RDkit pyodide support added

[stefdoerr]

Added the rdkit package with tests. I tested it a decent bit and it seems to work fine.
For transparency, this is 99% 🤖-generated code with Claude, I mostly intervened to keep it in line with our requirements and asking it to simplify things.

These are probably the only missing features compared to the full RDKit PyPI build:

● ┌──────────────────────────┬─────────────────────────────────────────────────────────┬──────────────────────────────────────┐
  │         Feature          │                      What it does                       │        Why missing in Pyodide        │
  ├──────────────────────────┼─────────────────────────────────────────────────────────┼──────────────────────────────────────┤
  │ RDK_BUILD_THREADSAFE_SSS │ Thread-safe substructure searching                      │ WASM lacks pthreads in most browsers │
  ├──────────────────────────┼─────────────────────────────────────────────────────────┼──────────────────────────────────────┤
  │ RDK_OPTIMIZE_POPCNT      │ SSE4.2 popcount CPU instruction for faster fingerprints │ x86-specific, not available in WASM  │
  ├──────────────────────────┼─────────────────────────────────────────────────────────┼──────────────────────────────────────┤
  │ RDK_USE_BOOST_STACKTRACE │ Verbose stack traces on invariant violations            │ Linux-only, not applicable to WASM   │
  ├──────────────────────────┼─────────────────────────────────────────────────────────┼──────────────────────────────────────┤
  │ RDK_TEST_MULTITHREADED   │ Run multithreaded tests                                 │ No threading in WASM                 │
  └──────────────────────────┴─────────────────────────────────────────────────────────┴──────────────────────────────────────┘

[stefdoerr]

This is interesting. It works on a Chrome browser which we tested yet fails here in the Chrome tests (Firefox tests and node passed). The error suggests that the core.so file at 22MB is too large to be loaded synchronously on Chrome so Claude now converted it to a dynlib so it can be loaded by pyodide asynchronously. To do that it had to split rdkit into rdkit and librdkit packages. Let's see if it's all in its imagination by running the tests here :P

[80](https://github.com/pyodide/pyodide-recipes/actions/runs/23238648273/job/67557269203#step:11:2881)
FAILED packages/rdkit/test_rdkit.py::test_smiles_parsing[chrome] - pyodide.ffi.JsException: RangeError: WebAssembly.Compile is disallowed on the main thread, if the buffer size is larger than 8MB. Use WebAssembly.compile, compile on a worker thread, or use the flag `--enable-features=WebAssemblyUnlimitedSyncCompilation`.[80](https://github.com/pyodide/pyodide-recipes/actions/runs/23238648273/job/67557269203#step:11:2881)
FAILED packages/rdkit/test_rdkit.py::test_smiles_parsing[chrome] - pyodide.ffi.JsException: RangeError: WebAssembly.Compile is disallowed on the main thread, if the buffer size is larger than 8MB. Use WebAssembly.compile, compile on a worker thread, or use the flag `--enable-features=WebAssemblyUnlimitedSyncCompilation`.

[stefdoerr]

Works now! I'll try one more thing to simplify the linking

[github-actions]

Package Build Results

Total packages built: 24
Total build time: 0:55:20

Package Build Times (click to expand)

Package	Build Time
librdkit	49m 41s
libboost-python	4m 39s
numpy	3m 1s
rdkit	39s
libzlib	19s
regex	11s
pydoc_data	4s
MarkupSafe	3s
atomicwrites	2s
micropip	1s
exceptiongroup	1s
more-itertools	1s
pytest-asyncio	1s
Jinja2	1s
attrs	1s
setuptools	1s
py	1s
pytz	1s
tblib	1s
pytest	1s
iniconfig	0s
pyparsing	0s
pluggy	0s
six	0s

Longest build: librdkit (49m 41s)
Packages built in more than 10 minutes: 1

[stefdoerr]

Ok, it's good to go now

[ryanking13]

@stefdoerr

Thanks for working on this! The PR looks good overall, but what I am concerned is the librdkit takes around 50mins to build. Regarding that this repository rebuild every package for each commit that goes to the main branch (at least for now), adding 50+ minutes of build time in our CI is a huge overhead.

Regarding you and @fxcoudert were discussing this in rdkit repository (rdkit/rdkit#7827), would you be possible to upstream this change to rdkit itself; i.e. building WASM version in rdkit CI, and only add the built wheel here?

For instance, we are doing the same thing for duckdb. It is built in a separate repository so that we don't need to rebuild it everytime.