Add rdkit package

[fxcoudert]

First try for now, it's a complicated process with Boost and Cmake

[fxcoudert]

OK, I have reached the stage where boost-python is successfully installed. I can see:

/home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_python313.a                                                                       
/home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_numpy313.a                                                                        
/home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_container.a                                                                       
/home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_graph.a                                                                           

🎉

Now, to get rdkit to work…

[fxcoudert]

Next issue was: boostorg/boost_install#82
Fixed by passing the right argument to boost build.

[fxcoudert]

Then, I encountered this rdkit issue: rdkit/rdkit#9150
Fixed by hacking the cmake file.

Now I get a problem with the INCHI-API dep, which isn't set up to build static libraries:

2026-03-04T15:43:16.1265127Z [ 36%] Building CXX object                                                      
2026-03-04T15:43:16.1265342Z External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o                    
2026-03-04T15:43:16.1265529Z [ 36%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so                 
2026-03-04T15:43:16.1265736Z em++: warning: -sSIDE_MODULE + pthreads is experimental [-Wexperimental]        
2026-03-04T15:43:16.1265969Z em++: warning: ignoring unsupported linker flag: `--allow-shlib-undefined`      
2026-03-04T15:43:16.1266112Z [-Wlinkflags]                                                                   
2026-03-04T15:43:16.1266319Z em++: warning: ignoring unsupported linker flag: `-rpath-link` [-Wlinkflags]    
2026-03-04T15:43:16.1266525Z em++: warning: ignoring unsupported linker flag: `--allow-shlib-undefined`      
2026-03-04T15:43:16.1266784Z [-Wlinkflags]                                                                   
2026-03-04T15:43:16.1266984Z em++: warning: ignoring unsupported linker flag: `-rpath-link` [-Wlinkflags]    
2026-03-04T15:43:16.1267177Z cache:INFO: generating system asset:                                            
2026-03-04T15:43:16.1267399Z sysroot/lib/wasm32-emscripten/pic/crtbegin.o... (this will be cached in         
2026-03-04T15:43:16.1267615Z "/home/runner/work/pyodide-recipes/pyodide-recipes/emsdk/upstream/emscripten/cac
2026-03-04T15:43:16.1267830Z he/sysroot/lib/wasm32-emscripten/pic/crtbegin.o" for subsequent builds)         
2026-03-04T15:43:16.1268020Z system_libs:INFO: compiled 1 inputs in 0.16s                                    
2026-03-04T15:43:16.1268173Z cache:INFO:  - ok                                                               
2026-03-04T15:43:16.1268339Z wasm-ld: error: cannot open                                                     
2026-03-04T15:43:16.1268572Z /home/runner/miniconda3/envs/pyodide-env/shared/python_compiler_compat: Is a    
2026-03-04T15:43:16.1268710Z directory                                                                       
2026-03-04T15:43:16.1268849Z em++: error:                                                                    
2026-03-04T15:43:16.1269067Z '/home/runner/work/pyodide-recipes/pyodide-recipes/emsdk/upstream/bin/wasm-ld -o
2026-03-04T15:43:16.1269243Z ../../../rdkit/Chem/rdinchi.so                                                  
2026-03-04T15:43:16.1269459Z /home/runner/miniconda3/envs/pyodide-env/shared/python_compiler_compat -rpath   
2026-03-04T15:43:16.1269661Z /home/runner/miniconda3/envs/pyodide-env/lib                                    
2026-03-04T15:43:16.1269867Z -L/home/runner/miniconda3/envs/pyodide-env/lib -rpath                           
2026-03-04T15:43:16.1270067Z /home/runner/miniconda3/envs/pyodide-env/lib                                    
2026-03-04T15:43:16.1270348Z -L/home/runner/miniconda3/envs/pyodide-env/lib                                  
2026-03-04T15:43:16.1279925Z -L/home/runner/.cache/.pyodide-xbuildenv-0.31.2.dev3+gb82593b9c/https_github_com
2026-03-04T15:43:16.1280231Z _pyodide_pyodide-build-environment-nightly_releases_download_20260201_xbuildenv_
2026-03-04T15:43:16.1280463Z tar_bz2/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/lib/              
2026-03-04T15:43:16.1280696Z -L/home/runner/.cache/.pyodide-xbuildenv-0.31.2.dev3+gb82593b9c/https_github_com
2026-03-04T15:43:16.1280930Z _pyodide_pyodide-build-environment-nightly_releases_download_20260201_xbuildenv_
2026-03-04T15:43:16.1281150Z tar_bz2/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/lib/              
2026-03-04T15:43:16.1281365Z -L/home/runner/.cache/.pyodide-xbuildenv-0.31.2.dev3+gb82593b9c/https_github_com
2026-03-04T15:43:16.1281604Z _pyodide_pyodide-build-environment-nightly_releases_download_20260201_xbuildenv_
2026-03-04T15:43:16.1281818Z tar_bz2/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/lib/              
2026-03-04T15:43:16.1282042Z -L/home/runner/.cache/.pyodide-xbuildenv-0.31.2.dev3+gb82593b9c/https_github_com
2026-03-04T15:43:16.1282395Z _pyodide_pyodide-build-environment-nightly_releases_download_20260201_xbuildenv_
2026-03-04T15:43:16.1282607Z tar_bz2/xbuildenv/pyodide-root/cpython/installs/python-3.13.2/lib/              
2026-03-04T15:43:16.1282822Z CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.a          
2026-03-04T15:43:16.1283016Z ../../../lib/libRDKitRDBoost.a ../../../lib/libRDKitInchi.a                     
2026-03-04T15:43:16.1283206Z ../../../lib/libRDKitDepictor.a ../../../lib/libRDKitcoordgen.a                 
2026-03-04T15:43:16.1283405Z ../../../lib/libRDKitMolAlign.a ../../../lib/libRDKitMolTransforms.a            
2026-03-04T15:43:16.1283600Z ../../../lib/libRDKitEigenSolvers.a ../../../lib/libRDKitAlignment.a            
2026-03-04T15:43:16.1283807Z ../../../lib/libRDKitSubstructMatch.a ../../../lib/libRDKitGenericGroups.a      
2026-03-04T15:43:16.1284169Z ../../../lib/libRDKitSmilesParse.a ../../../lib/libRDKitGraphMol.a              
2026-03-04T15:43:16.1284377Z ../../../lib/libRDKitRDGeometryLib.a ../../../lib/libRDKitDataStructs.a         
2026-03-04T15:43:16.1284613Z ../../../lib/libRDKitRingDecomposerLib.a                                        
2026-03-04T15:43:16.1284840Z /home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_nu
2026-03-04T15:43:16.1284972Z mpy313.a                                                                        
2026-03-04T15:43:16.1285192Z /home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_py
2026-03-04T15:43:16.1285323Z thon313.a                                                                       
2026-03-04T15:43:16.1285557Z /home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_co
2026-03-04T15:43:16.1285696Z ntainer.a                                                                       
2026-03-04T15:43:16.1285918Z /home/runner/work/pyodide-recipes/pyodide-recipes/packages/.libs/lib/libboost_gr
2026-03-04T15:43:16.1286102Z aph.a ../../../lib/libRDKitRDGeneral.a                                          
2026-03-04T15:43:16.1286321Z -L/home/runner/work/pyodide-recipes/pyodide-recipes/emsdk/upstream/emscripten/ca
2026-03-04T15:43:16.1286521Z che/sysroot/lib/wasm32-emscripten/pic                                           
2026-03-04T15:43:16.1286733Z -L/home/runner/work/pyodide-recipes/pyodide-recipes/emsdk/upstream/emscripten/sr
2026-03-04T15:43:16.1286861Z c/lib                                                                           
2026-03-04T15:43:16.1287085Z /home/runner/work/pyodide-recipes/pyodide-recipes/emsdk/upstream/emscripten/cach
2026-03-04T15:43:16.1287297Z e/sysroot/lib/wasm32-emscripten/pic/crtbegin.o -mllvm                           
2026-03-04T15:43:16.1287532Z -combiner-global-alias-analysis=false -mllvm -wasm-enable-sjlj -mllvm           
2026-03-04T15:43:16.1287754Z -wasm-use-legacy-eh -mllvm -disable-lsr -mllvm -wasm-enable-eh -mllvm           
2026-03-04T15:43:16.1288088Z -wasm-use-legacy-eh -mllvm -exception-model=wasm --import-memory --shared-memory
2026-03-04T15:43:16.1288300Z --strip-debug --export=__wasm_call_ctors --export=_emscripten_tls_init          
2026-03-04T15:43:16.1288507Z --export-if-defined=__start_em_asm --export-if-defined=__stop_em_asm            
2026-03-04T15:43:16.1288718Z --export-if-defined=__start_em_lib_deps --export-if-defined=__stop_em_lib_deps  
2026-03-04T15:43:16.1288913Z --export-if-defined=__start_em_js --export-if-defined=__stop_em_js              
2026-03-04T15:43:16.1289118Z --export-if-defined=main --export-if-defined=__main_argc_argv                   
2026-03-04T15:43:16.1289322Z --export-if-defined=__wasm_apply_data_relocs --experimental-pic                 
2026-03-04T15:43:16.1289544Z --unresolved-symbols=import-dynamic -shared --no-export-dynamic' failed         
2026-03-04T15:43:16.1289680Z (returned 1)                                                                    
2026-03-04T15:43:16.1289893Z make[2]: *** [External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make:123:    
2026-03-04T15:43:16.1290067Z rdkit/Chem/rdinchi.so] Error 1                                                  

Turning that off, the same problem occurs with Avalon:

[ 35%] Linking CXX shared module ../../../rdkit/Avalon/pyAvalonTools.so

Then freesasa:

[ 34%] Linking CXX shared module ../../../rdkit/Chem/rdFreeSASA.so

Then coordgen:

[ 32%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so              

Then YAeHMOP:

[ 37%] Building CXX object                                                      
External/YAeHMOP/CMakeFiles/testEHTLib1.dir/test1.cpp.o                         
[ 37%] Linking CXX executable testEHTLib1.js                                    

[fxcoudert]

Cleverer approach in #538