Apply Pyodide-specific patches to our Emscripten toolchain installation by agriyakhetarpal · Pull Request #2800 · pypa/cibuildwheel

agriyakhetarpal · 2026-03-25T01:20:03Z

Our Emscripten toolchain installation here has mostly remained vanilla-like, but pyodide-build and pyodide-recipes also apply some Pyodide-specific patches. This makes both mechanisms of building Pyodide wheels uniform by applying the patches here as well.

I have been wanting to get to this for a while now, having used a pesky combination of sparse-checking out the patches with actions/checkout and then applying them in the before-build stage in GHA before. My motivation to do this today came from flintlib/python-flint#382, so I thought I'd just put it in here!

N.B: We also have an install-and-patch-emscripten command thingy somewhere IIRC... this change is not that because that would be a bigger change to incorporate and should be discussed first; it would move the Emscripten installation from cibuildwheel's control to pyodide-build and thus would make changes to that scheme difficult (say, if pyodide-build were to break at a particular version for whatever reason, it would then start impacting all Pyodide builds for downstream users of cibuildwheel). I've gone ahead and implemented the pyodide xbuildenv install-emscripten command as that's what we ended up agreeing with at the end, in that it doesn't expose any pyodide-build internals to cibuildwheel.

cc: @oscarbenjamin

agriyakhetarpal · 2026-03-25T01:21:50Z

+        try:
+            subprocess.run(
+                f"cat {shlex.quote(str(patches_dir))}/*.patch | patch -p1 --verbose",
+                check=True,
+                shell=True,
+                cwd=emscripten_root,
+            )


We have some level of Windows support in pyodide-build, but not yet in cibuildwheel, so I stayed with the cat and patch commands here. We could think of a cross-platform solution later.

We have some level of Windows support in pyodide-build

We never considered windows as a valid target so I think it is fine.

agriyakhetarpal · 2026-03-25T01:38:59Z

You may see it working here: https://github.com/pypa/cibuildwheel/actions/runs/23520265886/job/68462021117?pr=2800#step:7:665. Note that the Pyodide 0.28.0 xbuildenvs were the first to include the Emscripten patches, so this is not applicable to the Pyodide 0.27.7 xbuildenvs/builds.

When we release Pyodide 0.30 in the next couple of months or so (or before that, or later), we should drop Pyodide 0.27 here and keep only Pyodide 0.29 and Pyodide 0.30. It still makes sense to keep Pyodide 0.27 for now, as it is beneficial for cibuildwheel to retain support for building wheels for two different Pyodide ABIs at a time.

agriyakhetarpal · 2026-03-25T01:40:01Z

I'll take a look at the failing tests later today. I don't immediately see what part of my changes might be causing them, though!

ryanking13

N.B: We also have an install-and-patch-emscripten command thingy somewhere IIRC... this change is not that because that would be a bigger change to incorporate and should be discussed first; it would move the Emscripten installation from cibuildwheel's control to pyodide-build and thus would make changes to that scheme difficult (say, if pyodide-build were to break at a particular version for whatever reason, it would then start impacting all Pyodide builds for downstream users of cibuildwheel).

I would like to go this way directly if possible. This PR already exposes pyodide-build internals (e.g. path to the emscripten patches) to cibuildwheel, which can silently be broken when we make changes in pyodide-build. I don't want to introduce more of that into cibuildwheel.

The pyodide-build >= 0.33 now installs emscripten and applies the patch in the background without calling any command explicitly. So I guess the thing we need to do is simply removing the emscripten installation part in cibuildwheel.

ryanking13 · 2026-03-25T04:55:27Z

+        try:
+            subprocess.run(
+                f"cat {shlex.quote(str(patches_dir))}/*.patch | patch -p1 --verbose",
+                check=True,
+                shell=True,
+                cwd=emscripten_root,
+            )


We have some level of Windows support in pyodide-build

We never considered windows as a valid target so I think it is fine.

joerick · 2026-04-01T13:04:50Z

I would like to go this way directly if possible. This PR already exposes pyodide-build internals (e.g. path to the emscripten patches) to cibuildwheel, which can silently be broken when we make changes in pyodide-build. I don't want to introduce more of that into cibuildwheel.

Agreed re. the coupling. If there's special magic needed for pyodide builds, let's keep as much of that as we can in pyodide-build, so it can be used without cibuildwheel.

That might be calling a command from pyodide-build that patches an existing emscripten install, or,
If we move the emscripten installation to pyodide-build, that's fine with me too. One asterisk - might be good to keep the vresion pin, if we go that way perhaps each pyodide-build version could pin an emscripten version? Or I suppose we could pass the version pin to pyodide-build.

ryanking13 · 2026-04-02T04:08:54Z

might be good to keep the vresion pin, if we go that way perhaps each pyodide-build version could pin an emscripten version? Or I suppose we could pass the version pin to pyodide-build.

The Emscripten version is defined by the Python version. pyodide-build will choose the right emscripten version (and Pyodide version) when the Python version is selected.

agriyakhetarpal · 2026-04-02T07:22:21Z

might be good to keep the vresion pin, if we go that way perhaps each pyodide-build version could pin an emscripten version? Or I suppose we could pass the version pin to pyodide-build.

The Emscripten version is defined by the Python version. pyodide-build will choose the right emscripten version (and Pyodide version) when the Python version is selected.

Yes, correct

N.B: We also have an install-and-patch-emscripten command thingy somewhere IIRC... this change is not that because that would be a bigger change to incorporate and should be discussed first; it would move the Emscripten installation from cibuildwheel's control to pyodide-build and thus would make changes to that scheme difficult (say, if pyodide-build were to break at a particular version for whatever reason, it would then start impacting all Pyodide builds for downstream users of cibuildwheel).

I would like to go this way directly if possible. This PR already exposes pyodide-build internals (e.g. path to the emscripten patches) to cibuildwheel, which can silently be broken when we make changes in pyodide-build. I don't want to introduce more of that into cibuildwheel.

Agreed re. the coupling. If there's special magic needed for pyodide builds, let's keep as much of that as we can in pyodide-build, so it can be used without cibuildwheel.

Okay, since both of you suggest that we should rely on pyodide-build's existing command-line machinery for the Emscripten installation, I'll update this PR to use it! We'll just have to ensure that pyodide-build doesn't start breaking :-) which it fortunately hasn't for a while now, so I'm all fine with it.

Co-authored-by: Joe Rickerby <joerick@mac.com>

agriyakhetarpal · 2026-04-02T14:25:16Z

@joerick, assuming that https://github.com/pypa/cibuildwheel/releases/tag/v3.4.1 was the upcoming release for which this PR was held, and that it occurred seven minutes after you added the label, this should be unblocked now – please let me know if I misunderstand! Thanks! :)

joerick · 2026-04-02T14:30:21Z

Yep you're right :)

ryanking13

LGTM. Plase make sure the pyodide-build version pinned in cibuildwheel supports install-emscripten command correctly.

ryanking13 · 2026-04-03T03:09:53Z

+    emcc_path = (
+        xbuildenv_cache_path / pyodide_version / "emsdk" / "upstream" / "emscripten" / "emcc"


Maybe we can make a config variable something like pyodide config get emscripten-path in the future so that this path is not hardcoded in cibuildwheel.

Maybe we can make a config variable something like pyodide config get emscripten-path in the future so that this path is not hardcoded in cibuildwheel.

Agreed. We already have one that points to the xbuildenv path, so why not!

Edit: working on this rn

agriyakhetarpal · 2026-04-03T04:06:59Z

LGTM. Plase make sure the pyodide-build version pinned in cibuildwheel supports install-emscripten command correctly.

Yes, it does – pyodide-build is at version 0.33.0 for both the Pyodide 0.27.7 and Pyodide 0.29.3 builds, and also thanks to our backwards compatibility setup through which we can install the older xbuildenvs.

cibuildwheel/cibuildwheel/resources/constraints-pyodide312.txt

Line 55 in 8d2b08b

pyodide-build==0.33.0

cibuildwheel/cibuildwheel/resources/constraints-pyodide313.txt

Line 55 in 8d2b08b

pyodide-build==0.33.0

agriyakhetarpal · 2026-04-03T05:22:35Z

I have opened pyodide/pyodide-build#321, and will make a release after merge.

ryanking13 · 2026-04-03T05:25:24Z

I have opened pyodide/pyodide-build#321, and will make a release after merge.

Thanks. Actually, you don't need to block this PR for pyodide-build change. My comment was a suggestion not a merge blocker.

agriyakhetarpal · 2026-04-03T05:35:50Z

Oh, sounds good! Thanks for the reviews, @ryanking13 and @joerick! I'll put together a follow-up PR later :)

agriyakhetarpal added 2 commits March 25, 2026 06:28

Apply Pyodide's patches to Emscripten

bbb6722

Quote the patch dir

45c1223

agriyakhetarpal requested review from hoodmane and ryanking13 as code owners March 25, 2026 01:20

agriyakhetarpal commented Mar 25, 2026

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ryanking13 reviewed Mar 25, 2026

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agriyakhetarpal mentioned this pull request Mar 30, 2026

Make install-emscripten command idempotent pyodide/pyodide-build#320

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agriyakhetarpal marked this pull request as draft April 2, 2026 07:28

agriyakhetarpal added 2 commits April 2, 2026 13:21

Rework: remove manual patches, use install-emscripten

9dc1940

Fix weird Emscripten version mismatch error due to symlink

c8d0766

agriyakhetarpal marked this pull request as ready for review April 2, 2026 09:50

agriyakhetarpal requested review from henryiii, joerick and ryanking13 April 2, 2026 09:50

joerick approved these changes Apr 2, 2026

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Comment thread cibuildwheel/platforms/pyodide.py Outdated

Remove comment that's no longer needed

2d7658d

Co-authored-by: Joe Rickerby <joerick@mac.com>

joerick added the Hold for future release This PR might be complete, but is scheduled to be merged in a future release. Don't merge yet. label Apr 2, 2026

joerick removed the Hold for future release This PR might be complete, but is scheduled to be merged in a future release. Don't merge yet. label Apr 2, 2026

ryanking13 approved these changes Apr 3, 2026

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agriyakhetarpal merged commit 8d75eb7 into pypa:main Apr 3, 2026
73 of 74 checks passed

agriyakhetarpal deleted the apply-pyodide-patches-to-emscripten branch April 3, 2026 05:36

This was referenced Apr 3, 2026

Expose emscripten_dir variable via config pyodide/pyodide-build#321

Merged

Pyodide updates: add 314.0 alpha, switch to pyemscripten platform tag (PEP 783), and remove hardcoded Emscripten location + update dependencies #2812

Open

		emcc_path = (
		xbuildenv_cache_path / pyodide_version / "emsdk" / "upstream" / "emscripten" / "emcc"

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