841d9c7fc1
GitOrigin-RevId: 3a8d7958a610cd3fec3a6f424480f91a1b259185
1604 lines
59 KiB
Markdown
1604 lines
59 KiB
Markdown
# Python {#python}
|
||
|
||
## User Guide {#user-guide}
|
||
|
||
### Using Python {#using-python}
|
||
|
||
#### Overview {#overview}
|
||
|
||
Several versions of the Python interpreter are available on Nix, as well as a
|
||
high amount of packages. The attribute `python3` refers to the default
|
||
interpreter, which is currently CPython 3.8. The attribute `python` refers to
|
||
CPython 2.7 for backwards-compatibility. It is also possible to refer to
|
||
specific versions, e.g. `python38` refers to CPython 3.8, and `pypy` refers to
|
||
the default PyPy interpreter.
|
||
|
||
Python is used a lot, and in different ways. This affects also how it is
|
||
packaged. In the case of Python on Nix, an important distinction is made between
|
||
whether the package is considered primarily an application, or whether it should
|
||
be used as a library, i.e., of primary interest are the modules in
|
||
`site-packages` that should be importable.
|
||
|
||
In the Nixpkgs tree Python applications can be found throughout, depending on
|
||
what they do, and are called from the main package set. Python libraries,
|
||
however, are in separate sets, with one set per interpreter version.
|
||
|
||
The interpreters have several common attributes. One of these attributes is
|
||
`pkgs`, which is a package set of Python libraries for this specific
|
||
interpreter. E.g., the `toolz` package corresponding to the default interpreter
|
||
is `python.pkgs.toolz`, and the CPython 3.8 version is `python38.pkgs.toolz`.
|
||
The main package set contains aliases to these package sets, e.g.
|
||
`pythonPackages` refers to `python.pkgs` and `python38Packages` to
|
||
`python38.pkgs`.
|
||
|
||
#### Installing Python and packages {#installing-python-and-packages}
|
||
|
||
The Nix and NixOS manuals explain how packages are generally installed. In the
|
||
case of Python and Nix, it is important to make a distinction between whether the
|
||
package is considered an application or a library.
|
||
|
||
Applications on Nix are typically installed 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. Python applications can be installed in
|
||
your profile, and will be wrapped to find their exact library dependencies,
|
||
without impacting other applications or polluting your user environment.
|
||
|
||
But Python libraries you would like to use for development cannot be installed,
|
||
at least not individually, because they won't be able to find each other
|
||
resulting in import errors. Instead, it is possible to create an environment
|
||
with `python.buildEnv` or `python.withPackages` where the interpreter and other
|
||
executables are wrapped to be able to find each other and all of the modules.
|
||
|
||
In the following examples we will start by creating a simple, ad-hoc environment
|
||
with a nix-shell that has `numpy` and `toolz` in Python 3.8; then we will create
|
||
a re-usable environment in a single-file Python script; then we will create a
|
||
full Python environment for development with this same environment.
|
||
|
||
Philosphically, this should be familiar to users who are used to a `venv` style
|
||
of development: individual projects create their own Python environments without
|
||
impacting the global environment or each other.
|
||
|
||
#### Ad-hoc temporary Python environment with `nix-shell` {#ad-hoc-temporary-python-environment-with-nix-shell}
|
||
|
||
The simplest way to start playing with the way nix wraps and sets up Python
|
||
environments is with `nix-shell` at the cmdline. These environments create a
|
||
temporary shell session with a Python and a *precise* list of packages (plus
|
||
their runtime dependencies), with no other Python packages in the Python
|
||
interpreter's scope.
|
||
|
||
To create a Python 3.8 session with `numpy` and `toolz` available, run:
|
||
|
||
```sh
|
||
$ nix-shell -p 'python38.withPackages(ps: with ps; [ numpy toolz ])'
|
||
```
|
||
|
||
By default `nix-shell` will start a `bash` session with this interpreter in our
|
||
`PATH`, so if we then run:
|
||
|
||
```Python console
|
||
[nix-shell:~/src/nixpkgs]$ python3
|
||
Python 3.8.1 (default, Dec 18 2019, 19:06:26)
|
||
[GCC 9.2.0] on linux
|
||
Type "help", "copyright", "credits" or "license" for more information.
|
||
>>> import numpy; import toolz
|
||
```
|
||
|
||
Note that no other modules are in scope, even if they were imperatively
|
||
installed into our user environment as a dependency of a Python application:
|
||
|
||
```Python console
|
||
>>> import requests
|
||
Traceback (most recent call last):
|
||
File "<stdin>", line 1, in <module>
|
||
ModuleNotFoundError: No module named 'requests'
|
||
```
|
||
|
||
We can add as many additional modules onto the `nix-shell` as we need, and we
|
||
will still get 1 wrapped Python interpreter. We can start the interpreter
|
||
directly like so:
|
||
|
||
```sh
|
||
$ nix-shell -p 'python38.withPackages(ps: with ps; [ numpy toolz requests ])' --run python3
|
||
these derivations will be built:
|
||
/nix/store/xbdsrqrsfa1yva5s7pzsra8k08gxlbz1-python3-3.8.1-env.drv
|
||
building '/nix/store/xbdsrqrsfa1yva5s7pzsra8k08gxlbz1-python3-3.8.1-env.drv'...
|
||
created 277 symlinks in user environment
|
||
Python 3.8.1 (default, Dec 18 2019, 19:06:26)
|
||
[GCC 9.2.0] on linux
|
||
Type "help", "copyright", "credits" or "license" for more information.
|
||
>>> import requests
|
||
>>>
|
||
```
|
||
|
||
Notice that this time it built a new Python environment, which now includes
|
||
`requests`. Building an environment just creates wrapper scripts that expose the
|
||
selected dependencies to the interpreter while re-using the actual modules. This
|
||
means if any other env has installed `requests` or `numpy` in a different
|
||
context, we don't need to recompile them -- we just recompile the wrapper script
|
||
that sets up an interpreter pointing to them. This matters much more for "big"
|
||
modules like `pytorch` or `tensorflow`.
|
||
|
||
Module names usually match their names on [pypi.org](https://pypi.org/), but
|
||
you can use the [Nixpkgs search website](https://nixos.org/nixos/packages.html)
|
||
to find them as well (along with non-python packages).
|
||
|
||
At this point we can create throwaway experimental Python environments with
|
||
arbitrary dependencies. This is a good way to get a feel for how the Python
|
||
interpreter and dependencies work in Nix and NixOS, but to do some actual
|
||
development, we'll want to make it a bit more persistent.
|
||
|
||
##### Running Python scripts and using `nix-shell` as shebang {#running-python-scripts-and-using-nix-shell-as-shebang}
|
||
|
||
Sometimes, we have a script whose header looks like this:
|
||
|
||
```python
|
||
#!/usr/bin/env python3
|
||
import numpy as np
|
||
a = np.array([1,2])
|
||
b = np.array([3,4])
|
||
print(f"The dot product of {a} and {b} is: {np.dot(a, b)}")
|
||
```
|
||
|
||
Executing this script requires a `python3` that has `numpy`. Using what we learned
|
||
in the previous section, we could startup a shell and just run it like so:
|
||
|
||
```ShellSession
|
||
$ nix-shell -p 'python38.withPackages(ps: with ps; [ numpy ])' --run 'python3 foo.py'
|
||
The dot product of [1 2] and [3 4] is: 11
|
||
```
|
||
|
||
But if we maintain the script ourselves, and if there are more dependencies, it
|
||
may be nice to encode those dependencies in source to make the script re-usable
|
||
without that bit of knowledge. That can be done by using `nix-shell` as a
|
||
[shebang](https://en.wikipedia.org/wiki/Shebang_(Unix)), like so:
|
||
|
||
```python
|
||
#!/usr/bin/env nix-shell
|
||
#!nix-shell -i python3 -p "python3.withPackages(ps: [ ps.numpy ])"
|
||
import numpy as np
|
||
a = np.array([1,2])
|
||
b = np.array([3,4])
|
||
print(f"The dot product of {a} and {b} is: {np.dot(a, b)}")
|
||
```
|
||
|
||
Then we simply execute it, without requiring any environment setup at all!
|
||
|
||
```sh
|
||
$ ./foo.py
|
||
The dot product of [1 2] and [3 4] is: 11
|
||
```
|
||
|
||
If the dependencies are not available on the host where `foo.py` is executed, it
|
||
will build or download them from a Nix binary cache prior to starting up, prior
|
||
that it is executed on a machine with a multi-user nix installation.
|
||
|
||
This provides a way to ship a self bootstrapping Python script, akin to a
|
||
statically linked binary, where it can be run on any machine (provided nix is
|
||
installed) without having to assume that `numpy` is installed globally on the
|
||
system.
|
||
|
||
By default it is pulling the import checkout of Nixpkgs itself from our nix
|
||
channel, which is nice as it cache aligns with our other package builds, but we
|
||
can make it fully reproducible by pinning the `nixpkgs` import:
|
||
|
||
```python
|
||
#!/usr/bin/env nix-shell
|
||
#!nix-shell -i python3 -p "python3.withPackages(ps: [ ps.numpy ])"
|
||
#!nix-shell -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/d373d80b1207d52621961b16aa4a3438e4f98167.tar.gz
|
||
import numpy as np
|
||
a = np.array([1,2])
|
||
b = np.array([3,4])
|
||
print(f"The dot product of {a} and {b} is: {np.dot(a, b)}")
|
||
```
|
||
|
||
This will execute with the exact same versions of Python 3.8, numpy, and system
|
||
dependencies a year from now as it does today, because it will always use
|
||
exactly git commit `d373d80b1207d52621961b16aa4a3438e4f98167` of Nixpkgs for all
|
||
of the package versions.
|
||
|
||
This is also a great way to ensure the script executes identically on different
|
||
servers.
|
||
|
||
##### Load environment from `.nix` expression {#load-environment-from-.nix-expression}
|
||
|
||
We've now seen how to create an ad-hoc temporary shell session, and how to
|
||
create a single script with Python dependencies, but in the course of normal
|
||
development we're usually working in an entire package repository.
|
||
|
||
As explained in the Nix manual, `nix-shell` can also load an expression from a
|
||
`.nix` file. Say we want to have Python 3.8, `numpy` and `toolz`, like before,
|
||
in an environment. We can add a `shell.nix` file describing our dependencies:
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
(python38.withPackages (ps: [ps.numpy ps.toolz])).env
|
||
```
|
||
|
||
And then at the command line, just typing `nix-shell` produces the same
|
||
environment as before. In a normal project, we'll likely have many more
|
||
dependencies; this can provide a way for developers to share the environments
|
||
with each other and with CI builders.
|
||
|
||
What's happening here?
|
||
|
||
1. We begin with importing the Nix Packages collections. `import <nixpkgs>`
|
||
imports the `<nixpkgs>` function, `{}` calls it and the `with` statement
|
||
brings all attributes of `nixpkgs` in the local scope. These attributes form
|
||
the main package set.
|
||
2. Then we create a Python 3.8 environment with the `withPackages` function, as before.
|
||
3. 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.
|
||
|
||
To combine this with `mkShell` you can:
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
let
|
||
pythonEnv = python38.withPackages (ps: [
|
||
ps.numpy
|
||
ps.toolz
|
||
]);
|
||
in mkShell {
|
||
packages = [
|
||
pythonEnv
|
||
|
||
black
|
||
mypy
|
||
|
||
libffi
|
||
openssl
|
||
];
|
||
}
|
||
```
|
||
|
||
This will create a unified environment that has not just our Python interpreter
|
||
and its Python dependencies, but also tools like `black` or `mypy` and libraries
|
||
like `libffi` the `openssl` in scope. This is generic and can span any number of
|
||
tools or languages across the Nixpkgs ecosystem.
|
||
|
||
##### Installing environments globally on the system {#installing-environments-globally-on-the-system}
|
||
|
||
Up to now, we've been creating environments scoped to an ad-hoc shell session,
|
||
or a single script, or a single project. This is generally advisable, as it
|
||
avoids pollution across contexts.
|
||
|
||
However, sometimes we know we will often want a Python with some basic packages,
|
||
and want this available without having to enter into a shell or build context.
|
||
This can be useful to have things like vim/emacs editors and plugins or shell
|
||
tools "just work" without having to set them up, or when running other software
|
||
that expects packages to be installed globally.
|
||
|
||
To create your own custom environment, create a file in `~/.config/nixpkgs/overlays/`
|
||
that looks like this:
|
||
|
||
```nix
|
||
# ~/.config/nixpkgs/overlays/myEnv.nix
|
||
self: super: {
|
||
myEnv = super.buildEnv {
|
||
name = "myEnv";
|
||
paths = [
|
||
# A Python 3 interpreter with some packages
|
||
(self.python3.withPackages (
|
||
ps: with ps; [
|
||
pyflakes
|
||
pytest
|
||
python-language-server
|
||
]
|
||
))
|
||
|
||
# Some other packages we'd like as part of this env
|
||
self.mypy
|
||
self.black
|
||
self.ripgrep
|
||
self.tmux
|
||
];
|
||
};
|
||
}
|
||
```
|
||
|
||
You can then build and install this to your profile with:
|
||
|
||
```sh
|
||
nix-env -iA myEnv
|
||
```
|
||
|
||
One limitation of this is that you can only have 1 Python env installed
|
||
globally, since they conflict on the `python` to load out of your `PATH`.
|
||
|
||
If you get a conflict or prefer to keep the setup clean, you can have `nix-env`
|
||
atomically *uninstall* all other imperatively installed packages and replace
|
||
your profile with just `myEnv` by using the `--replace` flag.
|
||
|
||
##### Environment defined in `/etc/nixos/configuration.nix` {#environment-defined-in-etcnixosconfiguration.nix}
|
||
|
||
For the sake of completeness, here's how to install the environment system-wide
|
||
on NixOS.
|
||
|
||
```nix
|
||
{ # ...
|
||
|
||
environment.systemPackages = with pkgs; [
|
||
(python38.withPackages(ps: with ps; [ numpy toolz ]))
|
||
];
|
||
}
|
||
```
|
||
|
||
### Developing with Python {#developing-with-python}
|
||
|
||
Above, we were mostly just focused on use cases and what to do to get started
|
||
creating working Python environments in nix.
|
||
|
||
Now that you know the basics to be up and running, it is time to take a step
|
||
back and take a deeper look at how Python packages are packaged on Nix. Then,
|
||
we will look at how you can use development mode with your code.
|
||
|
||
#### Python library packages in Nixpkgs {#python-library-packages-in-nixpkgs}
|
||
|
||
With Nix all packages are built by functions. The main function in Nix for
|
||
building Python libraries is `buildPythonPackage`. Let's see how we can build the
|
||
`toolz` package.
|
||
|
||
```nix
|
||
{ lib, buildPythonPackage, fetchPypi }:
|
||
|
||
buildPythonPackage rec {
|
||
pname = "toolz";
|
||
version = "0.10.0";
|
||
|
||
src = fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560";
|
||
};
|
||
|
||
doCheck = false;
|
||
|
||
meta = with lib; {
|
||
homepage = "https://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 PyPI using the helper function
|
||
`fetchPypi`. The argument `doCheck` is used to set whether tests should be run
|
||
when building the package. Furthermore, we specify some (optional) meta
|
||
information. The output of the function is a derivation.
|
||
|
||
An expression for `toolz` can be found in the Nixpkgs repository. As explained
|
||
in the introduction of this Python section, a derivation of `toolz` is available
|
||
for each interpreter version, e.g. `python38.pkgs.toolz` refers to the `toolz`
|
||
derivation corresponding to the CPython 3.8 interpreter.
|
||
|
||
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.
|
||
|
||
The following expression creates a derivation for the `toolz` package,
|
||
and adds it along with a `numpy` package to a Python environment.
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
( let
|
||
my_toolz = python38.pkgs.buildPythonPackage rec {
|
||
pname = "toolz";
|
||
version = "0.10.0";
|
||
|
||
src = python38.pkgs.fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560";
|
||
};
|
||
|
||
doCheck = false;
|
||
|
||
meta = {
|
||
homepage = "https://github.com/pytoolz/toolz/";
|
||
description = "List processing tools and functional utilities";
|
||
};
|
||
};
|
||
|
||
in python38.withPackages (ps: [ps.numpy my_toolz])
|
||
).env
|
||
```
|
||
|
||
Executing `nix-shell` will result in an environment in which you can use
|
||
Python 3.8 and the `toolz` package. As you can see we had to explicitly mention
|
||
for which Python version we want to build a package.
|
||
|
||
So, 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`, named `my_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`). We did not take
|
||
`toolz` from the Nixpkgs package set this time, but instead took our own version
|
||
that we introduced with the `let` expression.
|
||
|
||
#### Handling dependencies {#handling-dependencies}
|
||
|
||
Our example, `toolz`, does not 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 in `buildInputs`, but if it is (also) a runtime dependency, then it
|
||
should be added to `propagatedBuildInputs`. Test dependencies are considered
|
||
build-time dependencies and passed to `checkInputs`.
|
||
|
||
The following example shows which arguments are given to `buildPythonPackage` in
|
||
order to build [`datashape`](https://github.com/blaze/datashape).
|
||
|
||
```nix
|
||
{ lib, buildPythonPackage, fetchPypi, numpy, multipledispatch, dateutil, pytest }:
|
||
|
||
buildPythonPackage rec {
|
||
pname = "datashape";
|
||
version = "0.4.7";
|
||
|
||
src = fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "14b2ef766d4c9652ab813182e866f493475e65e558bed0822e38bf07bba1a278";
|
||
};
|
||
|
||
checkInputs = [ pytest ];
|
||
propagatedBuildInputs = [ numpy multipledispatch dateutil ];
|
||
|
||
meta = with lib; {
|
||
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 `checkInputs`, 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
|
||
{ lib, pkgs, buildPythonPackage, fetchPypi }:
|
||
|
||
buildPythonPackage rec {
|
||
pname = "lxml";
|
||
version = "3.4.4";
|
||
|
||
src = fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "16a0fa97hym9ysdk3rmqz32xdjqmy4w34ld3rm3jf5viqjx65lxk";
|
||
};
|
||
|
||
buildInputs = [ pkgs.libxml2 pkgs.libxslt ];
|
||
|
||
meta = with lib; {
|
||
description = "Pythonic binding for the libxml2 and libxslt libraries";
|
||
homepage = "https://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
|
||
{ lib, pkgs, buildPythonPackage, fetchPypi, numpy, scipy }:
|
||
|
||
buildPythonPackage rec {
|
||
pname = "pyFFTW";
|
||
version = "0.9.2";
|
||
|
||
src = fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "f6bbb6afa93085409ab24885a1a3cdb8909f095a142f4d49e346f2bd1b789074";
|
||
};
|
||
|
||
buildInputs = [ pkgs.fftw pkgs.fftwFloat pkgs.fftwLongDouble];
|
||
|
||
propagatedBuildInputs = [ 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 = with lib; {
|
||
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 ];
|
||
maintainers = with maintainers; [ fridh ];
|
||
};
|
||
}
|
||
```
|
||
|
||
Note also the line `doCheck = false;`, we explicitly disabled running the test-suite.
|
||
|
||
#### Testing Python Packages {#testing-python-packages}
|
||
|
||
It is highly encouraged to have testing as part of the package build. This
|
||
helps to avoid situations where the package was able to build and install,
|
||
but is not usable at runtime. Currently, all packages will use the `test`
|
||
command provided by the setup.py (i.e. `python setup.py test`). However,
|
||
this is currently deprecated https://github.com/pypa/setuptools/pull/1878
|
||
and your package should provide its own checkPhase.
|
||
|
||
*NOTE:* The `checkPhase` for python maps to the `installCheckPhase` on a
|
||
normal derivation. This is due to many python packages not behaving well
|
||
to the pre-installed version of the package. Version info, and natively
|
||
compiled extensions generally only exist in the install directory, and
|
||
thus can cause issues when a test suite asserts on that behavior.
|
||
|
||
*NOTE:* Tests should only be disabled if they don't agree with nix
|
||
(e.g. external dependencies, network access, flakey tests), however,
|
||
as many tests should be enabled as possible. Failing tests can still be
|
||
a good indication that the package is not in a valid state.
|
||
|
||
#### Using pytest {#using-pytest}
|
||
|
||
Pytest is the most common test runner for python repositories. A trivial
|
||
test run would be:
|
||
|
||
```
|
||
checkInputs = [ pytest ];
|
||
checkPhase = "pytest";
|
||
```
|
||
|
||
However, many repositories' test suites do not translate well to nix's build
|
||
sandbox, and will generally need many tests to be disabled.
|
||
|
||
To filter tests using pytest, one can do the following:
|
||
|
||
```
|
||
checkInputs = [ pytest ];
|
||
# avoid tests which need additional data or touch network
|
||
checkPhase = ''
|
||
pytest tests/ --ignore=tests/integration -k 'not download and not update'
|
||
'';
|
||
```
|
||
|
||
`--ignore` will tell pytest to ignore that file or directory from being
|
||
collected as part of a test run. This is useful is a file uses a package
|
||
which is not available in nixpkgs, thus skipping that test file is much
|
||
easier than having to create a new package.
|
||
|
||
`-k` is used to define a predicate for test names. In this example, we are
|
||
filtering out tests which contain `download` or `update` in their test case name.
|
||
Only one `-k` argument is allowed, and thus a long predicate should be concatenated
|
||
with “\\” and wrapped to the next line.
|
||
|
||
*NOTE:* In pytest==6.0.1, the use of “\\” to continue a line (e.g. `-k 'not download \'`) has
|
||
been removed, in this case, it's recommended to use `pytestCheckHook`.
|
||
|
||
#### Using pytestCheckHook {#using-pytestcheckhook}
|
||
|
||
`pytestCheckHook` is a convenient hook which will substitute the setuptools
|
||
`test` command for a checkPhase which runs `pytest`. This is also beneficial
|
||
when a package may need many items disabled to run the test suite.
|
||
|
||
Using the example above, the analagous pytestCheckHook usage would be:
|
||
|
||
```
|
||
checkInputs = [ pytestCheckHook ];
|
||
|
||
# requires additional data
|
||
pytestFlagsArray = [ "tests/" "--ignore=tests/integration" ];
|
||
|
||
disabledTests = [
|
||
# touches network
|
||
"download"
|
||
"update"
|
||
];
|
||
|
||
disabledTestPaths = [
|
||
"tests/test_failing.py"
|
||
];
|
||
```
|
||
|
||
This is expecially useful when tests need to be conditionallydisabled,
|
||
for example:
|
||
|
||
```
|
||
disabledTests = [
|
||
# touches network
|
||
"download"
|
||
"update"
|
||
] ++ lib.optionals (pythonAtLeast "3.8") [
|
||
# broken due to python3.8 async changes
|
||
"async"
|
||
] ++ lib.optionals stdenv.isDarwin [
|
||
# can fail when building with other packages
|
||
"socket"
|
||
];
|
||
```
|
||
Trying to concatenate the related strings to disable tests in a regular checkPhase
|
||
would be much harder to read. This also enables us to comment on why specific tests
|
||
are disabled.
|
||
|
||
#### Using pythonImportsCheck {#using-pythonimportscheck}
|
||
|
||
Although unit tests are highly prefered to validate correctness of a package, not
|
||
all packages have test suites that can be ran easily, and some have none at all.
|
||
To help ensure the package still works, `pythonImportsCheck` can attempt to import
|
||
the listed modules.
|
||
|
||
```
|
||
pythonImportsCheck = [ "requests" "urllib" ];
|
||
```
|
||
roughly translates to:
|
||
```
|
||
postCheck = ''
|
||
PYTHONPATH=$out/${python.sitePackages}:$PYTHONPATH
|
||
python -c "import requests; import urllib"
|
||
'';
|
||
```
|
||
However, this is done in it's own phase, and not dependent on whether `doCheck = true;`
|
||
|
||
This can also be useful in verifying that the package doesn't assume commonly
|
||
present packages (e.g. `setuptools`)
|
||
|
||
### Develop local package {#develop-local-package}
|
||
|
||
As a Python developer you're likely aware of [development mode](http://setuptools.readthedocs.io/en/latest/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. 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 3.8
|
||
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 python38Packages;
|
||
|
||
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 {#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 a repository with your
|
||
own packages. The important functions here are `import` and `callPackage`.
|
||
|
||
### Including a derivation using `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`
|
||
|
||
```nix
|
||
{ lib, buildPythonPackage }:
|
||
|
||
buildPythonPackage rec {
|
||
pname = "toolz";
|
||
version = "0.10.0";
|
||
|
||
src = fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "08fdd5ef7c96480ad11c12d472de21acd32359996f69a5259299b540feba4560";
|
||
};
|
||
|
||
meta = with lib; {
|
||
homepage = "https://github.com/pytoolz/toolz/";
|
||
description = "List processing tools and functional utilities";
|
||
license = licenses.bsd3;
|
||
maintainers = with maintainers; [ fridh ];
|
||
};
|
||
}
|
||
```
|
||
|
||
It takes an argument `buildPythonPackage`. We now call this function using
|
||
`callPackage` in the definition of our environment
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
( let
|
||
toolz = callPackage /path/to/toolz/release.nix {
|
||
buildPythonPackage = python38Packages.buildPythonPackage;
|
||
};
|
||
in python38.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 `python38Packages`,
|
||
and in this case the `python38` interpreter is automatically used.
|
||
|
||
## Reference {#reference}
|
||
|
||
### Interpreters {#interpreters}
|
||
|
||
Versions 2.7, 3.6, 3.7, 3.8 and 3.9 of the CPython interpreter are available as
|
||
respectively `python27`, `python36`, `python37`, `python38` and `python39`. The
|
||
aliases `python2` and `python3` correspond to respectively `python27` and
|
||
`python39`. The attribute `python` maps to `python2`. The PyPy interpreters
|
||
compatible with Python 2.7 and 3 are available as `pypy27` and `pypy3`, with
|
||
aliases `pypy2` mapping to `pypy27` and `pypy` mapping to `pypy2`. 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 {#missing-tkinter-module-standard-library}
|
||
|
||
To reduce closure size the `Tkinter`/`tkinter` is available as a separate package, `pythonPackages.tkinter`.
|
||
|
||
#### Attributes on interpreters packages {#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. `python3.8`.
|
||
- `pkgs`. Set of Python packages for that specific interpreter. The package set can be modified by overriding the interpreter and passing `packageOverrides`.
|
||
|
||
### Optimizations {#optimizations}
|
||
|
||
The Python interpreters are by default not build with optimizations enabled, because
|
||
the builds are in that case not reproducible. To enable optimizations, override the
|
||
interpreter of interest, e.g using
|
||
|
||
```
|
||
let
|
||
pkgs = import ./. {};
|
||
mypython = pkgs.python3.override {
|
||
enableOptimizations = true;
|
||
reproducibleBuild = false;
|
||
self = mypython;
|
||
};
|
||
in mypython
|
||
```
|
||
|
||
### Building packages and applications {#building-packages-and-applications}
|
||
|
||
Python libraries and applications that use `setuptools` or
|
||
`distutils` are typically built 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.python27Packages`
|
||
* `pkgs.python36Packages`
|
||
* `pkgs.python37Packages`
|
||
* `pkgs.python38Packages`
|
||
* `pkgs.python39Packages`
|
||
* `pkgs.pypyPackages`
|
||
|
||
and the aliases
|
||
|
||
* `pkgs.python2Packages` pointing to `pkgs.python27Packages`
|
||
* `pkgs.python3Packages` pointing to `pkgs.python38Packages`
|
||
* `pkgs.pythonPackages` pointing to `pkgs.python2Packages`
|
||
|
||
#### `buildPythonPackage` function {#buildpythonpackage-function}
|
||
|
||
The `buildPythonPackage` function is implemented in
|
||
`pkgs/development/interpreters/python/mk-python-derivation`
|
||
using setup hooks.
|
||
|
||
The following is an example:
|
||
|
||
```nix
|
||
{ lib, buildPythonPackage, fetchPypi, hypothesis, setuptools-scm, attrs, py, setuptools, six, pluggy }:
|
||
|
||
buildPythonPackage rec {
|
||
pname = "pytest";
|
||
version = "3.3.1";
|
||
|
||
src = fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "cf8436dc59d8695346fcd3ab296de46425ecab00d64096cebe79fb51ecb2eb93";
|
||
};
|
||
|
||
postPatch = ''
|
||
# don't test bash builtins
|
||
rm testing/test_argcomplete.py
|
||
'';
|
||
|
||
checkInputs = [ hypothesis ];
|
||
nativeBuildInputs = [ setuptools-scm ];
|
||
propagatedBuildInputs = [ attrs py setuptools six pluggy ];
|
||
|
||
meta = with lib; {
|
||
maintainers = with maintainers; [ domenkozar lovek323 madjar lsix ];
|
||
description = "Framework for writing tests";
|
||
};
|
||
}
|
||
```
|
||
|
||
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.
|
||
|
||
By default tests are run because `doCheck = true`. Test dependencies, like
|
||
e.g. the test runner, should be added to `checkInputs`.
|
||
|
||
By default `meta.platforms` is set to the same value
|
||
as the interpreter unless overridden otherwise.
|
||
|
||
##### `buildPythonPackage` parameters {#buildpythonpackage-parameters}
|
||
|
||
All parameters from `stdenv.mkDerivation` function are still supported. The
|
||
following are specific to `buildPythonPackage`:
|
||
|
||
* `catchConflicts ? true`: If `true`, abort package build if a package name
|
||
appears more than once in dependency tree. Default is `true`.
|
||
* `disabled` ? false: If `true`, package is not built for the particular Python
|
||
interpreter version.
|
||
* `dontWrapPythonPrograms ? false`: Skip wrapping of Python programs.
|
||
* `permitUserSite ? false`: Skip setting the `PYTHONNOUSERSITE` environment
|
||
variable in wrapped programs.
|
||
* `format ? "setuptools"`: Format of the source. Valid options are
|
||
`"setuptools"`, `"pyproject"`, `"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. Use `other` when a custom
|
||
`buildPhase` and/or `installPhase` is needed.
|
||
* `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"]`.
|
||
* `namePrefix`: Prepends text to `${name}` parameter. In case of libraries, this
|
||
defaults to `"python3.8-"` for Python 3.8, etc., and in case of applications
|
||
to `""`.
|
||
* `pipInstallFlags ? []`: A list of strings. Arguments to be passed to `pip
|
||
install`. To pass options to `python setup.py install`, use
|
||
`--install-option`. E.g., `pipInstallFlags=["--install-option='--cpp_implementation'"]`.
|
||
* `pythonPath ? []`: List of packages to be added into `$PYTHONPATH`. Packages
|
||
in `pythonPath` are not propagated (contrary to `propagatedBuildInputs`).
|
||
* `preShellHook`: Hook to execute commands before `shellHook`.
|
||
* `postShellHook`: Hook to execute commands after `shellHook`.
|
||
* `removeBinByteCode ? true`: Remove bytecode from `/bin`. Bytecode is only
|
||
created when the filenames end with `.py`.
|
||
* `setupPyGlobalFlags ? []`: List of flags passed to `setup.py` command.
|
||
* `setupPyBuildFlags ? []`: List of flags passed to `setup.py build_ext` command.
|
||
|
||
The `stdenv.mkDerivation` function accepts various parameters for describing
|
||
build inputs (see "Specifying dependencies"). The following are of special
|
||
interest for Python packages, either because these are primarily used, or
|
||
because their behaviour is different:
|
||
|
||
* `nativeBuildInputs ? []`: Build-time only dependencies. Typically executables
|
||
as well as the items listed in `setup_requires`.
|
||
* `buildInputs ? []`: Build and/or run-time dependencies that need to be
|
||
compiled for the host machine. Typically non-Python libraries which are being
|
||
linked.
|
||
* `checkInputs ? []`: Dependencies needed for running the `checkPhase`. These
|
||
are added to `nativeBuildInputs` when `doCheck = true`. Items listed in
|
||
`tests_require` go here.
|
||
* `propagatedBuildInputs ? []`: Aside from propagating dependencies,
|
||
`buildPythonPackage` also injects code into and wraps executables with the
|
||
paths included in this list. Items listed in `install_requires` go here.
|
||
|
||
##### Overriding Python packages {#overriding-python-packages}
|
||
|
||
The `buildPythonPackage` function has a `overridePythonAttrs` method that can be
|
||
used to override the package. In the following example we create an environment
|
||
where we have the `blaze` package using an older version of `pandas`. We
|
||
override first the Python interpreter and pass `packageOverrides` which contains
|
||
the overrides for packages in the package set.
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
(let
|
||
python = let
|
||
packageOverrides = self: super: {
|
||
pandas = super.pandas.overridePythonAttrs(old: rec {
|
||
version = "0.19.1";
|
||
src = super.fetchPypi {
|
||
pname = "pandas";
|
||
inherit version;
|
||
sha256 = "08blshqj9zj1wyjhhw3kl2vas75vhhicvv72flvf1z3jvapgw295";
|
||
};
|
||
});
|
||
};
|
||
in pkgs.python3.override {inherit packageOverrides; self = python;};
|
||
|
||
in python.withPackages(ps: [ps.blaze])).env
|
||
```
|
||
|
||
#### `buildPythonApplication` function {#buildpythonapplication-function}
|
||
|
||
The `buildPythonApplication` function is practically the same as
|
||
`buildPythonPackage`. The main purpose of this function is to build a Python
|
||
package where one is interested only in the executables, and not importable
|
||
modules. For that reason, when adding this package to a `python.buildEnv`, the
|
||
modules won't be made available.
|
||
|
||
Another difference is that `buildPythonPackage` by default prefixes the names of
|
||
the packages with the version of the interpreter. Because this is irrelevant for
|
||
applications, the prefix is omitted.
|
||
|
||
When packaging a Python application with `buildPythonApplication`, it should be
|
||
called with `callPackage` and passed `python` or `pythonPackages` (possibly
|
||
specifying an interpreter version), like this:
|
||
|
||
```nix
|
||
{ lib, python3Packages }:
|
||
|
||
python3Packages.buildPythonApplication rec {
|
||
pname = "luigi";
|
||
version = "2.7.9";
|
||
|
||
src = python3Packages.fetchPypi {
|
||
inherit pname version;
|
||
sha256 = "035w8gqql36zlan0xjrzz9j4lh9hs0qrsgnbyw07qs7lnkvbdv9x";
|
||
};
|
||
|
||
propagatedBuildInputs = with python3Packages; [ tornado_4 python-daemon ];
|
||
|
||
meta = with lib; {
|
||
...
|
||
};
|
||
}
|
||
```
|
||
|
||
This is then added to `all-packages.nix` just as any other application would be.
|
||
|
||
```nix
|
||
luigi = callPackage ../applications/networking/cluster/luigi { };
|
||
```
|
||
|
||
Since the package is an application, a consumer doesn't need to care about
|
||
Python versions or modules, which is why they don't go in `pythonPackages`.
|
||
|
||
#### `toPythonApplication` function {#topythonapplication-function}
|
||
|
||
A distinction is made between applications and libraries, however, sometimes a
|
||
package is used as both. In this case the package is added as a library to
|
||
`python-packages.nix` and as an application to `all-packages.nix`. To reduce
|
||
duplication the `toPythonApplication` can be used to convert a library to an
|
||
application.
|
||
|
||
The Nix expression shall use `buildPythonPackage` and be called from
|
||
`python-packages.nix`. A reference shall be created from `all-packages.nix` to
|
||
the attribute in `python-packages.nix`, and the `toPythonApplication` shall be
|
||
applied to the reference:
|
||
|
||
```nix
|
||
youtube-dl = with pythonPackages; toPythonApplication youtube-dl;
|
||
```
|
||
|
||
#### `toPythonModule` function {#topythonmodule-function}
|
||
|
||
In some cases, such as bindings, a package is created using
|
||
`stdenv.mkDerivation` and added as attribute in `all-packages.nix`. The Python
|
||
bindings should be made available from `python-packages.nix`. The
|
||
`toPythonModule` function takes a derivation and makes certain Python-specific
|
||
modifications.
|
||
|
||
```nix
|
||
opencv = toPythonModule (pkgs.opencv.override {
|
||
enablePython = true;
|
||
pythonPackages = self;
|
||
});
|
||
```
|
||
|
||
Do pay attention to passing in the right Python version!
|
||
|
||
#### `python.buildEnv` function {#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`
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
python.buildEnv.override {
|
||
extraLibs = [ 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`
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
(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 {#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`).
|
||
* `permitUserSite`: Skip setting the `PYTHONNOUSERSITE` environment variable in
|
||
wrapped binaries in the environment.
|
||
|
||
#### `python.withPackages` function {#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:
|
||
|
||
```nix
|
||
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:
|
||
|
||
```nix
|
||
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:
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
(python38.withPackages (ps: [ps.numpy ps.requests])).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`.
|
||
|
||
#### Setup hooks {#setup-hooks}
|
||
|
||
The following are setup hooks specifically for Python packages. Most of these
|
||
are used in `buildPythonPackage`.
|
||
|
||
- `eggUnpackhook` to move an egg to the correct folder so it can be installed
|
||
with the `eggInstallHook`
|
||
- `eggBuildHook` to skip building for eggs.
|
||
- `eggInstallHook` to install eggs.
|
||
- `flitBuildHook` to build a wheel using `flit`.
|
||
- `pipBuildHook` to build a wheel using `pip` and PEP 517. Note a build system
|
||
(e.g. `setuptools` or `flit`) should still be added as `nativeBuildInput`.
|
||
- `pipInstallHook` to install wheels.
|
||
- `pytestCheckHook` to run tests with `pytest`. See [example usage](#using-pytestcheckhook).
|
||
- `pythonCatchConflictsHook` to check whether a Python package is not already existing.
|
||
- `pythonImportsCheckHook` to check whether importing the listed modules works.
|
||
- `pythonRemoveBinBytecode` to remove bytecode from the `/bin` folder.
|
||
- `setuptoolsBuildHook` to build a wheel using `setuptools`.
|
||
- `setuptoolsCheckHook` to run tests with `python setup.py test`.
|
||
- `venvShellHook` to source a Python 3 `venv` at the `venvDir` location. A
|
||
`venv` is created if it does not yet exist. `postVenvCreation` can be used to
|
||
to run commands only after venv is first created.
|
||
- `wheelUnpackHook` to move a wheel to the correct folder so it can be installed
|
||
with the `pipInstallHook`.
|
||
|
||
### Development mode {#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`:
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
pythonPackages.buildPythonPackage {
|
||
name = "myproject";
|
||
buildInputs = with 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:
|
||
|
||
```shell
|
||
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 {#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.
|
||
|
||
- [pypi2nix](https://github.com/nix-community/pypi2nix): Generate Nix
|
||
expressions for your Python project. Note that [sharing derivations from
|
||
pypi2nix with nixpkgs is possible but not
|
||
encouraged](https://github.com/nix-community/pypi2nix/issues/222#issuecomment-443497376).
|
||
- [nixpkgs-pytools](https://github.com/nix-community/nixpkgs-pytools)
|
||
- [poetry2nix](https://github.com/nix-community/poetry2nix)
|
||
|
||
### Deterministic builds {#deterministic-builds}
|
||
|
||
The Python interpreters are now built deterministically. 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](https://docs.python.org/3.8/using/cmdline.html#envvar-PYTHONHASHSEED).
|
||
Both are also exported in `nix-shell`.
|
||
|
||
### Automatic tests {#automatic-tests}
|
||
|
||
It is recommended to test packages as part of the build process.
|
||
Source distributions (`sdist`) often include test files, but not always.
|
||
|
||
By default the command `python setup.py test` is run as part of the
|
||
`checkPhase`, but often it is necessary to pass a custom `checkPhase`. An
|
||
example of such a situation is when `py.test` is used.
|
||
|
||
#### Common issues {#common-issues}
|
||
|
||
* Non-working tests can often be deselected. By default `buildPythonPackage`
|
||
runs `python setup.py test`. Most Python modules follows the standard test
|
||
protocol where the pytest runner can be used instead. `py.test` supports a
|
||
`-k` parameter to ignore test methods or classes:
|
||
|
||
```nix
|
||
buildPythonPackage {
|
||
# ...
|
||
# assumes the tests are located in tests
|
||
checkInputs = [ pytest ];
|
||
checkPhase = ''
|
||
py.test -k 'not function_name and not other_function' tests
|
||
'';
|
||
}
|
||
```
|
||
|
||
* Tests that attempt to access `$HOME` can be fixed by using the following
|
||
work-around before running tests (e.g. `preCheck`): `export HOME=$(mktemp -d)`
|
||
|
||
## FAQ {#faq}
|
||
|
||
### How to solve circular dependencies? {#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? {#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.
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
(let
|
||
python = let
|
||
packageOverrides = self: super: {
|
||
pandas = super.pandas.overridePythonAttrs(old: {name="foo";});
|
||
};
|
||
in pkgs.python38.override {inherit packageOverrides;};
|
||
|
||
in python.withPackages(ps: [ps.pandas])).env
|
||
```
|
||
|
||
Using `nix-build` on this expression will build an environment that contains 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.
|
||
|
||
```nix
|
||
with import <nixpkgs> {};
|
||
|
||
( let
|
||
packageOverrides = self: super: {
|
||
scipy = super.scipy_0_17;
|
||
};
|
||
in (pkgs.python38.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`.
|
||
|
||
```nix
|
||
let
|
||
pkgs = import <nixpkgs> {};
|
||
newpkgs = import pkgs.path { overlays = [ (self: super: {
|
||
python38 = let
|
||
packageOverrides = python-self: python-super: {
|
||
numpy = python-super.numpy_1_18;
|
||
};
|
||
in super.python38.override {inherit packageOverrides;};
|
||
} ) ]; };
|
||
in newpkgs.inkscape
|
||
```
|
||
|
||
### `python setup.py bdist_wheel` cannot create .whl {#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 from the Nix store (which have a timestamp of the UNIX
|
||
epoch of January 1, 1970) are included in the .ZIP, but .ZIP archives follow the
|
||
DOS convention of counting timestamps from 1980.
|
||
|
||
The command `bdist_wheel` reads the `SOURCE_DATE_EPOCH` environment variable,
|
||
which `nix-shell` sets to 1. Unsetting this variable or giving it a value
|
||
corresponding to 1980 or later enables building wheels.
|
||
|
||
Use 1980 as timestamp:
|
||
|
||
```shell
|
||
nix-shell --run "SOURCE_DATE_EPOCH=315532800 python3 setup.py bdist_wheel"
|
||
```
|
||
|
||
or the current time:
|
||
|
||
```shell
|
||
nix-shell --run "SOURCE_DATE_EPOCH=$(date +%s) python3 setup.py bdist_wheel"
|
||
```
|
||
|
||
or unset `SOURCE_DATE_EPOCH`:
|
||
|
||
```shell
|
||
nix-shell --run "unset SOURCE_DATE_EPOCH; python3 setup.py bdist_wheel"
|
||
```
|
||
|
||
### `install_data` / `data_files` problems {#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://github.com/pypa/setuptools/issues/130) 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:
|
||
|
||
```shell
|
||
${python.interpreter} setup.py install_data --install-dir=$out --root=$out
|
||
sed -i '/ = data\_files/d' setup.py
|
||
```
|
||
|
||
### Rationale of non-existent global site-packages {#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 virtual environment like I am used to on other Operating Systems? {#how-to-consume-python-modules-using-pip-in-a-virtual-environment-like-i-am-used-to-on-other-operating-systems}
|
||
|
||
While this approach is not very idiomatic from Nix perspective, it can still be
|
||
useful when dealing with pre-existing projects or in situations where it's not
|
||
feasible or desired to write derivations for all required dependencies.
|
||
|
||
This is an example of a `default.nix` for a `nix-shell`, which allows to consume
|
||
a virtual environment created by `venv`, and install Python modules through
|
||
`pip` the traditional way.
|
||
|
||
Create this `default.nix` file, together with a `requirements.txt` and simply
|
||
execute `nix-shell`.
|
||
|
||
```nix
|
||
with import <nixpkgs> { };
|
||
|
||
let
|
||
pythonPackages = python3Packages;
|
||
in pkgs.mkShell rec {
|
||
name = "impurePythonEnv";
|
||
venvDir = "./.venv";
|
||
buildInputs = [
|
||
# A Python interpreter including the 'venv' module is required to bootstrap
|
||
# the environment.
|
||
pythonPackages.python
|
||
|
||
# This execute some shell code to initialize a venv in $venvDir before
|
||
# dropping into the shell
|
||
pythonPackages.venvShellHook
|
||
|
||
# Those are dependencies that we would like to use from nixpkgs, which will
|
||
# add them to PYTHONPATH and thus make them accessible from within the venv.
|
||
pythonPackages.numpy
|
||
pythonPackages.requests
|
||
|
||
# In this particular example, in order to compile any binary extensions they may
|
||
# require, the Python modules listed in the hypothetical requirements.txt need
|
||
# the following packages to be installed locally:
|
||
taglib
|
||
openssl
|
||
git
|
||
libxml2
|
||
libxslt
|
||
libzip
|
||
zlib
|
||
];
|
||
|
||
# Run this command, only after creating the virtual environment
|
||
postVenvCreation = ''
|
||
unset SOURCE_DATE_EPOCH
|
||
pip install -r requirements.txt
|
||
'';
|
||
|
||
# Now we can execute any commands within the virtual environment.
|
||
# This is optional and can be left out to run pip manually.
|
||
postShellHook = ''
|
||
# allow pip to install wheels
|
||
unset SOURCE_DATE_EPOCH
|
||
'';
|
||
|
||
}
|
||
```
|
||
|
||
In case the supplied venvShellHook is insufficient, or when Python 2 support is
|
||
needed, you can define your own shell hook and adapt to your needs like in the
|
||
following example:
|
||
|
||
```nix
|
||
with import <nixpkgs> { };
|
||
|
||
let
|
||
venvDir = "./.venv";
|
||
pythonPackages = python3Packages;
|
||
in pkgs.mkShell rec {
|
||
name = "impurePythonEnv";
|
||
buildInputs = [
|
||
pythonPackages.python
|
||
# Needed when using python 2.7
|
||
# pythonPackages.virtualenv
|
||
# ...
|
||
];
|
||
|
||
# This is very close to how venvShellHook is implemented, but
|
||
# adapted to use 'virtualenv'
|
||
shellHook = ''
|
||
SOURCE_DATE_EPOCH=$(date +%s)
|
||
|
||
if [ -d "${venvDir}" ]; then
|
||
echo "Skipping venv creation, '${venvDir}' already exists"
|
||
else
|
||
echo "Creating new venv environment in path: '${venvDir}'"
|
||
# Note that the module venv was only introduced in python 3, so for 2.7
|
||
# this needs to be replaced with a call to virtualenv
|
||
${pythonPackages.python.interpreter} -m venv "${venvDir}"
|
||
fi
|
||
|
||
# Under some circumstances it might be necessary to add your virtual
|
||
# environment to PYTHONPATH, which you can do here too;
|
||
# PYTHONPATH=$PWD/${venvDir}/${pythonPackages.python.sitePackages}/:$PYTHONPATH
|
||
|
||
source "${venvDir}/bin/activate"
|
||
|
||
# As in the previous example, this is optional.
|
||
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`? {#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:
|
||
|
||
```nix
|
||
nixpkgs.config.packageOverrides = super: {
|
||
python = super.python.override {
|
||
packageOverrides = python-self: python-super: {
|
||
twisted = python-super.twisted.overrideAttrs (oldAttrs: {
|
||
src = super.fetchPipy {
|
||
pname = "twisted";
|
||
version = "19.10.0";
|
||
sha256 = "7394ba7f272ae722a74f3d969dcf599bc4ef093bc392038748a490f1724a515d";
|
||
extension = "tar.bz2";
|
||
};
|
||
});
|
||
};
|
||
};
|
||
};
|
||
```
|
||
|
||
`pythonPackages.twisted` is now globally overridden.
|
||
All packages and also all NixOS services that reference `twisted`
|
||
(such as `services.buildbot-worker`) now use the new definition.
|
||
Note that `python-super` refers to the old package set and `python-self`
|
||
to the new, overridden version.
|
||
|
||
To modify only a Python package set instead of a whole Python derivation, use
|
||
this snippet:
|
||
|
||
```nix
|
||
myPythonPackages = pythonPackages.override {
|
||
overrides = self: super: {
|
||
twisted = ...;
|
||
};
|
||
}
|
||
```
|
||
|
||
### How to override a Python package using overlays? {#how-to-override-a-python-package-using-overlays}
|
||
|
||
Use the following overlay template:
|
||
|
||
```nix
|
||
self: super: {
|
||
python = super.python.override {
|
||
packageOverrides = python-self: python-super: {
|
||
twisted = python-super.twisted.overrideAttrs (oldAttrs: {
|
||
src = super.fetchPypi {
|
||
pname = "twisted";
|
||
version = "19.10.0";
|
||
sha256 = "7394ba7f272ae722a74f3d969dcf599bc4ef093bc392038748a490f1724a515d";
|
||
extension = "tar.bz2";
|
||
};
|
||
});
|
||
};
|
||
};
|
||
}
|
||
```
|
||
|
||
### How to use Intel’s MKL with numpy and scipy? {#how-to-use-intels-mkl-with-numpy-and-scipy}
|
||
|
||
MKL can be configured using an overlay. See the section "[Using overlays to
|
||
configure alternatives](#sec-overlays-alternatives-blas-lapack)".
|
||
|
||
### What inputs do `setup_requires`, `install_requires` and `tests_require` map to? {#what-inputs-do-setup_requires-install_requires-and-tests_require-map-to}
|
||
|
||
In a `setup.py` or `setup.cfg` it is common to declare dependencies:
|
||
|
||
* `setup_requires` corresponds to `nativeBuildInputs`
|
||
* `install_requires` corresponds to `propagatedBuildInputs`
|
||
* `tests_require` corresponds to `checkInputs`
|
||
|
||
## Contributing {#contributing}
|
||
|
||
### Contributing guidelines {#contributing-guidelines}
|
||
|
||
The following rules are desired to be respected:
|
||
|
||
* Python libraries are called from `python-packages.nix` and packaged with
|
||
`buildPythonPackage`. The expression of a library should be in
|
||
`pkgs/development/python-modules/<name>/default.nix`.
|
||
* 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 reflect that they are Python
|
||
libraries, so write for example `pythonPackages.numpy: 1.11 -> 1.12`.
|
||
* Attribute names in `python-packages.nix` as well as `pname`s should match the
|
||
library's name on PyPI, but be normalized according to [PEP
|
||
0503](https://www.python.org/dev/peps/pep-0503/#normalized-names). This means
|
||
that characters should be converted to lowercase and `.` and `_` should be
|
||
replaced by a single `-` (foo-bar-baz instead of Foo__Bar.baz).
|
||
If necessary, `pname` has to be given a different value within `fetchPypi`.
|
||
* Attribute names in `python-packages.nix` should be sorted alphanumerically to
|
||
avoid merge conflicts and ease locating attributes.
|