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scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Bug on scanpy, sc.pp.neighbors function #2160

Open RutBo opened 2 years ago

RutBo commented 2 years ago

Hi, I am working with a big dataset and I run into a problem when computing the neigbours. Find below an small example:

Minimal code sample


 import scanpy
import numpy
> 
tab = scvi.data.read_csv("C:/Users/RUTBO/AML-029-01-1E.gene.expression.matrix.tsv", delimiter='\t', first_column_names=True)

sc.tl.pca(tab, svd_solver='arpack')
sc.pp.neighbors(tab, n_neighbors=10, n_pcs=40)
traceback ```pytb > The error I get: > --------------------------------------------------------------------------- > File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\errors.py", line 823, in new_error_context yield File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 293, in lower_block self.lower_inst(inst) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 438, in lower_inst val = self.lower_assign(ty, inst) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 624, in lower_assign return self.lower_expr(ty, value) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 1159, in lower_expr res = self.lower_call(resty, expr) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 889, in lower_call res = self._lower_call_normal(fnty, expr, signature) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 1130, in _lower_call_normal res = impl(self.builder, argvals, self.loc) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\base.py", line 1201, in __call__ res = self._imp(self._context, builder, self._sig, args, loc=loc) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\base.py", line 1231, in wrapper return fn(*args, **kwargs) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\cpython\rangeobj.py", line 40, in range1_impl state.stop = stop File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\cgutils.py", line 164, in __setattr__ self[self._datamodel.get_field_position(field)] = value File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\cgutils.py", line 188, in __setitem__ raise TypeError("Invalid store of {value.type} to " TypeError: Invalid store of i64 to i32 in (trying to write member #1) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\RUTBO\PycharmProjects\pvalue\single cell analysis.py", line 44, in sc.pp.neighbors(tab, n_neighbors=10, n_pcs=40) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\neighbors\__init__.py", line 139, in neighbors neighbors.compute_neighbors( File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\neighbors\__init__.py", line 808, in compute_neighbors self._distances, self._connectivities = _compute_connectivities_umap( File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\scanpy\neighbors\__init__.py", line 387, in _compute_connectivities_umap from umap.umap_ import fuzzy_simplicial_set File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\__init__.py", line 2, in from .umap_ import UMAP File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\umap_.py", line 41, in from umap.layouts import ( File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\layouts.py", line 39, in def rdist(x, y): File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\decorators.py", line 219, in wrapper disp.compile(sig) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 965, in compile cres = self._compiler.compile(args, return_type) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 125, in compile status, retval = self._compile_cached(args, return_type) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 139, in _compile_cached retval = self._compile_core(args, return_type) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\dispatcher.py", line 152, in _compile_core cres = compiler.compile_extra(self.targetdescr.typing_context, File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 693, in compile_extra return pipeline.compile_extra(func) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 429, in compile_extra return self._compile_bytecode() File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 497, in _compile_bytecode return self._compile_core() File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 476, in _compile_core raise e File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler.py", line 463, in _compile_core pm.run(self.state) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 353, in run raise patched_exception File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 341, in run self._runPass(idx, pass_inst, state) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_lock.py", line 35, in _acquire_compile_lock return func(*args, **kwargs) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 296, in _runPass mutated |= check(pss.run_pass, internal_state) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\compiler_machinery.py", line 269, in check mangled = func(compiler_state) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\typed_passes.py", line 394, in run_pass lower.lower() File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 196, in lower self.lower_normal_function(self.fndesc) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 250, in lower_normal_function entry_block_tail = self.lower_function_body() File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 279, in lower_function_body self.lower_block(block) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\lowering.py", line 293, in lower_block self.lower_inst(inst) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\contextlib.py", line 135, in __exit__ self.gen.throw(type, value, traceback) File "C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\site-packages\numba\core\errors.py", line 837, in new_error_context raise newerr.with_traceback(tb) numba.core.errors.LoweringError: Failed in nopython mode pipeline (step: native lowering) Invalid store of i64 to i32 in (trying to write member #1) File "..\..\AppData\Local\Programs\Python\Python39\lib\umap\layouts.py", line 53: def rdist(x, y): dim = x.shape[0] for i in range(dim): ^ During: lowering "$20call_function.7 = call $16load_global.5(dim, func=$16load_global.5, args=[Var(dim, layouts.py:52)], kws=(), vararg=None, target=None)" at C:\Users\RUTBO\AppData\Local\Programs\Python\Python39\lib\umap\layouts.py (53) ```

I am running scanpy using python v3.9 with numba v0.55.

ivirshup commented 2 years ago

Are you able to run something like:

from umap import UMAP

embedding = UMAP()
embedding.fit_transform(adata.obsm["X_pca"])

I think this may be largely upstream and due to windows issues. Also is there any chance you are using a 32 bit system?

xiangrong7 commented 2 years ago

Hello,I am having the same problem. When I run this:

from umap import UMAP

It occurs this error.

TypeError                                 Traceback (most recent call last)
File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\errors.py:823, in new_error_context(fmt_, *args, **kwargs)
    [822](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=821) try:
--> [823](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=822)     yield
    [824](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=823) except NumbaError as e:

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:293, in BaseLower.lower_block(self, block)
    [291](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=290)     with new_error_context('lowering "{inst}" at {loc}', inst=inst,
    [292](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=291)                            loc=self.loc, errcls_=defaulterrcls):
--> [293](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=292)         self.lower_inst(inst)
    [294](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=293) self.post_block(block)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:438, in Lower.lower_inst(self, inst)
    [437](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=436) ty = self.typeof(inst.target.name)
--> [438](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=437) val = self.lower_assign(ty, inst)
    [439](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=438) argidx = None

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:624, in Lower.lower_assign(self, ty, inst)
    [623](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=622) elif isinstance(value, ir.Expr):
--> [624](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=623)     return self.lower_expr(ty, value)
    [626](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=625) elif isinstance(value, ir.Var):

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:1159, in Lower.lower_expr(self, resty, expr)
   [1158](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1157) elif expr.op == 'call':
-> [1159](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1158)     res = self.lower_call(resty, expr)
   [1160](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1159)     return res

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:889, in Lower.lower_call(self, resty, expr)
    [888](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=887) else:
--> [889](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=888)     res = self._lower_call_normal(fnty, expr, signature)
    [891](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=890) # If lowering the call returned None, interpret that as returning dummy
    [892](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=891) # value if the return type of the function is void, otherwise there is
    [893](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=892) # a problem

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:1130, in Lower._lower_call_normal(self, fnty, expr, signature)
   [1128](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1127)     argvals = [the_self] + list(argvals)
-> [1130](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1129) res = impl(self.builder, argvals, self.loc)
   [1131](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=1130) return res

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\base.py:1201, in _wrap_impl.__call__(self, builder, args, loc)
   [1200](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1199) def __call__(self, builder, args, loc=None):
-> [1201](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1200)     res = self._imp(self._context, builder, self._sig, args, loc=loc)
   [1202](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1201)     self._context.add_linking_libs(getattr(self, 'libs', ()))

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\base.py:1231, in _wrap_missing_loc.__call__.<locals>.wrapper(*args, **kwargs)
   [1230](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1229) kwargs.pop('loc')     # drop unused loc
-> [1231](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/base.py?line=1230) return fn(*args, **kwargs)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\cpython\rangeobj.py:40, in make_range_impl.<locals>.range1_impl(context, builder, sig, args)
     [39](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/cpython/rangeobj.py?line=38) state.start = context.get_constant(int_type, 0)
---> [40](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/cpython/rangeobj.py?line=39) state.stop = stop
     [41](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/cpython/rangeobj.py?line=40) state.step = context.get_constant(int_type, 1)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\cgutils.py:164, in _StructProxy.__setattr__(self, field, value)
    [163](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=162)     return super(_StructProxy, self).__setattr__(field, value)
--> [164](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=163) self[self._datamodel.get_field_position(field)] = value

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\cgutils.py:188, in _StructProxy.__setitem__(self, index, value)
    [187](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=186)     else:
--> [188](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=187)         raise TypeError("Invalid store of {value.type} to "
    [189](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=188)                         "{ptr.type.pointee} in "
    [190](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=189)                         "{self._datamodel} "
    [191](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=190)                         "(trying to write member #{index})"
    [192](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=191)                         .format(value=value, ptr=ptr, self=self,
    [193](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=192)                                 index=index))
    [194](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/cgutils.py?line=193) self._builder.store(value, ptr)

TypeError: Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x00000242239BD700> (trying to write member #1)

During handling of the above exception, another exception occurred:

LoweringError                             Traceback (most recent call last)
e:\Drosophila\ST\04.yao\E8-10_b_analysis\E8-10_b_analysis\8_cellbin_clustering\cellbin_scsq.ipynb Cell 10' in <cell line: 1>()
----> [1](vscode-notebook-cell:/e%3A/Drosophila/ST/04.yao/E8-10_b_analysis/E8-10_b_analysis/8_cellbin_clustering/cellbin_scsq.ipynb#ch0000016?line=0) from umap import UMAP

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\__init__.py:2, in <module>
      [1](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=0) from warnings import warn, catch_warnings, simplefilter
----> [2](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=1) from .umap_ import UMAP
      [4](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=3) try:
      [5](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/__init__.py?line=4)     with catch_warnings():

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\umap_.py:41, in <module>
     [34](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=33) from umap.utils import (
     [35](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=34)     submatrix,
     [36](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=35)     ts,
     [37](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=36)     csr_unique,
     [38](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=37)     fast_knn_indices,
     [39](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=38) )
     [40](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=39) from umap.spectral import spectral_layout
---> [41](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=40) from umap.layouts import (
     [42](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=41)     optimize_layout_euclidean,
     [43](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=42)     optimize_layout_generic,
     [44](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=43)     optimize_layout_inverse,
     [45](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=44) )
     [47](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=46) from pynndescent import NNDescent
     [48](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/umap_.py?line=47) from pynndescent.distances import named_distances as pynn_named_distances

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\layouts.py:39, in <module>
     [25](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=24)     else:
     [26](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=25)         return val
     [29](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=28) @numba.njit(
     [30](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=29)     "f4(f4[::1],f4[::1])",
     [31](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=30)     fastmath=True,
     [32](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=31)     cache=True,
     [33](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=32)     locals={
     [34](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=33)         "result": numba.types.float32,
     [35](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=34)         "diff": numba.types.float32,
     [36](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=35)         "dim": numba.types.int32,
     [37](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=36)     },
     [38](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=37) )
---> [39](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=38) def rdist(x, y):
     [40](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=39)     """Reduced Euclidean distance.
     [41](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=40) 
     [42](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=41)     Parameters
   (...)
     [49](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=48)     The squared euclidean distance between x and y
     [50](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=49)     """
     [51](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/umap/layouts.py?line=50)     result = 0.0

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\decorators.py:219, in _jit.<locals>.wrapper(func)
    [217](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=216)     with typeinfer.register_dispatcher(disp):
    [218](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=217)         for sig in sigs:
--> [219](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=218)             disp.compile(sig)
    [220](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=219)         disp.disable_compile()
    [221](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/decorators.py?line=220) return disp

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:965, in Dispatcher.compile(self, sig)
    [963](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=962) with ev.trigger_event("numba:compile", data=ev_details):
    [964](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=963)     try:
--> [965](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=964)         cres = self._compiler.compile(args, return_type)
    [966](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=965)     except errors.ForceLiteralArg as e:
    [967](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=966)         def folded(args, kws):

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:125, in _FunctionCompiler.compile(self, args, return_type)
    [124](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=123) def compile(self, args, return_type):
--> [125](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=124)     status, retval = self._compile_cached(args, return_type)
    [126](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=125)     if status:
    [127](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=126)         return retval

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:139, in _FunctionCompiler._compile_cached(self, args, return_type)
    [136](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=135)     pass
    [138](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=137) try:
--> [139](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=138)     retval = self._compile_core(args, return_type)
    [140](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=139) except errors.TypingError as e:
    [141](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=140)     self._failed_cache[key] = e

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\dispatcher.py:152, in _FunctionCompiler._compile_core(self, args, return_type)
    [149](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=148) flags = self._customize_flags(flags)
    [151](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=150) impl = self._get_implementation(args, {})
--> [152](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=151) cres = compiler.compile_extra(self.targetdescr.typing_context,
    [153](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=152)                               self.targetdescr.target_context,
    [154](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=153)                               impl,
    [155](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=154)                               args=args, return_type=return_type,
    [156](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=155)                               flags=flags, locals=self.locals,
    [157](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=156)                               pipeline_class=self.pipeline_class)
    [158](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=157) # Check typing error if object mode is used
    [159](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/dispatcher.py?line=158) if cres.typing_error is not None and not flags.enable_pyobject:

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:693, in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class)
    [669](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=668) """Compiler entry point
    [670](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=669) 
    [671](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=670) Parameter
   (...)
    [689](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=688)     compiler pipeline
    [690](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=689) """
    [691](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=690) pipeline = pipeline_class(typingctx, targetctx, library,
    [692](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=691)                           args, return_type, flags, locals)
--> [693](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=692) return pipeline.compile_extra(func)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:429, in CompilerBase.compile_extra(self, func)
    [427](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=426) self.state.lifted = ()
    [428](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=427) self.state.lifted_from = None
--> [429](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=428) return self._compile_bytecode()

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:497, in CompilerBase._compile_bytecode(self)
    [493](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=492) """
    [494](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=493) Populate and run pipeline for bytecode input
    [495](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=494) """
    [496](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=495) assert self.state.func_ir is None
--> [497](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=496) return self._compile_core()

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:476, in CompilerBase._compile_core(self)
    [474](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=473)         self.state.status.fail_reason = e
    [475](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=474)         if is_final_pipeline:
--> [476](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=475)             raise e
    [477](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=476) else:
    [478](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=477)     raise CompilerError("All available pipelines exhausted")

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler.py:463, in CompilerBase._compile_core(self)
    [461](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=460) res = None
    [462](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=461) try:
--> [463](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=462)     pm.run(self.state)
    [464](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=463)     if self.state.cr is not None:
    [465](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler.py?line=464)         break

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:353, in PassManager.run(self, state)
    [350](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=349) msg = "Failed in %s mode pipeline (step: %s)" % \
    [351](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=350)     (self.pipeline_name, pass_desc)
    [352](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=351) patched_exception = self._patch_error(msg, e)
--> [353](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=352) raise patched_exception

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:341, in PassManager.run(self, state)
    [339](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=338) pass_inst = _pass_registry.get(pss).pass_inst
    [340](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=339) if isinstance(pass_inst, CompilerPass):
--> [341](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=340)     self._runPass(idx, pass_inst, state)
    [342](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=341) else:
    [343](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=342)     raise BaseException("Legacy pass in use")

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_lock.py:35, in _CompilerLock.__call__.<locals>._acquire_compile_lock(*args, **kwargs)
     [32](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=31) @functools.wraps(func)
     [33](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=32) def _acquire_compile_lock(*args, **kwargs):
     [34](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=33)     with self:
---> [35](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_lock.py?line=34)         return func(*args, **kwargs)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:296, in PassManager._runPass(self, index, pss, internal_state)
    [294](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=293)     mutated |= check(pss.run_initialization, internal_state)
    [295](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=294) with SimpleTimer() as pass_time:
--> [296](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=295)     mutated |= check(pss.run_pass, internal_state)
    [297](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=296) with SimpleTimer() as finalize_time:
    [298](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=297)     mutated |= check(pss.run_finalizer, internal_state)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\compiler_machinery.py:269, in PassManager._runPass.<locals>.check(func, compiler_state)
    [268](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=267) def check(func, compiler_state):
--> [269](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=268)     mangled = func(compiler_state)
    [270](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=269)     if mangled not in (True, False):
    [271](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=270)         msg = ("CompilerPass implementations should return True/False. "
    [272](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/compiler_machinery.py?line=271)                "CompilerPass with name '%s' did not.")

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\typed_passes.py:394, in NativeLowering.run_pass(self, state)
    [391](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=390) with targetctx.push_code_library(library):
    [392](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=391)     lower = lowering.Lower(targetctx, library, fndesc, interp,
    [393](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=392)                            metadata=metadata)
--> [394](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=393)     lower.lower()
    [395](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=394)     if not flags.no_cpython_wrapper:
    [396](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/typed_passes.py?line=395)         lower.create_cpython_wrapper(flags.release_gil)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:196, in BaseLower.lower(self)
    [194](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=193) if self.generator_info is None:
    [195](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=194)     self.genlower = None
--> [196](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=195)     self.lower_normal_function(self.fndesc)
    [197](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=196) else:
    [198](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=197)     self.genlower = self.GeneratorLower(self)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:250, in BaseLower.lower_normal_function(self, fndesc)
    [248](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=247) # Init argument values
    [249](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=248) self.extract_function_arguments()
--> [250](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=249) entry_block_tail = self.lower_function_body()
    [252](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=251) # Close tail of entry block, do not emit debug metadata else the
    [253](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=252) # unconditional jump gets associated with the metadata from the function
    [254](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=253) # body end.
    [255](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=254) with debuginfo.suspend_emission(self.builder):

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:279, in BaseLower.lower_function_body(self)
    [277](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=276)     bb = self.blkmap[offset]
    [278](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=277)     self.builder.position_at_end(bb)
--> [279](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=278)     self.lower_block(block)
    [280](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=279) self.post_lower()
    [281](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=280) return entry_block_tail

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\lowering.py:293, in BaseLower.lower_block(self, block)
    [290](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=289)     defaulterrcls = partial(LoweringError, loc=self.loc)
    [291](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=290)     with new_error_context('lowering "{inst}" at {loc}', inst=inst,
    [292](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=291)                            loc=self.loc, errcls_=defaulterrcls):
--> [293](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=292)         self.lower_inst(inst)
    [294](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/lowering.py?line=293) self.post_block(block)

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\contextlib.py:131, in _GeneratorContextManager.__exit__(self, type, value, traceback)
    [129](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=128)     value = type()
    [130](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=129) try:
--> [131](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=130)     self.gen.throw(type, value, traceback)
    [132](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=131) except StopIteration as exc:
    [133](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=132)     # Suppress StopIteration *unless* it's the same exception that
    [134](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=133)     # was passed to throw().  This prevents a StopIteration
    [135](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=134)     # raised inside the "with" statement from being suppressed.
    [136](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/contextlib.py?line=135)     return exc is not value

File D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\numba\core\errors.py:837, in new_error_context(fmt_, *args, **kwargs)
    [835](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=834)     else:
    [836](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=835)         tb = None
--> [837](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=836)     raise newerr.with_traceback(tb)
    [838](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=837) elif use_new_style_errors():
    [839](file:///d%3A/Users/xiangrong1/Miniconda3/envs/py48/lib/site-packages/numba/core/errors.py?line=838)     raise e

LoweringError: Failed in nopython mode pipeline (step: native lowering)
Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x00000242239BD700> (trying to write member #1)

File "D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\layouts.py", line 53:
def rdist(x, y):
    <source elided>
    dim = x.shape[0]
    for i in range(dim):
    ^

During: lowering "$20call_function.7 = call $16load_global.5(dim, func=$16load_global.5, args=[Var(dim, layouts.py:52)], kws=(), vararg=None, target=None)" at D:\Users\xiangrong1\Miniconda3\envs\py48\lib\site-packages\umap\layouts.py (53)