mirrors/nixpkgs
1
0
Fork 1
mirror of https://github.com/NixOS/nixpkgs.git synced 2024-12-03 11:02:05 +00:00
Code Issues Wiki Activity

Documentation: rewrite Python

Browse source 
- Rewrite current documentation
- Add introduction/tutorial
- Convert to markdown
This commit is contained in:
Frederik Rietdijk 2016-02-21 20:13:44 +01:00
parent ce6a1a6cea
commit 4c1525c1f8
3 changed files with 718 additions and 447 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
doc/default.nix
View file

@ -45,6 +45,10 @@ stdenv.mkDerivation {
+ toDocbook {
inputFile = ./introduction.md;
outputFile = "introduction.xml";
}
+ toDocbook {
inputFile = ./languages-frameworks/python.md;
outputFile = "./languages-frameworks/python.xml";
useChapters = true;
}
+ toDocbook {

714
doc/languages-frameworks/python.md Normal file
View file

@ -0,0 +1,714 @@
# 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
```sh
$ 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)
```sh
[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
```sh
$ nix-shell -p python35Packages.numpy python35Packages.toolz --run "python3"
```
This way you can use the `--run` option also to directly run a script
```sh
$ 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](https://en.wikipedia.org/wiki/Shebang_(Unix)) 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.
```py
#! /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
```nix
with import <nixpkgs> {};
(pkgs.python35.buildEnv.override {
extraLibs = with pkgs.python35Packages; [ numpy toolz ];
}).env
```
executing `nix-shell` gives you again a Nix shell from which you can run Python.
What's happening here?
1. 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`.
2. Then we create a Python 3.5 environment with `pkgs.buildEnv`. Because we want to use it with a custom set of Python packages, we override it.
3. The `extraLibs` argument of the original `buildEnv` function can be used to specify which packages should be included. We want `numpy` and `toolz`. Again, we use the `with` statement to bring a set of attributes into the local scope.
4. And finally, for in interactive use we return the environment.
### 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`](https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/python-modules/generic/default.nix).
Let's see how we would build the `toolz` package. According to [`python-packages.nix`](https://raw.githubusercontent.com/NixOS/nixpkgs/master/pkgs/top-level/python-packages.nix) `toolz` is build using
```nix
toolz = buildPythonPackage rec{
name = "toolz-${version}";
version = "0.7.4";
src = pkgs.fetchurl{
url = "https://pypi.python.org/packages/source/t/toolz/toolz-${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`](http://nixos.org/nix/manual/#sec-constructs)).
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](http://nixos.org/nixpkgs/manual/#chap-meta).
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 `python27Packages`, `python34Packages`, `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
```nix
with import <nixpkgs> {};
pkgs.python35Packages.buildPythonPackage rec {
name = "toolz-${version}";
version = "0.7.4";
src = pkgs.fetchurl{
url = "https://pypi.python.org/packages/source/t/toolz/toolz-${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 ];
};
}
```
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
```nix
with import <nixpkgs> {};
( let
toolz = pkgs.python35Packages.buildPythonPackage rec {
name = "toolz-${version}";
version = "0.7.4";
src = pkgs.fetchurl{
url = "https://pypi.python.org/packages/source/t/toolz/toolz-${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 ];
};
};
in pkgs.python35.buildEnv.override rec {
extraLibs = [ pkgs.python35Packages.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
`buildEnv.override` we used a
[`let`](http://nixos.org/nix/manual/#sec-constructs) expression.
### 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`](https://github.com/blaze/datashape).
```nix
datashape = buildPythonPackage rec {
name = "datashape-${version}";
version = "0.4.7";
src = pkgs.fetchurl {
url = "https://pypi.python.org/packages/source/D/DataShape/${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`.
```nix
lxml = buildPythonPackage rec {
name = "lxml-3.4.4";
src = pkgs.fetchurl {
url = "http://pypi.python.org/packages/source/l/lxml/${name}.tar.gz";
sha256 = "16a0fa97hym9ysdk3rmqz32xdjqmy4w34ld3rm3jf5viqjx65lxk";
};
buildInputs = with self; [ pkgs.libxml2 pkgs.libxslt ];
meta = {
description = "Pythonic binding for the libxml2 and libxslt libraries";
homepage = http://lxml.de;
license = licenses.bsd3;
maintainers = with maintainers; [ sjourdois ];
};
};
```
In this example `lxml` and Nix are able to work out exactly where the relevant
files of the dependencies are. This is not always the case.
The example below shows bindings to The Fastest Fourier Transform in the West, commonly known as
FFTW. On Nix we have separate packages of FFTW for the different types of floats
(`"single"`, `"double"`, `"long-double"`). The bindings need all three types,
and therefore we add all three as `buildInputs`. The bindings don't expect to
find each of them in a different folder, and therefore we have to set `LDFLAGS`
and `CFLAGS`.
```nix
pyfftw = buildPythonPackage rec {
name = "pyfftw-${version}";
version = "0.9.2";
src = pkgs.fetchurl {
url = "https://pypi.python.org/packages/source/p/pyFFTW/pyFFTW-${version}.tar.gz";
sha256 = "f6bbb6afa93085409ab24885a1a3cdb8909f095a142f4d49e346f2bd1b789074";
};
buildInputs = [ pkgs.fftw pkgs.fftwFloat pkgs.fftwLongDouble];
propagatedBuildInputs = with self; [ numpy scipy ];
# Tests cannot import pyfftw. pyfftw works fine though.
doCheck = false;
LDFLAGS="-L${pkgs.fftw}/lib -L${pkgs.fftwFloat}/lib -L${pkgs.fftwLongDouble}/lib"
CFLAGS="-I${pkgs.fftw}/include -I${pkgs.fftwFloat}/include -I${pkgs.fftwLongDouble}/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](http://pythonhosted.org/setuptools/setuptools.html#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 on Nix as [explained](http://nixos.org/nixpkgs/manual/#ssec-python-development) in the Nixpkgs manual.
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
```nix
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`.
```nix
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 `buildEnv`, 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`
```nix
{ pkgs, buildPythonPackage }:
buildPythonPackage rec {
name = "toolz-${version}";
version = "0.7.4";
src = pkgs.fetchurl{
url = "https://pypi.python.org/packages/source/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
```nix
with import <nixpkgs> {};
( let
toolz = pkgs.callPackage ~/path/to/toolz/release.nix { pkgs=pkgs; buildPythonPackage=pkgs.python35Packages.buildPythonPackage; };
in pkgs.python35.buildEnv.override rec {
extraLibs = [ pkgs.python35Packages.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 2.6, 2.7, 3.3, 3.4 and 3.5 of the CPython interpreter are available on
Nix and are available as `python26`, `python27`, `python33`, `python34` and
`python35`. The PyPy interpreter is also available as `pypy`. Currently, the
aliases `python` and `python3` correspond to respectively `python27` and
`python35`. The Nix expressions for the interpreters can be found in
`pkgs/development/interpreters/python`.
#### Missing modules standard library
The interpreters `python26` and `python27` do not include modules that
require external dependencies. This is done in order to reduce the closure size.
The following modules need to be added as `buildInput` explicitly:
* `python.modules.bsddb`
* `python.modules.curses`
* `python.modules.curses_panel`
* `python.modules.crypt`
* `python.modules.gdbm`
* `python.modules.sqlite3`
* `python.modules.tkinter`
* `python.modules.readline`
For convenience `python27Full` and `python26Full` are provided with all
modules included.
All packages depending on any Python interpreter get appended
`out/{python.sitePackages}` to `$PYTHONPATH` if such directory
exists.
#### 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/${executable}`.
- `buildEnv`. Function to build python interpreter environments with extra packages bundled together. See section *python.buildEnv function* for usage and documentation.
- `sitePackages`. Alias for `lib/${libPrefix}/site-packages`.
- `executable`. Name of the interpreter executable, ie `python3.4`.
### Building packages and applications
Python packages (libraries) and applications that use `setuptools` or
`distutils` are typically built with respectively the `buildPythonPackage` and
`buildPythonApplication` functions.
All Python packages reside in `pkgs/top-level/python-packages.nix` and all
applications elsewhere. Some packages are also defined in
`pkgs/development/python-modules`. It is important that these packages are
called in `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.pypyPackages`
and the aliases
* `pkgs.pythonPackages` pointing to `pkgs.python27Packages`
* `pkgs.python3Packages` pointing to `pkgs.python35Packages`
#### `buildPythonPackage` function
The `buildPythonPackage` function is implemented in
`pkgs/development/python-modules/generic/default.nix`
and can be used as:
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 `$PYTHONPATH` and `$PATH` environment variables.
* 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'"].
#### `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 {};
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 {};
(python3.buildEnv.override {
extraLibs = with python3Packages; [ numpy requests ];
}).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`).
### 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 {};
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 build 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](https://github.com/proger/python2nix) by Vladimir Kirillov
- [pypi2nix](https://github.com/garbas/pypi2nix) by Rok Garbas
- [pypi2nix](https://github.com/offlinehacker/pypi2nix) by Jaka Hudoklin
## FAQ
### 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?
Recursively updating a package can be done with `pkgs.overridePackages` as explained in the Nixpkgs manual.
Python attribute sets are created for each interpreter version. We will therefore override the attribute set for the interpreter version we're interested.
In the following example we change the name of the package `pandas` to `foo`.
```
newpkgs = pkgs.overridePackages(self: super: rec {
python35Packages = super.python35Packages.override {
self = python35Packages // { pandas = python35Packages.pandas.override{name="foo";};};
};
});
```
This can be tested with
```
with import <nixpkgs> {};
(let
newpkgs = pkgs.overridePackages(self: super: rec {
python35Packages = super.python35Packages.override {
self = python35Packages // { pandas = python35Packages.pandas.override{name="foo";};};
};
});
in newpkgs.python35.buildEnv.override{
extraLibs = [newpkgs.python35Packages.blaze ];
}).env
```
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`. All packages in `newpkgs` will now use the updated `scipy` version.
```
with import <nixpkgs> {};
(let
newpkgs = pkgs.overridePackages(self: super: rec {
python35Packages = super.python35Packages.override {
self = python35Packages // { scipy = python35Packages.scipy_0_16;};
};
});
in pkgs.python35.buildEnv.override{
extraLibs = [newpkgs.python35Packages.blaze ];
}).env
```
The requested package `blaze` depends upon `pandas` which itself depends on `scipy`.
### `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](https://bitbucket.org/pypa/setuptools/issue/130/install_data-doesnt-respect-prefix) 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.
## Contributing
### Contributing guidelines
Following rules are desired to be respected:
* Make sure package builds for all python interpreters. Use `disabled` argument to `buildPythonPackage` to set unsupported interpreters.
* If tests need to be disabled for a package, make sure you leave a comment about reasoning.
* Packages in `pkgs/top-level/python-packages.nix` are sorted quasi-alphabetically to avoid merge conflicts.
* Python libraries are supposed to be in `python-packages.nix` and packaged with `buildPythonPackage`. Python applications live outside of `python-packages.nix` and are packaged with `buildPythonApplication`.

447
doc/languages-frameworks/python.xml
View file

@ -1,447 +0,0 @@
<section xmlns="http://docbook.org/ns/docbook"
xmlns:xlink="http://www.w3.org/1999/xlink"
xml:id="sec-python">
<title>Python</title>
<para>
Currently supported interpreters are <varname>python26</varname>, <varname>python27</varname>,
<varname>python33</varname>, <varname>python34</varname>, <varname>python35</varname>
and <varname>pypy</varname>.
</para>
<para>
<varname>python</varname> is an alias to <varname>python27</varname> and <varname>python3</varname> is an alias to <varname>python34</varname>.
</para>
<para>
<varname>python26</varname> and <varname>python27</varname> do not include modules that require
external dependencies (to reduce dependency bloat). Following modules need to be added as
<varname>buildInput</varname> explicitly:
</para>
<itemizedlist>
<listitem><para><varname>python.modules.bsddb</varname></para></listitem>
<listitem><para><varname>python.modules.curses</varname></para></listitem>
<listitem><para><varname>python.modules.curses_panel</varname></para></listitem>
<listitem><para><varname>python.modules.crypt</varname></para></listitem>
<listitem><para><varname>python.modules.gdbm</varname></para></listitem>
<listitem><para><varname>python.modules.sqlite3</varname></para></listitem>
<listitem><para><varname>python.modules.tkinter</varname></para></listitem>
<listitem><para><varname>python.modules.readline</varname></para></listitem>
</itemizedlist>
<para>For convenience <varname>python27Full</varname> and <varname>python26Full</varname>
are provided with all modules included.</para>
<para>
Python packages that
use <link xlink:href="http://pypi.python.org/pypi/setuptools/"><literal>setuptools</literal></link> or <literal>distutils</literal>,
can be built using the <varname>buildPythonPackage</varname> function as documented below.
</para>
<para>
All packages depending on any Python interpreter get appended <varname>$out/${python.sitePackages}</varname>
to <literal>$PYTHONPATH</literal> if such directory exists.
</para>
<variablelist>
<title>
Useful attributes on interpreters packages:
</title>
<varlistentry>
<term><varname>libPrefix</varname></term>
<listitem><para>
Name of the folder in <literal>${python}/lib/</literal> for corresponding interpreter.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>interpreter</varname></term>
<listitem><para>
Alias for <literal>${python}/bin/${executable}.</literal>
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>buildEnv</varname></term>
<listitem><para>
Function to build python interpreter environments with extra packages bundled together.
See <xref linkend="ssec-python-build-env" /> for usage and documentation.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>sitePackages</varname></term>
<listitem><para>
Alias for <literal>lib/${libPrefix}/site-packages</literal>.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>executable</varname></term>
<listitem><para>
Name of the interpreter executable, ie <literal>python3.4</literal>.
</para></listitem>
</varlistentry>
</variablelist>
<section xml:id="ssec-build-python-package"><title><varname>buildPythonPackage</varname> function</title>
<para>
The function is implemented in <link xlink:href="https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/python-modules/generic/default.nix">
<filename>pkgs/development/python-modules/generic/default.nix</filename></link>.
Example usage:
<programlisting language="nix">
twisted = buildPythonPackage {
name = "twisted-8.1.0";
src = pkgs.fetchurl {
url = http://tmrc.mit.edu/mirror/twisted/Twisted/8.1/Twisted-8.1.0.tar.bz2;
sha256 = "0q25zbr4xzknaghha72mq57kh53qw1bf8csgp63pm9sfi72qhirl";
};
propagatedBuildInputs = [ self.ZopeInterface ];
meta = {
homepage = http://twistedmatrix.com/;
description = "Twisted, an event-driven networking engine written in Python";
license = stdenv.lib.licenses.mit;
};
};
</programlisting>
Most of Python packages that use <varname>buildPythonPackage</varname> are defined
in <link xlink:href="https://github.com/NixOS/nixpkgs/blob/master/pkgs/top-level/python-packages.nix"><filename>pkgs/top-level/python-packages.nix</filename></link>
and generated for each python interpreter separately into attribute sets <varname>python26Packages</varname>,
<varname>python27Packages</varname>, <varname>python35Packages</varname>, <varname>python33Packages</varname>,
<varname>python34Packages</varname> and <varname>pypyPackages</varname>.
</para>
<para>
<function>buildPythonPackage</function> mainly does four things:
<orderedlist>
<listitem><para>
In the <varname>buildPhase</varname>, it calls
<literal>${python.interpreter} setup.py bdist_wheel</literal> to build a wheel binary zipfile.
</para></listitem>
<listitem><para>
In the <varname>installPhase</varname>, it installs the wheel file using
<literal>pip install *.whl</literal>.
</para></listitem>
<listitem><para>
In the <varname>postFixup</varname> phase, <literal>wrapPythonPrograms</literal>
bash function is called to wrap all programs in <filename>$out/bin/*</filename>
directory to include <literal>$PYTHONPATH</literal> and <literal>$PATH</literal>
environment variables.
</para></listitem>
<listitem><para>
In the <varname>installCheck</varname> phase, <literal>${python.interpreter} setup.py test</literal>
is ran.
</para></listitem>
</orderedlist>
</para>
<para>By default <varname>doCheck = true</varname> is set</para>
<para>
As in Perl, dependencies on other Python packages can be specified in the
<varname>buildInputs</varname> and
<varname>propagatedBuildInputs</varname> attributes. If something is
exclusively a build-time dependency, use
<varname>buildInputs</varname>; if it’s (also) a runtime dependency,
use <varname>propagatedBuildInputs</varname>.
</para>
<para>
By default <varname>meta.platforms</varname> is set to the same value
as the interpreter unless overriden otherwise.
</para>
<variablelist>
<title>
<varname>buildPythonPackage</varname> parameters
(all parameters from <varname>mkDerivation</varname> function are still supported)
</title>
<varlistentry>
<term><varname>namePrefix</varname></term>
<listitem><para>
Prepended text to <varname>${name}</varname> parameter.
Defaults to <literal>"python3.3-"</literal> for Python 3.3, etc. Set it to
<literal>""</literal>
if you're packaging an application or a command line tool.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>disabled</varname></term>
<listitem><para>
If <varname>true</varname>, package is not build for
particular python interpreter version. Grep around
<filename>pkgs/top-level/python-packages.nix</filename>
for examples.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>setupPyBuildFlags</varname></term>
<listitem><para>
List of flags passed to <command>setup.py build_ext</command> command.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>pythonPath</varname></term>
<listitem><para>
List of packages to be added into <literal>$PYTHONPATH</literal>.
Packages in <varname>pythonPath</varname> are not propagated
(contrary to <varname>propagatedBuildInputs</varname>).
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>preShellHook</varname></term>
<listitem><para>
Hook to execute commands before <varname>shellHook</varname>.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>postShellHook</varname></term>
<listitem><para>
Hook to execute commands after <varname>shellHook</varname>.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>makeWrapperArgs</varname></term>
<listitem><para>
A list of strings. Arguments to be passed to
<varname>makeWrapper</varname>, which wraps generated binaries. By
default, the arguments to <varname>makeWrapper</varname> set
<varname>PATH</varname> and <varname>PYTHONPATH</varname> 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,
<varname>makeWrapperArgs = ["--set FOO BAR" "--set BAZ QUX"]</varname>.
</para></listitem>
</varlistentry>
</variablelist>
</section>
<section xml:id="ssec-python-build-env"><title><function>python.buildEnv</function> function</title>
<para>
Create Python environments using low-level <function>pkgs.buildEnv</function> function. Example <filename>default.nix</filename>:
<programlisting language="nix">
<![CDATA[with import <nixpkgs> {};
python.buildEnv.override {
extraLibs = [ pkgs.pythonPackages.pyramid ];
ignoreCollisions = true;
}]]>
</programlisting>
Running <command>nix-build</command> will create
<filename>/nix/store/cf1xhjwzmdki7fasgr4kz6di72ykicl5-python-2.7.8-env</filename>
with wrapped binaries in <filename>bin/</filename>.
</para>
<para>
You can also use <varname>env</varname> attribute to create local
environments with needed packages installed (somewhat comparable to
<literal>virtualenv</literal>). For example, with the following
<filename>shell.nix</filename>:
<programlisting language="nix">
<![CDATA[with import <nixpkgs> {};
(python3.buildEnv.override {
extraLibs = with python3Packages;
[ numpy
requests
];
}).env]]>
</programlisting>
Running <command>nix-shell</command> will drop you into a shell where
<command>python</command> will have specified packages in its path.
</para>
<variablelist>
<title>
<function>python.buildEnv</function> arguments
</title>
<varlistentry>
<term><varname>extraLibs</varname></term>
<listitem><para>
List of packages installed inside the environment.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>postBuild</varname></term>
<listitem><para>
Shell command executed after the build of environment.
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>ignoreCollisions</varname></term>
<listitem><para>
Ignore file collisions inside the environment (default is <varname>false</varname>).
</para></listitem>
</varlistentry>
</variablelist>
</section>
<section xml:id="ssec-python-tools"><title>Tools</title>
<para>Packages inside nixpkgs are written by hand. However many tools
exist in community to help save time. No tool is preferred at the moment.
</para>
<itemizedlist>
<listitem><para>
<link xlink:href="https://github.com/proger/python2nix">python2nix</link>
by Vladimir Kirillov
</para></listitem>
<listitem><para>
<link xlink:href="https://github.com/garbas/pypi2nix">pypi2nix</link>
by Rok Garbas
</para></listitem>
<listitem><para>
<link xlink:href="https://github.com/offlinehacker/pypi2nix">pypi2nix</link>
by Jaka Hudoklin
</para></listitem>
</itemizedlist>
</section>
<section xml:id="ssec-python-development"><title>Development</title>
<para>
To develop Python packages <function>buildPythonPackage</function> has
additional logic inside <varname>shellPhase</varname> to run
<command>pip install -e . --prefix $TMPDIR/</command> for the package.
</para>
<warning><para><varname>shellPhase</varname> is executed only if <filename>setup.py</filename>
exists.</para></warning>
<para>
Given a <filename>default.nix</filename>:
<programlisting language="nix">
<![CDATA[with import <nixpkgs> {};
buildPythonPackage {
name = "myproject";
buildInputs = with pkgs.pythonPackages; [ pyramid ];
src = ./.;
}]]>
</programlisting>
Running <command>nix-shell</command> with no arguments should give you
the environment in which the package would be build with
<command>nix-build</command>.
</para>
<para>
Shortcut to setup environments with C headers/libraries and python packages:
<programlisting language="bash">$ nix-shell -p pythonPackages.pyramid zlib libjpeg git</programlisting>
</para>
<note><para>
There is a boolean value <varname>lib.inNixShell</varname> set to
<varname>true</varname> if nix-shell is invoked.
</para></note>
</section>
<section xml:id="ssec-python-faq"><title>FAQ</title>
<variablelist>
<varlistentry>
<term>How to solve circular dependencies?</term>
<listitem><para>
If you have packages <varname>A</varname> and <varname>B</varname> that
depend on each other, when packaging <varname>B</varname> override package
<varname>A</varname> not to depend on <varname>B</varname> as input
(and also the other way around).
</para></listitem>
</varlistentry>
<varlistentry>
<term><varname>install_data / data_files</varname> problems resulting into <literal>error: could not create '/nix/store/6l1bvljpy8gazlsw2aw9skwwp4pmvyxw-python-2.7.8/etc': Permission denied</literal></term>
<listitem><para>
<link xlink:href="https://bitbucket.org/pypa/setuptools/issue/130/install_data-doesnt-respect-prefix">
Known bug in setuptools <varname>install_data</varname> does not respect --prefix</link>. Example of
such package using the feature is <filename>pkgs/tools/X11/xpra/default.nix</filename>. As workaround
install it as an extra <varname>preInstall</varname> step:
<programlisting>${python.interpreter} setup.py install_data --install-dir=$out --root=$out
sed -i '/ = data_files/d' setup.py</programlisting>
</para></listitem>
</varlistentry>
<varlistentry>
<term>Rationale of non-existent global site-packages</term>
<listitem><para>
There is no need to have global site-packages in Nix. Each package has isolated
dependency tree and installing any python package will only populate <varname>$PATH</varname>
inside user environment. See <xref linkend="ssec-python-build-env" /> to create self-contained
interpreter with a set of packages.
</para></listitem>
</varlistentry>
</variablelist>
</section>
<section xml:id="ssec-python-contrib"><title>Contributing guidelines</title>
<para>
Following rules are desired to be respected:
</para>
<itemizedlist>
<listitem><para>
Make sure package builds for all python interpreters. Use <varname>disabled</varname> argument to
<function>buildPythonPackage</function> to set unsupported interpreters.
</para></listitem>
<listitem><para>
If tests need to be disabled for a package, make sure you leave a comment about reasoning.
</para></listitem>
<listitem><para>
Packages in <link xlink:href="https://github.com/NixOS/nixpkgs/blob/master/pkgs/top-level/python-packages.nix"><filename>pkgs/top-level/python-packages.nix</filename></link>
are sorted quasi-alphabetically to avoid merge conflicts.
</para></listitem>
</itemizedlist>
</section>
</section>