Update numpy to 1.25.2

[rgommers]

Description

This is the last version of numpy that defaults to a distutils/setup.py-based build. I am also looking into moving the build to Meson (xref numpy/numpy#24603), but I thought it'd be good to make this update in case anything changed in the 1.25.x release series.

Checklists

• Add a CHANGELOG entry
• Add / update tests
• Add new / update outdated documentation

[hoodmane]

Thanks @rgommers! It seems to be mad about -std=c++17? I'll try building it locally.

[rgommers]

Argh, I was hoping it would be smooth sailing. I tried building locally in a conda env following the contributor guide, but that had some hiccup. I will try with the recommended Docker setup instead.

And yes indeed, more C++ in this release. This snippet from the release notes may also be relevant:

C++ standard library usage
--------------------------
NumPy builds now depend on the C++ standard library, because
the ``numpy.core._multiarray_umath`` extension is linked with
the C++ linker.

C++17 is no problem in principle I assume, right?

EDIT: build failure for future reference:

creating tmp/tmpr8en6c1l                                                        
INFO: compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core   
-Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath     
-Inumpy/core/src/npysort -Inumpy/core/src/_simd                                 
-I/tmp/build-env-2vd3bsq6/include                                               
-I/usr/share/miniconda/envs/pyodide-env/include/python3.11                      
-Ibuild/src.emscripten_3_1_45_wasm32-3.11/numpy/core/src/common                 
-Ibuild/src.emscripten_3_1_45_wasm32-3.11/numpy/core/src/npymath -c'            
INFO: c++: /tmp/tmpr8en6c1l/test.cpp                                            
/tmp/tmpr8en6c1l/test.cpp:4:41: error: no template named 'is_const_v' in        
namespace 'std'; did you mean 'is_const'?                                       
    4 | constexpr bool test_fold = (... && std::is_const_v<T>);                 
      |                                    ~~~~~^~~~~~~~~~                      
      |                                         is_const                        
/home/runner/work/pyodide/pyodide/emsdk/emsdk/upstream/emscripten/cache/sysroot/
include/c++/v1/__type_traits/is_const.h:24:29: note: 'is_const' declared here   
   24 | struct _LIBCPP_TEMPLATE_VIS is_const : _BoolConstant<__is_const(_Tp)> { 
};                                                                              
      |                             ^                                           
/tmp/tmpr8en6c1l/test.cpp:4:54: error: expected '(' for function-style cast or  
type construction                                                               
    4 | constexpr bool test_fold = (... && std::is_const_v<T>);                 
      |                                    ~~~~~~~~~~~~~~~~~~^                  
/tmp/tmpr8en6c1l/test.cpp:4:16: error: constexpr variable 'test_fold<int, const 
int>' must be initialized by a constant expression                              
    4 | constexpr bool test_fold = (... && std::is_const_v<T>);                 
      |                ^                                                        
      |                          = false                                        
/tmp/tmpr8en6c1l/test.cpp:7:9: note: in instantiation of variable template      
specialization 'test_fold<int, const int>' requested here                       
    7 |     if (test_fold<int, const int>) {                                    
      |         ^                                                               
3 errors generated.                                                             
em++: error: '/home/runner/work/pyodide/pyodide/emsdk/emsdk/upstream/bin/clang++
-target wasm32-unknown-emscripten -fignore-exceptions -fvisibility=default      
-mllvm -combiner-global-alias-analysis=false -mllvm -enable-emscripten-sjlj     
-mllvm -disable-lsr -DEMSCRIPTEN                                                
--sysroot=/home/runner/work/pyodide/pyodide/emsdk/emsdk/upstream/emscripten/cach
e/sysroot -Xclang -iwithsysroot/include/fakesdl -Xclang                         
-iwithsysroot/include/compat -g3 -fwrapv -O3 -Wall -O2 -g0 -fPIC                
-Werror=implicit-function-declaration -Werror=mismatched-parameter-types        
-Werror=return-type -Wno-return-type -O2 -g0 -fPIC -std=c++14 -DNDEBUG          
-DPY_CALL_TRAMPOLINE -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core      
-Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath     
-Inumpy/core/src/npysort -Inumpy/core/src/_simd                                 
-I/tmp/build-env-2vd3bsq6/include                                               
-Ibuild/src.emscripten_3_1_45_wasm32-3.11/numpy/core/src/common                 
-Ibuild/src.emscripten_3_1_45_wasm32-3.11/numpy/core/src/npymath                
-I/home/runner/work/pyodide/pyodide/cpython/installs/python-3.11.3/include/pytho
n3.11                                                                           
-I/home/runner/work/pyodide/pyodide/cpython/installs/python-3.11.3/include/pytho
n3.11 -c -MMD -MF tmp/tmpr8en6c1l/test.o.d -fcolor-diagnostics                  
/tmp/tmpr8en6c1l/test.cpp -o tmp/tmpr8en6c1l/test.o' failed (returned 1)        
INFO: C compiler: /tmp/tmpdoblrjdq/c++ -DNDEBUG -g -fwrapv -O3 -Wall -O2 -g0    
-fPIC -DPY_CALL_TRAMPOLINE                 

...

RuntimeError: Broken toolchain during testing C++ compiler.                     
A compiler with support for C++17 language features is required.                
Triggered the following error: Command "/tmp/tmpdoblrjdq/c++ -DNDEBUG -g -fwrapv
-O3 -Wall -O2 -g0 -fPIC -DPY_CALL_TRAMPOLINE -Inumpy/core/src/common            
-Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath                          
-Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort     
-Inumpy/core/src/_simd -I/tmp/build-env-2vd3bsq6/include                        
-I/usr/share/miniconda/envs/pyodide-env/include/python3.11                      
-Ibuild/src.emscripten_3_1_45_wasm32-3.11/numpy/core/src/common                 
-Ibuild/src.emscripten_3_1_45_wasm32-3.11/numpy/core/src/npymath -c             
/tmp/tmpr8en6c1l/test.cpp -o tmp/tmpr8en6c1l/test.o -MMD -MF                    
tmp/tmpr8en6c1l/test.o.d -std=c++17" failed with exit status 1.                                     

[hoodmane]

Are there any simple tricks to leave tmp files in the file system after compilation fails? I always have this problem where the failing command takes arguments that were in /tmp and now they are gone...

[hoodmane]

Ah but this test is hard coded into setup.py so it's easy to create my own.

[rgommers]

Yes, that is usually a pain. If you build via pip install, then --no-clean is helpful. Or otherwise yes, peek in the source of test.c and it's typically only a one-liner.

[hoodmane]

Okay found the problem.

[hoodmane]

It built really fast, 1m 31s, tests pass. Did you change something to improve the build speed?

[rgommers]

Not that I know of. Locally 1m 31s isn't unusual for a local parallel build though. I just tried on Linux:

$ time python setup.py build_ext -i -j4
real    1m21,634s
user    3m36,304s
sys     0m13,231s

It'll get a lot faster still from 1.26.0 onwards, due to the Meson rewrite:

$ time python -m build -wnx
real    0m40,042s
user    7m1,368s
sys     0m22,224s

[rgommers]

The macOS job failure looks unrelated. Something that picked up the system Python 2.7 in the final check-size step.

[hoodmane]

Yeah the github macos job flakes a lot so I tend not to pay much attention to it especially if the circleci safari tests pass.

[rgommers]

I can reproduce the initial failure and the completed build after your fix locally now. Thanks for the help!

[hoodmane]

Thanks again @rgommers!