Ingest of scanpy cannot work because of problems in numpy in colab platform

[HelloWorldLTY]

Sorry to disturb, but it seems that the ingest method in scanpy meets some problems caused by pynndescent and numba. Here are the details:
KeyError Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/numba/core/caching.py in save(self, key, data)
486 # If key already exists, we will overwrite the file
--> 487 data_name = overloads[key]
488 except KeyError:

KeyError: ((array(int32, 1d, C), array(int32, 1d, C), array(float32, 1d, C), array(float32, 2d, C), type(CPUDispatcher(<function squared_euclidean at 0x7fdefdb13830>)), array(int64, 1d, C), float64), ('x86_64-unknown-linux-gnu', 'broadwell', '+64bit,+adx,+aes,+avx,+avx2,-avx512bf16,-avx512bitalg,-avx512bw,-avx512cd,-avx512dq,-avx512er,-avx512f,-avx512ifma,-avx512pf,-avx512vbmi,-avx512vbmi2,-avx512vl,-avx512vnni,-avx512vpopcntdq,+bmi,+bmi2,-cldemote,-clflushopt,-clwb,-clzero,+cmov,+cx16,+cx8,-enqcmd,+f16c,+fma,-fma4,+fsgsbase,+fxsr,-gfni,+invpcid,-lwp,+lzcnt,+mmx,+movbe,-movdir64b,-movdiri,-mwaitx,+pclmul,-pconfig,-pku,+popcnt,-prefetchwt1,+prfchw,-ptwrite,-rdpid,+rdrnd,+rdseed,+rtm,+sahf,-sgx,-sha,-shstk,+sse,+sse2,+sse3,+sse4.1,+sse4.2,-sse4a,+ssse3,-tbm,-vaes,-vpclmulqdq,-waitpkg,-wbnoinvd,-xop,+xsave,-xsavec,+xsaveopt,-xsaves'), ('308c49885ad3c35a475c360e21af1359caa88c78eb495fa0f5e8c6676ae5019e', 'e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'))

During handling of the above exception, another exception occurred:

TypeError Traceback (most recent call last)
13 frames
in ()
----> 1 sc.tl.ingest(adata, adata_ref, obs='louvain') #ingest

/usr/local/lib/python3.7/dist-packages/scanpy/tools/_ingest.py in ingest(adata, adata_ref, obs, embedding_method, labeling_method, neighbors_key, inplace, **kwargs)
131
132 if obs is not None:
--> 133 ing.neighbors(**kwargs)
134 for i, col in enumerate(obs):
135 ing.map_labels(col, labeling_method[i])

/usr/local/lib/python3.7/dist-packages/scanpy/tools/_ingest.py in neighbors(self, k, queue_size, epsilon, random_state)
469 self._nnd_idx.search_rng_state = rng_state
470
--> 471 self._indices, self._distances = self._nnd_idx.query(test, k, epsilon)
472
473 else:

/usr/local/lib/python3.7/dist-packages/pynndescent/pynndescent_.py in query(self, query_data, k, epsilon)
1564 """
1565 if not hasattr(self, "_search_graph"):
-> 1566 self._init_search_graph()
1567
1568 if not self._is_sparse:

/usr/local/lib/python3.7/dist-packages/pynndescent/pynndescent_.py in _init_search_graph(self)
1061 self._distance_func,
1062 self.rng_state,
-> 1063 self.diversify_prob,
1064 )
1065 reverse_graph.eliminate_zeros()

/usr/local/lib/python3.7/dist-packages/numba/core/dispatcher.py in _compile_for_args(self, *args, **kws)
432 e.patch_message('\n'.join((str(e).rstrip(), help_msg)))
433 # ignore the FULL_TRACEBACKS config, this needs reporting!
--> 434 raise e
435
436 def inspect_llvm(self, signature=None):

/usr/local/lib/python3.7/dist-packages/numba/core/dispatcher.py in _compile_for_args(self, *args, **kws)
365 argtypes.append(self.typeof_pyval(a))
366 try:
--> 367 return self.compile(tuple(argtypes))
368 except errors.ForceLiteralArg as e:
369 # Received request for compiler re-entry with the list of arguments

/usr/local/lib/python3.7/dist-packages/numba/core/compiler_lock.py in _acquire_compile_lock(*args, **kwargs)
30 def _acquire_compile_lock(*args, **kwargs):
31 with self:
---> 32 return func(*args, **kwargs)
33 return _acquire_compile_lock
34

/usr/local/lib/python3.7/dist-packages/numba/core/dispatcher.py in compile(self, sig)
823 raise e.bind_fold_arguments(folded)
824 self.add_overload(cres)
--> 825 self._cache.save_overload(sig, cres)
826 return cres.entry_point
827

/usr/local/lib/python3.7/dist-packages/numba/core/caching.py in save_overload(self, sig, data)
669 """
670 with self._guard_against_spurious_io_errors():
--> 671 self._save_overload(sig, data)
672
673 def _save_overload(self, sig, data):

/usr/local/lib/python3.7/dist-packages/numba/core/caching.py in _save_overload(self, sig, data)
679 key = self._index_key(sig, _get_codegen(data))
680 data = self._impl.reduce(data)
--> 681 self._cache_file.save(key, data)
682
683 @contextlib.contextmanager

/usr/local/lib/python3.7/dist-packages/numba/core/caching.py in save(self, key, data)
494 break
495 overloads[key] = data_name
--> 496 self._save_index(overloads)
497 self._save_data(data_name, data)
498

/usr/local/lib/python3.7/dist-packages/numba/core/caching.py in _save_index(self, overloads)
540 def _save_index(self, overloads):
541 data = self._source_stamp, overloads
--> 542 data = self._dump(data)
543 with self._open_for_write(self._index_path) as f:
544 pickle.dump(self._version, f, protocol=-1)

/usr/local/lib/python3.7/dist-packages/numba/core/caching.py in _dump(self, obj)
568
569 def _dump(self, obj):
--> 570 return pickle.dumps(obj, protocol=-1)
571
572 @contextlib.contextmanager

TypeError: can't pickle weakref objects

How to solve this problem? Thanks.
The code comes from :https://scanpy-tutorials.readthedocs.io/en/latest/integrating-data-using-ingest.html

[HelloWorldLTY]

For more details, please take a look at:
lmcinnes/pynndescent#133

[rkern]

It doesn't look like this has anything to do with numpy. Did you mean to post this to the numba repo?