Unexpected prefix value in .../lib/pkgconfig/python-3.<minor>.pc

[Matiiss]

I am aware that this is a documented quirk:

On Linux, our distributions are built in containers. The container has a custom build of Clang in a custom filesystem location. And Python is installed to the prefix /install. So you may see references to /install in Linux distributions.

- https://gregoryszorc.com/docs/python-build-standalone/main/quirks.html#references-to-build-time-paths

Nonetheless, I was asked to open this issue as it seems it might get resolved for once 🥳

I was trying to compile a C extension using meson and it kept throwing an error that it couldn't find Python.h for the specified Python version and upon closer inspection it looked like it was not including the correct directory because the directory it was attempting to include started with /install which is not a path on my machine, so I went to the file mentioned in the title and found that it contains this (the <minor> was actually the version I had, in this case 3.12):

# See: man pkg-config
prefix=/install
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include

Name: Python
Description: Build a C extension for Python
Requires:
Version: 3.<minor>
Libs.private: -lpthread -ldl  -lutil
Libs: -L${libdir} 
Cflags: -I${includedir}/python3.<minor>

So the prefix=/install was unexpected, what I would have expected would have been (in my particular case)

prefix=/home/matiiss/.local/share/uv/python/cpython-3.12.8-linux-x86_64-gnu

After editing the file manually and trying to run meson again, it worked.

[charliermarsh]

I think we need to solve this in uv by patching pkgconfig, like we do with sysconfig, so I'm gonna transfer to the uv repo.

[neutrinoceros]

I'm encountering a very similar, possibly same, issue with uv 0.5.14

setup:

$ git clone https://github.com/numpy/numpy
$ cd numpy
$ git submodule update --init

then

$ uv build
Building source distribution...
+ /Users/clm/.cache/uv/builds-v0/.tmpcUq9Nd/bin/python /private/tmp/numpy/vendored-meson/meson/meson.py setup /private/tmp/numpy /private/tmp/numpy/.mesonpy-xqqxtm9n -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/private/tmp/numpy/.mesonpy-xqqxtm9n/meson-python-native-file.ini
The Meson build system
Version: 1.5.2
Source dir: /private/tmp/numpy
Build dir: /private/tmp/numpy/.mesonpy-xqqxtm9n
Build type: native build
Project name: NumPy
Project version: 2.3.0.dev0+git20241226.a07c6c5
C compiler for the host machine: cc (clang 16.0.0 "Apple clang version 16.0.0 (clang-1600.0.26.6)")
C linker for the host machine: cc ld64 1115.7.3
C++ compiler for the host machine: c++ (clang 16.0.0 "Apple clang version 16.0.0 (clang-1600.0.26.6)")
C++ linker for the host machine: c++ ld64 1115.7.3
Cython compiler for the host machine: cython (cython 3.0.11)
Host machine cpu family: aarch64
Host machine cpu: aarch64
Program python found: YES (/Users/clm/.cache/uv/builds-v0/.tmpcUq9Nd/bin/python)
Found pkg-config: YES (/opt/homebrew/bin/pkg-config) 2.3.0
Run-time dependency python found: YES 3.13
Has header "Python.h" with dependency python-3.13: NO

../meson.build:44:2: ERROR: Problem encountered: Cannot compile `Python.h`. Perhaps you need to install python-dev|python-devel

A full log can be found at /private/tmp/numpy/.mesonpy-xqqxtm9n/meson-logs/meson-log.txt
  × Failed to build `/private/tmp/numpy`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `mesonpy.build_sdist` failed (exit status: 1)
      hint: This usually indicates a problem with the package or the build environment.

I made sure to reinstall Python 3.13 after I upgraded uv to 0.5.14.

I already had this issue with earlier versions of uv but didn't have time to report it at the time. I found this issue from uv 0.5.14's release notes.

[neutrinoceros]

I opened a separate issue at #10558