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BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data
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numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend) #300

Open tangsanpang2 opened 3 months ago

tangsanpang2 commented 3 months ago

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)
    ^

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