SciPy v1.16.0 #141

agriyakhetarpal · 2025-06-29T18:02:28Z

Description

This PR bumps SciPy to version 1.16.0, released on 22nd June, 2025: https://github.com/scipy/scipy/releases/tag/v1.16.0. Here are a few points:

The number of patches has been reduced; we now have fourteen patches from the previous eighteen (although there is always scope to add a few more once this is implemented).
- The patch previously applied for id_dist has been dropped, and a patch for ARPACK based on the C port ENH:MAINT: sparse.linalg: rewrite ARPACK in C scipy/scipy#22748 has been introduced.
- A lot of other troublesome FORTRAN77 code has been removed since v1.14.1 notably: MINPACK, QUADPACK, L-BFGS-B, SLSQP, NNLS, linalg.expm, id_dist, and other Fortran codes that are not listed here; please view META: FORTRAN Code inventory scipy/scipy#18566 for more.
The problem of not being able to use the f2py entry point directly via Meson generators remains, and we have to resort to using python -m numpy.f2py and custom targets until Stop excluding unisolated packages from build dependencies pyodide-build#21 is resolved.
Many new C-rewritten packages also have the same problem of alternate returns, which means that we need to patch their signatures to match the ones coming from OpenBLAS, which means voids are transformed to ints in the code for the ARPACK, the _matfuncs family, FITPACK, SLSQP, NNLS, and the L-BFGS-B extension modules.
Most of the diff of 50K lines added here comes from the ARPACK code; and the patch is more or less the same as the aforementioned upstream PR with hardly any differences. The removal of 20K lines comes from dropping the id_dist patch,
Unfortunately, I tried testing the previous tests that we used to run via scipy-pytest.js, but the tests always hang on my macOS machine locally at the ~14-15% stage at various points, despite skipping many of them. I suggest that we leave the extra testing for another PR, as the necessary infrastructure to get those tests up and running is a follow-up task that I'd be happy to assign myself to.

Tip

This PR depends on https://github.com/pyodide/pyodide-recipes#140, which, at the time of writing, contains a patch that allows compilation to proceed to completion and succeed. That PR also depends on another PR (pyodide/pyodide-build#168). Please review those PRs first (starting with the latter) before coming back to this one, as this will reduce the diff to the relevant files. Thank you!

PR stack

Please review the following PRs in the order listed below:

Additional context

SciPy was previously updated in pyodide/pyodide#5031 to version 1.14.1.

Follow-up tasks after this PR:

Sync this update to Pyodide, and address Bump to NumPy 2.3.1, and split out numpy-tests (backport of pyodide/pyodide-recipes#86) pyodide#5715
Remove unvendor-tests: true and use -Cinstall-args=--tags=runtime,python-runtime,devel
Start working on llvm-flang + scipy progress tracker pyodide#5268
Port Fix SciPy LAPACK larf function signature mismatch pyodide#5060

Tagging the recipe maintainers and our previous collaborators here, like I've done in the past: @lesteve, @steppi, and @rgommers

Thank you for your time!

github-actions · 2025-06-29T18:34:24Z

Package Build Results

Total packages built: 33
Total build time: 0:18:31

Package Build Times (click to expand)

Package	Build Time
scipy	9m 34s
openblas	7m 19s
openssl	5m 43s
boost-cpp	5m 7s
numpy	5m 5s
sqlite3	1m 52s
liblzma	1m 3s
test	37s
libf2c	32s
regex	22s
lzma	9s
ssl	9s
MarkupSafe	7s
hashlib	7s
pydecimal	6s
pydoc_data	6s
atomicwrites	5s
packaging	4s
pytz	2s
py	2s
setuptools	2s
pyparsing	2s
Jinja2	1s
attrs	1s
tblib	1s
more-itertools	1s
six	1s
pytest-asyncio	1s
pytest	1s
micropip	1s
exceptiongroup	1s
iniconfig	1s
pluggy	1s

Longest build: scipy (9m 34s)
Packages built in more than 10 minutes: 0

agriyakhetarpal · 2025-06-30T11:03:04Z

Hi @rgommers, I experimented a bit with the f2py generator definition code to make find_program() use python -m numpy.f2py instead of just f2py, but I didn't get very far with this – I thought that would be good to get done with to drop one more patch (patch 0014) here to get to thirteen patches in total. Would it make sense to add a fallback of sorts? The comment at https://github.com/scipy/scipy/blob/07942c2a8222a6169a7e69c6935541f8c5430cb3/scipy/meson.build#L205-L212 already suggests the possibility of adding one. I could put together a PR for this if yes, or explore this further if there are any other options (xref scipy/scipy#14812).

Either way, it's not a blocker here, so this PR is ready for review. Thanks!

packages/scipy/patches/0007-MAINT-linalg-Remove-id_dist-Fortran-files.patch

agriyakhetarpal · 2025-06-30T22:34:11Z

All the errors in the test suite are coming from _dierckx.cpython-313-wasm32-emscripten.so, so I guess it's now time to perform some surgery on it and get some diagnostics.

agriyakhetarpal · 2025-06-30T23:14:55Z

wasm-objdump /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so -j Export -x

suggests that the symbol does exist:

_dierckx.cpython-313-wasm32-emscripten.so:      file format wasm 0x1

Section Details:

Export[4]:
 - func[39] <__wasm_call_ctors> -> "__wasm_call_ctors"
 - func[42] <PyInit__dierckx> -> "PyInit__dierckx"
 - func[59] <_ZNSt3__212__tuple_implINS_15__tuple_indicesIJLm0ELm1EEEEJNS_6vectorIdNS_9allocatorIdEEEENS3_IxNS4_IxEEEEEEC2B8ne190106IJLm0ELm1EEJS6_S8_ETpTnmJEJEJRS6_RS8_EEENS1_IJXspT_EEEENS_13__tuple_typesIJDpT0_EEENS1_IJXspT1_EEEENSE_IJDpT2_EEEDpOT3_> -> "_ZNSt3__212__tuple_implINS_15__tuple_indicesIJLm0ELm1EEEEJNS_6vectorIdNS_9allocatorIdEEEENS3_IxNS4_IxEEEEEEC2B8ne190106IJLm0ELm1EEJS6_S8_ETpTnmJEJEJRS6_RS8_EEENS1_IJXspT_EEEENS_13__tuple_typesIJDpT0_EEENS1_IJXspT1_EEEENSE_IJDpT2_EEEDpOT3_"
 - func[40] <__wasm_apply_data_relocs> -> "__wasm_apply_data_relocs"

and from the Type section dump:

type[2] () -> nil
type[4] () -> i32

And from the Function section:

func[42] sig=4 <PyInit__dierckx>

So PyInit__dierckx has signature type[4] which is () -> i32. This is correct.

Perhaps I missed patching a DLARTG somewhere?

ryanking13 · 2025-07-01T08:16:27Z

Thanks for the investigation, @agriyakhetarpal. The error happens while loading the library,

Failed to load lib  /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so
Error: Failed to load dynamic library /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so: 0

Because of the error during the loading step, the symbols will not be filled out in the GOT table. That's why the

ImportError: dynamic module does not define module export function (PyInit__dierckx)

error happens.

So I think we'll need to investigate why the library loading fails in the test (It ddidn't fail when I tried to load scipy locally in my browser). To see a more helpful error log, try with a debug build of Pyodide, which is available by passing the following flag PYODIDE_SYMBOLS=1 when building the Pyodide runtime. It will show a much richer message in the library loading process.

agriyakhetarpal · 2025-07-01T08:19:09Z

Thanks, @ryanking13! I wonder if we could also release an xbuildenv-debug.tar.bz2 in the same GitHub nightly/scheduled release, so that we won't have to compile it ourselves? We could also expand to debugoptimized, debug, and release builds (but only document the released ones for now, like we've been doing).

ryanking13 · 2025-07-01T08:19:52Z

Failed to load lib /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so
Error: Failed to load dynamic library /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so: 0

But I think this error only happens in the pyodide venv environment, so the hang in the unittest might have a different reason. pyodide venv has its own issues such as (pyodide/pyodide#5709), which isn't related to individual packages I guess.

ryanking13 · 2025-07-01T08:21:11Z

Thanks, @ryanking13! I wonder if we could also release an xbuildenv-debug.tar.bz2 in the same GitHub nightly/scheduled release, so that we won't have to compile it ourselves? We could also expand to debugoptimized, debug, and release builds (but only document the released ones for now, like we've been doing).

Sounds good to me. Would you like to update https://github.com/pyodide/pyodide-build-environment-nightly to support that feature?

agriyakhetarpal · 2025-07-01T08:25:34Z

Failed to load lib /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so
Error: Failed to load dynamic library /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so: 0

But I think this error only happens in the pyodide venv environment, so the hang in the unittest might have a different reason.

Oh, actually, another test in TestBSplines (when I was running the test suite locally) was hanging for the same reason (when I skipped this test to allow the test suite to proceed), so I think it must be related to _dierckx – it goes through the same code paths. So the scipy-pytest.js script with node also likely has the same error with loading this lib, but the error is not being reported in stdout/stderr and the script is not crashing/halting execution/failing here when it should.

Thanks, @ryanking13! I wonder if we could also release an xbuildenv-debug.tar.bz2 in the same GitHub nightly/scheduled release, so that we won't have to compile it ourselves? We could also expand to debugoptimized, debug, and release builds (but only document the released ones for now, like we've been doing).

Sounds good to me. Would you like to update pyodide/pyodide-build-environment-nightly to support that feature?

Yes, I'll put together a PR!

ryanking13 · 2025-07-01T08:35:04Z

Meanwhile, I ran the hanging test locally and was able to reproduce it in my browser:

from scipy import stats
from scipy.differentiate import derivative
from js import console

distcont = stats._distr_params.distcont
for idx, case in enumerate(distcont):
	distname, params = case
	console.log("handling case: ", idx, distname, params)
	dist = getattr(stats, distname)(*params)
	x = dist.median() + 0.1
	res = derivative(dist.cdf, x)
	ref = dist.pdf(x)

The derivative function (which was introduced in scipy 1.15) hangs when it the case is

    ['irwinhall', (10,)],

agriyakhetarpal · 2025-07-01T08:45:29Z

Thanks! Yes, there might be a few more broken libraries besides _dierckx, as I had at least 6-7 test cases that were hanging. However, I didn't check if they were all going through _dierckx, as it is the only one being reported right now.

Perhaps we could test individual test modules (scipy.stats, scipy.io, scipy.special, etc.) in the test suite to isolate this issue more effectively.

agriyakhetarpal · 2025-07-03T00:12:59Z

With the new debug xbuildenv from https://github.com/pyodide/pyodide-build-environment-nightly/releases/tag/20250703 that we added, I can see this when I try to run a reproducer:

Tap to expand logs

dlsym_js: PyInit__pocketfft_umath
dlsym_js: PyInit__pocketfft_umath getting table slot for: function 46() { [native code] }
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growMemory: 90439680 (+15073280 bytes / 230 pages)
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  '/Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/sparse/csgraph/_tools.cpython-313-wasm32-emscripten.so',
  '/Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/sparse/csgraph/_traversal.cpython-313-wasm32-emscripten.so',
  '/Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/sparse/linalg/_dsolve/_superlu.cpython-313-wasm32-emscripten.so',
  '/Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/sparse/linalg/_propack/_cpropack.cpython-313-wasm32-emscripten.so',
  ... 28 more items
]
dlsym_js: PyInit__dierckx
dlSetError: Tried to lookup unknown symbol "PyInit__dierckx" in dynamic lib: /Users/agriyakhetarpal/Desktop/pyodide-recipes/packages/scipy/.venv-pyodide/lib/python3.13/site-packages/scipy/interpolate/_dierckx.cpython-313-wasm32-emscripten.so

When I check the output from wasm-objdump, I see that the symbol PyInit__dierckx definitely exists in /_dierckx.cpython-313-wasm32-emscripten.so and is exported by it as well. I checked for dlartg_, and it imports it as expected: - func[35] sig=8 <env.dlartg_> <- env.dlartg_. libopenblas.so exports dlartg_ as well.

~~I'm going to try with a slightly older xbuildenv from May and see if something turns up, or if we will have the same issue.~~ Older xbuildenvs have NumPy 2.0.2 which fails to compile with newer AppleClang, never mind. Trying with 20250601 🤞🏻

Update: 20250601 has the same issue, unfortunately.

agriyakhetarpal · 2025-07-03T00:32:29Z

In the meantime, I pushed a commit to build from 20250703-debug so that we can both have artifacts to examine.

agriyakhetarpal · 2025-07-03T00:46:46Z

Also, may I ask how you are testing SciPy in your browser? When I copy the Pyodide runtime using the provided script and copy the OpenBLAS libs and other libs from the .libs/ directory into dist/, and run Pyodide through a basic test.html file in the dist/ directory, it complains about not being able to find the OpenBLAS lib in the directory. Subsequently, it fails to load the _dop module (much earlier than attempting to load _dierckx). I'm sure that I'm doing something wrong there!

ryanking13 · 2025-07-03T09:44:15Z

Also, may I ask how you are testing SciPy in your browser? When I copy the Pyodide runtime using the provided script and copy the OpenBLAS libs and other libs from the .libs/ directory into dist/, and run Pyodide through a basic test.html file in the dist/ directory, it complains about not being able to find the OpenBLAS lib in the directory. Subsequently, it fails to load the _dop module (much earlier than attempting to load _dierckx). I'm sure that I'm doing something wrong there!

For pyodide venv I think it is because the nightly buildenv does not have corresponding packages in the CDN. When running Pyodide in node, we dynamically download the package from the CDN (1, 2) when the package is not available in the filesystem using the version number in the Pyodide runtime, but for nightly buildenv, the version number would be something like 0.28.0dev0 so it probably fails to download packages like openblas.

If you are using the browser, copying the pyodide runtime to the dist directory containing the packages, and running the server in that directory will work (similar to how we do in our CI)

agriyakhetarpal · 2025-07-15T14:27:20Z

Yes, it hangs at test_differentiate.py::TestDerivative::test_accuracy[numpy-case51], still. We don't use pyodide venv here, though, just a JS script with Node.js. I'll switch to pyodide venv as it will report errors early, at least, instead of hanging.

agriyakhetarpal · 2025-10-03T13:29:04Z

@ryanking13 thanks for handling the NumPy version conflicts for Pyodide 0.29. I think this was inadvertently closed due to the "fix #141" string in the PR description 😅 Reopening it.

ryanking13 · 2025-10-03T13:32:33Z

oops... thanks 😅

ilayn · 2025-10-07T12:14:44Z

Just a heads up; PROPACK Fortran77 code is translated to C scipy/scipy#23531 (due SciPy version 1.17) so it might make things easier, hopefully that is.

For the remaining F77 crust (ODEPACK, FITPACK and BLAS/LAPACK wrappers), I am really hoping that it will be completed in SciPy version 1.18 so I can get my life back 😅 (but realistically it will be 1.19 I guess).

rgommers · 2025-10-07T16:59:45Z

🚀 @ilayn 🎉

For the remaining F77 crust (ODEPACK, FITPACK and BLAS/LAPACK wrappers), I am really hoping that it will be completed in SciPy version 1.18 so I can get my life back 😅 (but realistically it will be 1.19 I guess).

I'll note that Evgeni and Gagan are making a good dent in FITPACK at the moment, and BLAS/LAPACK wrappers aren't actually in Fortran so shouldn't matter for the purposes of Pyodide - hence I have some hope for the more optimistic timeline 🤞🏼

ryanking13 · 2025-10-08T07:49:39Z

@ilayn That's really good news! Thanks for sharing. Is there a planned timeline for the scipy 1.17 release?

agriyakhetarpal added 19 commits June 29, 2025 08:35

Port initial SciPy 1.15 patches

d91d593

Update patch registry for SciPy 1.15

fb47341

Bump to SciPy 1.16

a27718d

Drop MVNDST patch

6e8840e

Don't link COBYLA, SLSQP, and MVN with OpenBLAS

e0d627a

Drop test Fortran modules, reorder f2py-gen patch

ff7e366

The sf_error_state_lib module no longer exists

cbe09a8

Refresh LARFG function signature patch

79c45cf

Port ARPACK C-rewrite as a patch

f6f428e

Remove some more f2py generators

36ef800

Fix invalid patch for ARPACK that's valid on macOS

fb82c26

Use numpy.f2py to call f2py-based custom targets

25279a7

Fix alternate returns for linalg array utils

dea5c54

More patching for FITPACK

efe0f6c

Update signatures for NNLS and SLSQP

fb05300

Update signatures for ARPACK

eaea9cf

Update signatures for _matfuncs_* modules

03319d1

Update signatures for L-BFGS-B module headers

a485397

Add pyodide-build with my branch as a submodule

e9a929a

This was referenced Jun 29, 2025

Add pyodide-build repository as a submodule #140

Merged

Debug SciPy 1.16 builds on my fork agriyakhetarpal/pyodide-recipes#1

Closed

llvm-flang + scipy progress tracker pyodide/pyodide#5268

Open

Merge branch 'main' into scipy-1.16

bcad9e9

ryanking13 approved these changes Jun 30, 2025

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packages/scipy/patches/0007-MAINT-linalg-Remove-id_dist-Fortran-files.patch Show resolved Hide resolved

Merge main

6032858

Use debug xbuildenv from 20250703

541ed5b

Merge branch 'main' into scipy-1.16

96b2431

ryanking13 mentioned this pull request Jul 30, 2025

Bump numpy 2.3.2 #303

Draft

agriyakhetarpal mentioned this pull request Aug 6, 2025

MAINT:optimize.minimize: Restructure solver C code and some fixes scipy/scipy#23433

Open

agriyakhetarpal added 3 commits August 23, 2025 19:21

Update to xbuildenvs from 20th August

8e265d8

Run tests in pyodide venv instead of node

6de0fa8

Handle unvendor-tests: key when testing SciPy

3797abf

ryanking13 mentioned this pull request Oct 2, 2025

Revert numpy version to 2.2.5 until we update Scipy #382

Merged

ryanking13 closed this in #382 Oct 3, 2025

agriyakhetarpal reopened this Oct 3, 2025

SciPy v1.16.0 #141

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SciPy v1.16.0 #141

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