BUG: build graph non-determinism

[mathstuf]

Describe your issue.

It seems that some Cython code needs more dependencies specified. Namely, some Cython generation requires from scipy.special cimport cython_special to work. While trying to ninja -k0 in order to ninja -j1 to isolate the error message, the problem went away. This tells me that dependencies probably just need better ordered.

Reproducing Code Example

N/A

Error message

[674/845] Generating 'scipy/special/_ellip_harm_2.cpython-39-darwin.so.p/_ellip_harm_2.c'
FAILED: scipy/special/_ellip_harm_2.cpython-39-darwin.so.p/_ellip_harm_2.c
/Users/ben.boeckel/code/superbuild/build/install/bin/cython -3 --fast-fail --output-file scipy/special/_ellip_harm_2.cpython-39-darwin.so.p/_ellip_harm_2.c --include-dir . ../../scipy/special/_ellip_harm_2.pyx

Error compiling Cython file:
------------------------------------------------------------
...
from scipy.special cimport cython_special
^
------------------------------------------------------------

SciPy/NumPy/Python version and system information

SciPy 1.11.2
MesonPy 0.13.2
Meson 1.2.1
Cython 3.0.0

[mathstuf]

I suspect that adding cython_special as a dependency to the relevant py3.extension_module calls is needed…trying to figure out enough Meson to verify this hypothesis.

[rgommers]

Thanks for the report. 0.13.2 is the meson-python version. Can you add the meson and Cython versions? This should be automatic, but it's very well possible that we're missing an explicit dependency here and that triggering the resulting problem is difficult.

[mathstuf]

So I tracked it down to these two rules which should reproduce anywhere (may need a ninja -t clean first depending on how you get your builddir and hacking mesonpy (see Bartpab/meson-py#4) to get access to such a build directory):

% <generate meson build>
% ninja scipy/special/_ellip_harm_2.cpython-39-darwin.so.p/_ellip_harm_2.c
<fails as above>
% ninja scipy/special/cython_special.cpython-39-darwin.so
<works>
% ninja scipy/special/_ellip_harm_2.cpython-39-darwin.so.p/_ellip_harm_2.c
<now works>

[rgommers]

Thanks! Yes, this is a clear bug. I've had on my wish/idea list for a long time to build every target separately to smoke out issues like these.

Here's how I reproduce it, from a clean repo:

$ meson setup build  # configure the build dir
$ # find an exact target name:
$ ninja -C build -t targets depth 0 | rg ".*ellip_harm.*.so"
$ # try to build only that target:
$ ninja -C build scipy/special/_ellip_harm_2.cpython-310-x86_64-linux-gnu.so
ninja: Entering directory `build'
[1/3] Generating 'scipy/special/_ellip_harm_2.cpython-310-x86_64-linux-gnu.so.p/_ellip_harm_2.c'.
FAILED: scipy/special/_ellip_harm_2.cpython-310-x86_64-linux-gnu.so.p/_ellip_harm_2.c 
/home/rgommers/mambaforge/envs/scipy-dev/bin/cython -3 --fast-fail --output-file scipy/special/_ellip_harm_2.cpython-310-x86_64-linux-gnu.so.p/_ellip_harm_2.c --include-dir . ../scipy/special/_ellip_harm_2.pyx

Error compiling Cython file:
------------------------------------------------------------
...
from scipy.special cimport cython_special
^
------------------------------------------------------------

/home/rgommers/code/scipy/scipy/special.pxd:1:0: 'scipy/special/cython_special.pxd' not found
ninja: build stopped: subcommand failed.

Meson is good at automatically adding dependencies, but it will miss the ones that come through a custom_target where we use a Python script to generate Cython source files which are then needed for a next target.

[mathstuf]

I'm unsure of how many places need this added, but I suppose grepping pyx files for scipy imports would be a good guide.

[rgommers]

I think it's only the places that use the output of a _generate_pyx.py script - that's easy to grep for.