When a PEP 517 project file is present, pip will not install
prerequisites in `site-packages`:
https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
For the shell hook, this has the consequence that the generated
temporary directory that is added to PYTHONPATH does not contain
`site.py`. As a result, Python does not discover the Python
module. Thus when a user executes nix-shell in a project, they cannot
import the project's Python module.
This change adds the `--no-build-isolation` option to pip when
creating the editable environment, to correctly generate `site.py`,
even when a `pyproject.toml` is present.
I took a close look at how Debian builds the Python interpreter,
because I noticed it ran substantially faster than the one in nixpkgs
and I was curious why.
One thing that I found made a material difference in performance was
this pair of linker flags (passed to the compiler):
-Wl,-O1 -Wl,-Bsymbolic-functions
In other words, effectively the linker gets passed the flags:
-O1 -Bsymbolic-functions
Doing the same thing in nixpkgs turns out to make the interpreter
run about 6% faster, which is quite a big win for such an easy
change. So, let's apply it.
---
I had not known there was a `-O1` flag for the *linker*!
But indeed there is.
These flags are unrelated to "link-time optimization" (LTO), despite
the latter's name. LTO means doing classic compiler optimizations
on the actual code, at the linking step when it becomes possible to
do them with cross-object-file information. These two flags, by
contrast, cause the linker to make certain optimizations within the
scope of its job as the linker.
Documentation is here, though sparse:
https://sourceware.org/binutils/docs-2.31/ld/Options.html
The meaning of -O1 was explained in more detail in this LWN article:
https://lwn.net/Articles/192624/
Apparently it makes the resulting symbol table use a bigger hash
table, so the load factor is smaller and lookups are faster. Cool.
As for -Bsymbolic-functions, the documentation indicates that it's a
way of saving lookups through the symbol table entirely. There can
apparently be situations where it changes the behavior of a program,
specifically if the program relies on linker tricks to provide
customization features:
https://bugs.launchpad.net/ubuntu/+source/xfe/+bug/644645https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=637184#35
But I'm pretty sure CPython doesn't permit that kind of trick: you
don't load a shared object that tries to redefine some symbol found
in the interpreter core.
The stronger reason I'm confident using -Bsymbolic-functions is
safe, though, is empirical. Both Debian and Ubuntu have been
shipping a Python built this way since forever -- it was introduced
for the Python 2.4 and 2.5 in Ubuntu "hardy", and Debian "lenny",
released in 2008 and 2009. In those 12 years they haven't seen a
need to drop this flag; and I've been unable to locate any reports
of trouble related to it, either on the Web in general or on the
Debian bug tracker. (There are reports of a handful of other
programs breaking with it, but not Python/CPython.) So that seems
like about as thorough testing as one could hope for.
---
As for the performance impact: I ran CPython upstream's preferred
benchmark suite, "pyperformance", in the same way as described in
the previous commit. On top of that commit's change, the results
across the 60 benchmarks in the suite are:
The median is 6% faster.
The middle half (aka interquartile range) is from 4% to 8% faster.
Out of 60 benchmarks, 3 come out slower, by 1-4%. At the other end,
5 are at least 10% faster, and one is 17% faster.
So, that's quite a material speedup! I don't know how big the
effect of these flags is for other software; but certainly CPython
tends to do plenty of dynamic linking, as that's how it loads
extension modules, which are ubiquitous in the stdlib as well as
popular third-party libraries. So perhaps that helps explain why
optimizing the dynamic linker has such an impact.
Without this flag, the configure script prints a warning at the end,
like this (reformatted):
If you want a release build with all stable optimizations active
(PGO, etc), please run ./configure --enable-optimizations
We're doing a build to distribute to people for day-to-day use,
doing things other than developing the Python interpreter. So
that's certainly a release build -- we're the target audience for
this recommendation.
---
And, trying it out, upstream isn't kidding! I ran the standard
benchmark suite that the CPython developers use for performance
work, "pyperformance". Following its usage instructions:
https://pyperformance.readthedocs.io/usage.html
I ran the whole suite, like so:
$ nix-shell -p ./result."$variant" --run '
cd $(mktemp -d); python -m venv venv; . venv/bin/activate
pip install pyperformance
pyperformance run -o ~/tmp/result.'"$variant"'.json
'
and then examined the results with commands like:
$ python -m pyperf compare_to --table -G \
~/tmp/result.{$before,$after}.json
Across all the benchmarks in the suite, the median speedup was 16%.
(Meaning 1.16x faster; 14% less time).
The middle half of them ranged from a 13% to a 22% speedup.
Each of the 60 benchmarks in the suite got faster, by speedups
ranging from 3% to 53%.
---
One reason this isn't just the default to begin with is that, until
recently, it made the build a lot slower. What it does is turn on
profile-guided optimization, which means first build for profiling,
then run some task to get a profile, then build again using the
profile. And, short of further customization, the task it would use
would be nearly the full test suite, which includes a lot of
expensive and slow tests, and can easily take half an hour to run.
Happily, in 2019 an upstream developer did the work to carefully
select a more appropriate set of tests to use for the profile:
https://github.com/python/cpython/commit/4e16a4a31https://bugs.python.org/issue36044
This suite takes just 2 minutes to run. And the resulting final
build is actually slightly faster than with the much longer suite,
at least as measured by those standard "pyperformance" benchmarks.
That work went into the 3.8 release, but the same list works great
if used on older releases too.
So, start passing that --enable-optimizations flag; and backport
that good-for-PGO set of tests, so that we use it on all releases.
Some PECLs depend on other PECLs and, like internal PHP extension
dependencies, need to be loaded in the correct order. This makes this
possible by adding the argument "peclDeps" to buildPecl, which adds
the extension to buildInputs and is treated the same way as
internalDeps when the extension config is generated.
@the-kenny did a good job in the past and is set as maintainer in many package,
however since 2017-2018 he stopped contributing. To create less confusion
in pull requests when people try to request his feedback, I removed him as
maintainer from all packages.
This should enable (manual) building of RPMs from python projects using
the `python setup.py bdist_rpm` command on systems where `rpmbuild` is
not located in `/usr/bin/`. (e.g. NixOS)
The discovery of the rpmbuild command was fixed upstream in Python 3.8,
so this commit backports the relevant patch to our currently supported
Python 3 versions.
Fixes: #85204
At the moment, using .withExtensions on a PHP derivation will
produce something which can't be used inside an
environment.systemPackages array, because outputsToInstall refers
to an output which doesn't exist on the final derivation.
Instead, override it back to just containing the single output
"out".
Also passthrough the meta of the package to have description,
homepage, license, maintainers and other metadata passed through to
the commonly used attribute.
Instead of using two different php packages in php-packages.nix, one
wrapper and one unwrapped, simply use the wrapper and use its
"unwrapped" attribute when necessary. Also, get rid of the packages
and extensions attributes from the base package, since they're no
longer needed.
Since the introduction of php.unwrapped there's no real need for the
phpXXbase attributes, so let's remove them to lessen potential
confusion and clutter. Also update the docs to make it clear how to
get hold of an unwrapped PHP if needed.
Some extensions depend on other extensions. Previously, these had to
be added manually to the list of included extensions, or we got a
cryptic error message pointing to strings-with-deps.nix, which wasn't
very helpful. This makes sure all required extensions are included in
the set from which textClosureList chooses its snippets.
Rework withExtensions / buildEnv to handle currently enabled
extensions better and make them compatible with override. They now
accept a function with the named arguments enabled and all, where
enabled is a list of currently enabled extensions and all is the set
of all extensions. This gives us several nice properties:
- You always get the right version of the list of currently enabled
extensions
- Invocations chain
- It works well with overridden PHP packages - you always get the
correct versions of extensions
As a contrived example of what's possible, you can add ImageMagick,
then override the version and disable fpm, then disable cgi, and
lastly remove the zip extension like this:
{ pkgs ? (import <nixpkgs>) {} }:
with pkgs;
let
phpWithImagick = php74.withExtensions ({ all, enabled }: enabled ++ [ all.imagick ]);
phpWithImagickWithoutFpm743 = phpWithImagick.override {
version = "7.4.3";
sha256 = "wVF7pJV4+y3MZMc6Ptx21PxQfEp6xjmYFYTMfTtMbRQ=";
fpmSupport = false;
};
phpWithImagickWithoutFpmZip743 = phpWithImagickWithoutFpm743.withExtensions (
{ enabled, all }:
lib.filter (e: e != all.zip) enabled);
phpWithImagickWithoutFpmZipCgi743 = phpWithImagickWithoutFpmZip743.override {
cgiSupport = false;
};
in
phpWithImagickWithoutFpmZipCgi743
Make buildEnv take earlier overridden values into account by
forwarding all arguments (a merge of generic's arguments, all previous
arguments and the current arguments) to the next invocation of
buildEnv.
Make all arguments to a PHP build overridable; i.e, both configuration
flags, such as valgrindSupport, and packages, such as valgrind:
php.override { valgrindSupport = false; valgrind = valgrind-light; }
This applies to packages built by generic and buildEnv/withExtensions;
i.e, it works with both phpXX and phpXXBase packages.
The following changes were also made to facilitate this:
- generic and generic' are merged into one function
- generic now takes all required arguments for a complete build and
is meant to be called by callPackage
- The main function called from all-packages.nix no longer takes all
required arguments for a complete build - all arguments passed to it
are however forwarded to the individual builds, thus default
arguments can still be overridden from all-packages.nix
This implements the override pattern for builds done with buildEnv, so
that we can, for example, write
php.override { fpmSupport = false; }
and get a PHP package with the default extensions enabled, but PHP
compiled without fpm support.
Also passthrough the meta of the package to have description,
homepage, license, maintainers and other metadata passed through to
the commonly used attribute.
This is a better name since we have multiple 64-bit things that could
be referred to.
LP64 : integer=32, long=64, pointer=64
ILP64 : integer=64, long=64, pointer=64
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.
treewide: cleanup from blas/lapack changes
A few issues in the original treewide:
- can’t assume blas64 is a bool
- unused commented code
This is to fix a regression in upstream Racket packaging, the upstream
bug tracking this is here:
https://github.com/racket/racket/issues/3046
When the bug is fixed this workaround will be unnecessary.
mkDerivation uses the dev output in buildInputs if it exits, hence the
php-with-extensions package was never built or put into the path of
packages dependent on it during build. With this fix, the php packages
built with buildEnv or withExtensions don't have any dev outputs;
packages which need the dev output can refer to the phpXXbase packages
instead.
This provides a means to build a PHP package based on a list of
extensions from another.
For example, to generate a package with all default extensions
enabled, except opcache, but with ImageMagick:
php.withExtensions (e:
(lib.filter (e: e != php.extensions.opcache) php.enabledExtensions)
++ [ e.imagick ])
So now we have only packages for human interaction in php.packages and
only extensions in php.extensions. With this php.packages.exts have
been merged into the same attribute set as all the other extensions to
make it flat and nice.
The nextcloud module have been updated to reflect this change as well
as the documentation.
Make mkExtension put headers in the dev output and use them, instead of
a different part of the current source tree, when referring to another
extension by using internalDeps.
This means external extensions can be built against the internal ones.
This means php packages can now refer to other php packages by looking
them up in the php.packages attribute and gets rid of the internal
recursive set previously defined in php-packages.nix. This also means
that in applications where previously both the php package and the
corresponding version of the phpPackages package set had to be
specified, the php package will now suffice.
This also adds the phpWithExtensions parameter to the
php-packages.nix, which can be used by extensions that need a fully
featured PHP executable.
A slight rewrite of buildEnv which:
1. Makes buildEnv recursively add itself to its output, so that it can
be accessed from any php derivation.
2. Orders the extension text strings according to their internalDeps
attribute - dependencies have to be put before dependants in the
php.ini or they will fail to load due to missing symbols.
This moves yet more extensions from the base build to
phpPackages.ext. Some of the extensions are a bit quirky and need
patching for this to work, most notably mysqlnd and opcache.
Two new parameters are introduced for mkExtension - internalDeps and
postPhpize. internalDeps is used to specify which other internal
extensions the current extension depends on, in order to provide them
at build time. postPhpize is for when patches and quirks need to be
applied after running phpize.
Patch notes:
- For opcache, older versions of PHP have a bug where header files are
included in the wrong order.
- For mysqlnd, the config.h is never included, so we include it in the
main header file, mysqlnd.h. Also, the configure script doesn't add
the necessary library link flags, so we add them to the variable
configure should have added them to.
Also, add opcache to default extensions since it significantly
increases PHP's performance and is by default enabled on Debian based
distributions. Not having it enabled by default results in a puzzling
performance loss for anyone attempting to migrate from Debian/Ubuntu
to NixOS who is unaware of this. Therefore, enable it by default. /talyz
The ./configure script prints a warning when passed this flag,
starting with 3.7:
configure: WARNING: unrecognized options: --with-threads
The reason is that there's no longer such a thing as a build
without threads.
Eliminate the warning, by only passing the flag on the older releases
that accept it.
Upstream change and discussion:
https://github.com/python/cpython/commit/a6a4dc816https://bugs.python.org/issue31370
The prefix will now be correct in case of Nix env.
Note, however, that creating a venv from a Nix env still does not function. This does not seem to be possible
with the current approach either, because venv will copy or symlink our Python wrapper. In case it symlinks
(the default) it won't see a pyvenv.cfg. If it is copied I think it should function but it does not...
This is needed in case of `python.buildEnv` to make sure site.PREFIXES
does not only point to the unwrapped executable prefix.
--------------------------------------------------------------------------------
This PR is a story where your valiant hero sets out on a very simple adventure but ends up having to slay dragons, starts questioning his own sanity and finally manages to gain enough knowledge to slay the evil dragon and finally win the proverbial price.
It all started out on sunny spring day with trying to tackle the Nixops plugin infrastructure and make that nice enough to work with.
Our story begins in the shanty town of [NixOps-AWS](https://github.com/nixos/nixops-aws) where [mypy](http://mypy-lang.org/) type checking has not yet been seen.
As our deuteragonist (@grahamc) has made great strides in the capital city of [NixOps](https://github.com/nixos/nixops) our hero wanted to bring this out into the land and let the people rejoice in reliability and a wonderful development experience.
The plugin work itself was straight forward and our hero quickly slayed the first small dragon, at this point things felt good and our hero thought he was going to reach the town of NixOps-AWS very quickly.
But alas! Mypy did not want to go, it said:
`Cannot find implementation or library stub for module named 'nixops'`
Our hero felt a small sliver of life escape from his body. Things were not going to be so easy.
After some frustration our hero discovered there was a [rule of the land of Python](https://www.python.org/dev/peps/pep-0561/) that governed the import of types into the kingdom, more specificaly a very special document (file) called `py.typed`.
Things were looking good.
But no, what the law said did not seem to match reality. How could things be so?
After some frustrating debugging our valiant hero thought to himself "Hmm, I wonder if this is simply a Nix idiosyncrasy", and it turns out indeed it was.
Things that were working in the blessed way of the land of Python (inside a `virtualenv`) were not working the way they were from his home town of Nix (`nix-shell` + `python.withPackages`).
After even more frustrating attempts at reading the mypy documentation and trying to understand how things were supposed to work our hero started questioning his sanity.
This is where things started to get truly interesting.
Our hero started to use a number of powerful weapons, both forged in the land of Python (pdb) & by the mages of UNIX (printf-style-debugging & strace).
After first trying to slay the dragon simply by `strace` and a keen eye our hero did not spot any weak points.
Time to break out a more powerful sword (`pdb`) which also did not divulge any secrets about what was wrong.
Our hero went back to the `strace` output and after a fair bit of thought and analysis a pattern started to emerge. Mypy was looking in the wrong place (i.e. not in in the environment created by `python.withPackages` but in the interpreter store path) and our princess was in another castle!
Our hero went to the pub full of old grumpy men giving out the inner workings of the open source universe (Github) and acquired a copy of Mypy.
He littered the code with print statements & break points.
After a fierce battle full of blood, sweat & tears he ended up in 20f7f2dd71/mypy/sitepkgs.py and realised that everything came down to the Python `site` module and more specifically https://docs.python.org/3.7/library/site.html#site.getsitepackages which in turn relies on https://docs.python.org/3.7/library/site.html#site.PREFIXES .
Our hero created a copy of the environment created by `python.withPackages` and manually modified it to confirm his findings, and it turned out it was indeed the case.
Our hero had damaged the dragon and it was time for a celebration.
He went out and acquired some mead which he ingested while he typed up his story and waited for the dragon to finally die (the commit caused a mass-rebuild, I had to wait for my repro).
In the end all was good in [NixOps-AWS](https://github.com/nixos/nixops-aws)-town and type checks could run. (PR for that incoming tomorrow).
