numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)

[tangsanpang2]

Hi,
Thank you very much for developing such excellent tools. However, I encountered an error while using them. Could you tell me what could be the reason for this?
st.tl.cci.run(adata, lrs,
... min_spots = 5, #Filter out any LR pairs with no scores for less than min_spots
... distance=0, # None defaults to spot+immediate neighbours; distance=0 for within-spot mode
... n_pairs=100, # Number of random pairs to generate; low as example, recommend ~10,000
... n_cpus=4 # Number of CPUs for parallel. If None, detects & use all available.
... )
Calculating neighbours...
0 spots with no neighbours, 1 median spot neighbours.
Spot neighbour indices stored in adata.obsm['spot_neighbours'] & adata.obsm['spot_neigh_bcs'].
Traceback (most recent call last):
File "", line 1, in
File "/bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/analysis.py", line 325, in run
lr_scores, lrs = get_lrs_scores(adata, lrs, neighbours, het_vals, min_expr)
File "/bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py", line 131, in get_lrs_scores
lr_scores = get_scores(
File "/bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/numba/core/dispatcher.py", line 468, in _compile_for_args
error_rewrite(e, 'typing')
File "/bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/numba/core/dispatcher.py", line 409, in error_rewrite
raise e.with_traceback(None)
numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Failed in nopython mode pipeline (step: nopython frontend)
Cannot unify array(float64, 1d, C) and array(int64, 1d, C) for 'nb_expr_mean.2', defined at /bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py (264)

File "../../anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py", line 264:
def lr_core(

nb_expr_mean = nb_expr.sum(axis=0)
nb_lr2[i, :] = nb_expr_mean
^

During: typing of assignment at /bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py (264)

File "../../anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py", line 264:
def lr_core(

nb_expr_mean = nb_expr.sum(axis=0)
nb_lr2[i, :] = nb_expr_mean
^

During: resolving callee type: type(CPUDispatcher(<function lr_core at 0x7f9579955310>))
During: typing of call at /bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py (340)

During: resolving callee type: type(CPUDispatcher(<function lr_core at 0x7f9579955310>))
During: typing of call at /bioccWL/Student/yinxz/anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py (340)

File "../../anaconda3/envs/stlearn/lib/python3.8/site-packages/stlearn/tools/microenv/cci/base.py", line 340:
def get_scores(

spot_lr1, spot_lr2 = spot_lr1s[:, i_ : (i_ + 2)], spot_lr2s[:, i_ : (i_ + 2)]
lr_scores = lr_core(spot_lr1, spot_lr2, neighbours, min_expr, spot_indices)
^

package Version Build Channel
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zlib 1.2.13 h5eee18b_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main

[durr1602]

Hi! I've run some tests lately and I get a similar issue with st.tl.cci.run_cci(). I also had a related issue with st.tl.cci.adj_pvals(). All these seem to be linked to numba choking on object dtypes. What's tricky is to identify which variable exactly causes the problem and it's not always patchable without modifying the source code :/. In some cases, converting to int64 or float64 does the trick.

[newmana]

This is now fixed.