferred location for library expressions is in pkgs/development/python-modules. It is important that these packages are called from pkgs/top-level/python-packages.nix and not elsewhere, to guarantee the right version of the package is built.

Based on the packages defined in pkgs/top-level/python-packages.nix an attribute set is created for each available Python interpreter. The available sets are

pkgs.python26Packages
pkgs.python27Packages
pkgs.python33Packages
pkgs.python34Packages
pkgs.python35Packages
pkgs.python36Packages
pkgs.pypyPackages

and the aliases

pkgs.python2Packages pointing to pkgs.python27Packages
pkgs.python3Packages pointing to pkgs.python35Packages
pkgs.pythonPackages pointing to pkgs.python2Packages

`buildPythonPackage` function

The buildPythonPackage function is implemented in pkgs/development/interpreters/python/build-python-package.nix

The following is an example:

{ # ...

  twisted = buildPythonPackage {
    name = "twisted-8.1.0";

    src = pkgs.fetchurl {
      url = http://tmrc.mit.edu/mirror/twisted/Twisted/8.1/Twisted-8.1.0.tar.bz2;
      sha256 = "0q25zbr4xzknaghha72mq57kh53qw1bf8csgp63pm9sfi72qhirl";
    };

    propagatedBuildInputs = [ self.ZopeInterface ];

    meta = {
      homepage = http://twistedmatrix.com/;
      description = "Twisted, an event-driven networking engine written in Python";
      license = stdenv.lib.licenses.mit;
    };
  };
}

The buildPythonPackage mainly does four things:

In the buildPhase, it calls ${python.interpreter} setup.py bdist_wheel to build a wheel binary zipfile.
In the installPhase, it installs the wheel file using pip install *.whl.
In the postFixup phase, the wrapPythonPrograms bash function is called to wrap all programs in the $out/bin/* directory to include $PATH environment variable and add dependent libraries to script's sys.path.
In the installCheck phase, ${python.interpreter} setup.py test is ran.

As in Perl, dependencies on other Python packages can be specified in the buildInputs and propagatedBuildInputs attributes. If something is exclusively a build-time dependency, use buildInputs; if it’s (also) a runtime dependency, use propagatedBuildInputs.

By default tests are run because doCheck = true. Test dependencies, like e.g. the test runner, should be added to buildInputs.

By default meta.platforms is set to the same value as the interpreter unless overriden otherwise.

`buildPythonPackage` parameters

All parameters from mkDerivation function are still supported.

namePrefix: Prepended text to ${name} parameter. Defaults to "python3.3-" for Python 3.3, etc. Set it to "" if you're packaging an application or a command line tool.
disabled: If true, package is not build for particular python interpreter version. Grep around pkgs/top-level/python-packages.nix for examples.
setupPyBuildFlags: List of flags passed to setup.py build_ext command.
pythonPath: List of packages to be added into $PYTHONPATH. Packages in pythonPath are not propagated (contrary to propagatedBuildInputs).
preShellHook: Hook to execute commands before shellHook.
postShellHook: Hook to execute commands after shellHook.
makeWrapperArgs: A list of strings. Arguments to be passed to makeWrapper, which wraps generated binaries. By default, the arguments to makeWrapper set PATH and PYTHONPATH environment variables before calling the binary. Additional arguments here can allow a developer to set environment variables which will be available when the binary is run. For example, makeWrapperArgs = ["--set FOO BAR" "--set BAZ QUX"].
installFlags: A list of strings. Arguments to be passed to pip install. To pass options to python setup.py install, use --install-option. E.g., `installFlags=["--install-option='--cpp_implementation'"].
format: Format of the source. Valid options are setuptools (default), flit, wheel, and other. setuptools is for when the source has a setup.py and setuptools is used to build a wheel, flit, in case flit should be used to build a wheel, and wheel in case a wheel is provided. In case you need to provide your own buildPhase and installPhase you can use other.
catchConflicts If true, abort package build if a package name appears more than once in dependency tree. Default is true.
checkInputs Dependencies needed for running the checkPhase. These are added to buildInputs when doCheck = true.

`buildPythonApplication` function

The buildPythonApplication function is practically the same as buildPythonPackage. The difference is that buildPythonPackage by default prefixes the names of the packages with the version of the interpreter. Because with an application we're not interested in multiple version the prefix is dropped.

python.buildEnv function

Python environments can be created using the low-level pkgs.buildEnv function. This example shows how to create an environment that has the Pyramid Web Framework. Saving the following as default.nix

with import <nixpkgs> {};

python.buildEnv.override {
  extraLibs = [ pkgs.pythonPackages.pyramid ];
  ignoreCollisions = true;
}

and running nix-build will create

/nix/store/cf1xhjwzmdki7fasgr4kz6di72ykicl5-python-2.7.8-env

with wrapped binaries in bin/.

You can also use the env attribute to create local environments with needed packages installed. This is somewhat comparable to virtualenv. For example, running nix-shell with the following shell.nix

with import <nixpkgs> {};

(python3.buildEnv.override {
  extraLibs = with python3Packages; [ numpy requests2 ];
}).env

will drop you into a shell where Python will have the specified packages in its path.

`python.buildEnv` arguments

extraLibs: List of packages installed inside the environment.
postBuild: Shell command executed after the build of environment.
ignoreCollisions: Ignore file collisions inside the environment (default is false).

python.withPackages function

The python.withPackages function provides a simpler interface to the python.buildEnv functionality. It takes a function as an argument that is passed the set of python packages and returns the list of the packages to be included in the environment. Using the withPackages function, the previous example for the Pyramid Web Framework environment can be written like this:

with import <nixpkgs> {};

python.withPackages (ps: [ps.pyramid])

withPackages passes the correct package set for the specific interpreter version as an argument to the function. In the above example, ps equals pythonPackages. But you can also easily switch to using python3:

with import <nixpkgs> {};

python3.withPackages (ps: [ps.pyramid])

Now, ps is set to python3Packages, matching the version of the interpreter.

As python.withPackages simply uses python.buildEnv under the hood, it also supports the env attribute. The shell.nix file from the previous section can thus be also written like this:

with import <nixpkgs> {};

(python33.withPackages (ps: [ps.numpy ps.requests2])).env

In contrast to python.buildEnv, python.withPackages does not support the more advanced options such as ignoreCollisions = true or postBuild. If you need them, you have to use python.buildEnv.

Python 2 namespace packages may provide __init__.py that collide. In that case python.buildEnv should be used with ignoreCollisions = true.

Development mode

Development or editable mode is supported. To develop Python packages buildPythonPackage has additional logic inside shellPhase to run pip install -e . --prefix $TMPDIR/for the package.

Warning: shellPhase is executed only if setup.py exists.

Given a default.nix:

with import <nixpkgs> {};

buildPythonPackage { name = "myproject";

buildInputs = with pkgs.pythonPackages; [ pyramid ];

src = ./.; }

Running nix-shell with no arguments should give you the environment in which the package would be built with nix-build.

Shortcut to setup environments with C headers/libraries and python packages:

nix-shell -p pythonPackages.pyramid zlib libjpeg git

Note: There is a boolean value lib.inNixShell set to true if nix-shell is invoked.

Tools

Packages inside nixpkgs are written by hand. However many tools exist in community to help save time. No tool is preferred at the moment.

python2nix by Vladimir Kirillov
pypi2nix by Rok Garbas
pypi2nix by Jaka Hudoklin

Deterministic builds

Python 2.7, 3.5 and 3.6 are now built deterministically and 3.4 mostly. Minor modifications had to be made to the interpreters in order to generate deterministic bytecode. This has security implications and is relevant for those using Python in a nix-shell.

When the environment variable DETERMINISTIC_BUILD is set, all bytecode will have timestamp 1. The buildPythonPackage function sets DETERMINISTIC_BUILD=1 and PYTHONHASHSEED=0. Both are also exported in nix-shell.

FAQ

How can I install a working Python environment?

As explained in the user's guide installing individual Python packages imperatively with nix-env -i or declaratively in environment.systemPackages is not supported. However, it is possible to install a Python environment with packages (python.buildEnv).

In the following examples we create an environment with Python 3.5, numpy and ipython. As you might imagine there is one limitation here, and that's you can install only one environment at a time. You will notice the complaints about collisions when you try to install a second environment.

Environment defined in separate `.nix` file

Create a file, e.g. build.nix, with the following expression

with import <nixpkgs> {};

pkgs.python35.withPackages (ps: with ps; [ numpy ipython ])

and install it in your profile with

nix-env -if build.nix

Now you can use the Python interpreter, as well as the extra packages that you added to the environment.

Environment defined in `~/.nixpkgs/config.nix`

If you prefer to, you could also add the environment as a package override to the Nixpkgs set.

{ # ...

  packageOverrides = pkgs: with pkgs; {
    myEnv = python35.withPackages (ps: with ps; [ numpy ipython ]);
  };
}

and install it in your profile with

nix-env -iA nixpkgs.myEnv

We're installing using the attribute path and assume the channels is named nixpkgs. Note that I'm using the attribute path here.

Environment defined in `/etc/nixos/configuration.nix`

For the sake of completeness, here's another example how to install the environment system-wide.

{ # ...

  environment.systemPackages = with pkgs; [
    (python35.withPackages(ps: with ps; [ numpy ipython ]))
  ];
}

How to solve circular dependencies?

Consider the packages A and B that depend on each other. When packaging B, a solution is to override package A not to depend on B as an input. The same should also be done when packaging A.

How to override a Python package?

We can override the interpreter and pass packageOverrides. In the following example we rename the pandas package and build it.

with import <nixpkgs> {};

let
  python = let
    packageOverrides = self: super: {
      pandas = super.pandas.override {name="foo";};
    };
  in pkgs.python35.override {inherit packageOverrides;};

in python.pkgs.pandas

Using nix-build on this expression will build the package pandas but with the new name foo.

All packages in the package set will use the renamed package. A typical use case is to switch to another version of a certain package. For example, in the Nixpkgs repository we have multiple versions of django and scipy. In the following example we use a different version of scipy and create an environment that uses it. All packages in the Python package set will now use the updated scipy version.

with import <nixpkgs> {};

( let
    packageOverrides = self: super: {
      scipy = super.scipy_0_17;
    };
  in (pkgs.python35.override {inherit packageOverrides;}).withPackages (ps: [ps.blaze])
).env

The requested package blaze depends on pandas which itself depends on scipy.

If you want the whole of Nixpkgs to use your modifications, then you can use overlays as explained in this manual. In the following example we build a inkscape using a different version of numpy.

let
  pkgs = import <nixpkgs> {};
  newpkgs = import pkgs.path { overlays = [ (pkgsself: pkgssuper: {
    python27 = let
      packageOverrides = self: super: {
        numpy = super.numpy_1_10;
      };
    in pkgssuper.python27.override {inherit packageOverrides;};
  } ) ]; };
in newpkgs.inkscape

`python setup.py bdist_wheel` cannot create .whl

Executing python setup.py bdist_wheel in a nix-shell fails with

ValueError: ZIP does not support timestamps before 1980

This is because files are included that depend on items in the Nix store which have a timestamp of, that is, it corresponds to January the 1st, 1970 at 00:00:00. And as the error informs you, ZIP does not support that. The command bdist_wheel takes into account SOURCE_DATE_EPOCH, and nix-shell sets this to 1. By setting it to a value corresponding to 1980 or later, or by unsetting it, it is possible to build wheels.

Use 1980 as timestamp:

nix-shell --run "SOURCE_DATE_EPOCH=315532800 python3 setup.py bdist_wheel"

or the current time:

nix-shell --run "SOURCE_DATE_EPOCH=$(date +%s) python3 setup.py bdist_wheel"

or unset:

nix-shell --run "unset SOURCE_DATE_EPOCH; python3 setup.py bdist_wheel"

`install_data` / `data_files` problems

If you get the following error:

could not create '/nix/store/6l1bvljpy8gazlsw2aw9skwwp4pmvyxw-python-2.7.8/etc':
Permission denied

This is a known bug in setuptools. Setuptools install_data does not respect --prefix. An example of such package using the feature is pkgs/tools/X11/xpra/default.nix. As workaround install it as an extra preInstall step:

${python.interpreter} setup.py install_data --install-dir=$out --root=$out
sed -i '/ = data\_files/d' setup.py

Rationale of non-existent global site-packages

On most operating systems a global site-packages is maintained. This however becomes problematic if you want to run multiple Python versions or have multiple versions of certain libraries for your projects. Generally, you would solve such issues by creating virtual environments using virtualenv.

On Nix each package has an isolated dependency tree which, in the case of Python, guarantees the right versions of the interpreter and libraries or packages are available. There is therefore no need to maintain a global site-packages.

If you want to create a Python environment for development, then the recommended method is to use nix-shell, either with or without the python.buildEnv function.

How to consume python modules using pip in a virtualenv like I am used to on other Operating Systems ?

This is an example of a default.nix for a nix-shell, which allows to consume a virtualenv environment, and install python modules through pip the traditional way.

Create this default.nix file, together with a requirements.txt and simply execute nix-shell.

with import <nixpkgs> {};
with pkgs.python27Packages;

stdenv.mkDerivation {
  name = "impurePythonEnv";
  buildInputs = [
    # these packages are required for virtualenv and pip to work:
    #
    python27Full
    python27Packages.virtualenv
    python27Packages.pip
    # the following packages are related to the dependencies of your python
    # project.
    # In this particular example the python modules listed in the
    # requirements.tx require the following packages to be installed locally
    # in order to compile any binary extensions they may require.
    #
    taglib
    openssl
    git
    libxml2
    libxslt
    libzip
    stdenv
    zlib ];
  src = null;
  shellHook = ''
  # set SOURCE_DATE_EPOCH so that we can use python wheels
  SOURCE_DATE_EPOCH=$(date +%s)
  virtualenv --no-setuptools venv
  export PATH=$PWD/venv/bin:$PATH
  pip install -r requirements.txt
  '';
}

Note that the pip install is an imperative action. So every time nix-shell is executed it will attempt to download the python modules listed in requirements.txt. However these will be cached locally within the virtualenv folder and not downloaded again.

How to override a Python package from `configuration.nix`?

If you need to change a package's attribute(s) from configuration.nix you could do:

  nixpkgs.config.packageOverrides = superP: {
    pythonPackages = superP.pythonPackages.override {
      overrides = self: super: {
        bepasty-server = super.bepasty-server.overrideAttrs ( oldAttrs: {
          src = pkgs.fetchgit {
            url = "https://github.com/bepasty/bepasty-server";
            sha256 = "9ziqshmsf0rjvdhhca55sm0x8jz76fsf2q4rwh4m6lpcf8wr0nps";
            rev = "e2516e8cf4f2afb5185337073607eb9e84a61d2d";
          };
        });
      };
    };
  };

If you are using the bepasty-server package somewhere, for example in systemPackages or indirectly from services.bepasty, then a nixos-rebuild switch will rebuild the system but with the bepasty-server package using a different src attribute. This way one can modify python based software/libraries easily. Using self and super one can also alter dependencies (buildInputs) between the old state (self) and new state (super).

Contributing

Contributing guidelines

Following rules are desired to be respected:

Python libraries are supposed to be called from python-packages.nix and packaged with buildPythonPackage. The expression of a library should be in pkgs/development/python-modules/<name>/default.nix. Libraries in pkgs/top-level/python-packages.nix are sorted quasi-alphabetically to avoid merge conflicts.
Python applications live outside of python-packages.nix and are packaged with buildPythonApplication.
Make sure libraries build for all Python interpreters.
By default we enable tests. Make sure the tests are found and, in the case of libraries, are passing for all interpreters. If certain tests fail they can be disabled individually. Try to avoid disabling the tests altogether. In any case, when you disable tests, leave a comment explaining why.
Commit names of Python libraries should include pythonPackages, for example pythonPackages.numpy: 1.11 -> 1.12.

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