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Merged
merged 1 commit into from
May 28, 2025
Merged

Backport PR #3353 on branch 1.11.x (Speed up categorical regressor with numba) #3654

merged 1 commit into from
May 28, 2025

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Backports #3353

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❌ 7 Tests Failed:

Tests completed Failed Passed Skipped
1988 7 1981 107
View the top 2 failed test(s) by shortest run time 
tests/test_preprocessing.py::test_regress_out_int[uint64]
Stack Traces | 0.05s run time 
dtype = dtype('float64')

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mdtype#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [np.uint32, np.float64, np.uint64])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_regress_out_int#x1B[39;49;00m(dtype):#x1B[90m#x1B[39;49;00m
        adata = pbmc3k()[:#x1B[94m200#x1B[39;49;00m, :#x1B[94m200#x1B[39;49;00m].copy()#x1B[90m#x1B[39;49;00m
        adata.X = adata.X.astype(np.float64 #x1B[94mif#x1B[39;49;00m dtype != np.uint32 #x1B[94melse#x1B[39;49;00m np.float32)#x1B[90m#x1B[39;49;00m
        dtype = adata.X.dtype#x1B[90m#x1B[39;49;00m
        adata.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mlabels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = pd.Categorical(#x1B[90m#x1B[39;49;00m
            ([#x1B[33m"#x1B[39;49;00m#x1B[33mA#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] * (adata.X.shape[#x1B[94m0#x1B[39;49;00m] - #x1B[94m100#x1B[39;49;00m)) + ([#x1B[33m"#x1B[39;49;00m#x1B[33mB#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] * #x1B[94m100#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        adata_other = adata.copy()#x1B[90m#x1B[39;49;00m
        adata_other.X = adata_other.X.astype(dtype)#x1B[90m#x1B[39;49;00m
        #x1B[90m# results using only one processor#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>       sc.pp.regress_out(adata, keys=[#x1B[33m"#x1B[39;49;00m#x1B[33mlabels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_preprocessing.py#x1B[0m:416: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/preprocessing/_simple.py#x1B[0m:806: in regress_out
    #x1B[0mres = Parallel(n_jobs=n_jobs)(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12....../site-packages/joblib/parallel.py#x1B[0m:1986: in __call__
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m output #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.return_generator #x1B[94melse#x1B[39;49;00m #x1B[96mlist#x1B[39;49;00m(output)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12....../site-packages/joblib/parallel.py#x1B[0m:1914: in _get_sequential_output
    #x1B[0mres = func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/preprocessing/_simple.py#x1B[0m:828: in _regress_out_chunk
    #x1B[0m#x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mstatsmodels#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mapi#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mas#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96msm#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../site-packages/statsmodels/api.py#x1B[0m:76: in <module>
    #x1B[0m#x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m datasets, distributions, iolib, regression, robust, tools#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../statsmodels/distributions/__init__.py#x1B[0m:7: in <module>
    #x1B[0m#x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdiscrete#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m (#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

    #x1B[0m#x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mnumpy#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mas#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mnp#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
    #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mstats#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m rv_discrete, poisson, nbinom#x1B[90m#x1B[39;49;00m
    #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mspecial#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m gammaln#x1B[90m#x1B[39;49;00m
>   #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_lib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_util#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m _lazywhere#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE   ImportError: cannot import name '_lazywhere' from 'scipy._lib._util' (/home/runner/..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../scipy/_lib/_util.py)#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../statsmodels/distributions/discrete.py#x1B[0m:5: ImportError
tests/test_preprocessing.py::test_regress_out_int[uint32]
Stack Traces | 0.07s run time 
dtype = dtype('float32')

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mdtype#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [np.uint32, np.float64, np.uint64])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_regress_out_int#x1B[39;49;00m(dtype):#x1B[90m#x1B[39;49;00m
        adata = pbmc3k()[:#x1B[94m200#x1B[39;49;00m, :#x1B[94m200#x1B[39;49;00m].copy()#x1B[90m#x1B[39;49;00m
        adata.X = adata.X.astype(np.float64 #x1B[94mif#x1B[39;49;00m dtype != np.uint32 #x1B[94melse#x1B[39;49;00m np.float32)#x1B[90m#x1B[39;49;00m
        dtype = adata.X.dtype#x1B[90m#x1B[39;49;00m
        adata.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mlabels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = pd.Categorical(#x1B[90m#x1B[39;49;00m
            ([#x1B[33m"#x1B[39;49;00m#x1B[33mA#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] * (adata.X.shape[#x1B[94m0#x1B[39;49;00m] - #x1B[94m100#x1B[39;49;00m)) + ([#x1B[33m"#x1B[39;49;00m#x1B[33mB#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] * #x1B[94m100#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        adata_other = adata.copy()#x1B[90m#x1B[39;49;00m
        adata_other.X = adata_other.X.astype(dtype)#x1B[90m#x1B[39;49;00m
        #x1B[90m# results using only one processor#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>       sc.pp.regress_out(adata, keys=[#x1B[33m"#x1B[39;49;00m#x1B[33mlabels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_preprocessing.py#x1B[0m:416: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/preprocessing/_simple.py#x1B[0m:806: in regress_out
    #x1B[0mres = Parallel(n_jobs=n_jobs)(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12....../site-packages/joblib/parallel.py#x1B[0m:1986: in __call__
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m output #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.return_generator #x1B[94melse#x1B[39;49;00m #x1B[96mlist#x1B[39;49;00m(output)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12....../site-packages/joblib/parallel.py#x1B[0m:1914: in _get_sequential_output
    #x1B[0mres = func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/preprocessing/_simple.py#x1B[0m:828: in _regress_out_chunk
    #x1B[0m#x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mstatsmodels#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mapi#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mas#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96msm#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../site-packages/statsmodels/api.py#x1B[0m:76: in <module>
    #x1B[0m#x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m datasets, distributions, iolib, regression, robust, tools#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../statsmodels/distributions/__init__.py#x1B[0m:7: in <module>
    #x1B[0m#x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdiscrete#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m (#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

    #x1B[0m#x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mnumpy#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mas#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mnp#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
    #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mstats#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m rv_discrete, poisson, nbinom#x1B[90m#x1B[39;49;00m
    #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mspecial#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m gammaln#x1B[90m#x1B[39;49;00m
>   #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_lib#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96m_util#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m _lazywhere#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE   ImportError: cannot import name '_lazywhere' from 'scipy._lib._util' (/home/runner/..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../scipy/_lib/_util.py)#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../statsmodels/distributions/discrete.py#x1B[0m:5: ImportError
View the full list of 1 ❄️ flaky tests 
tests/test_preprocessing.py::test_regress_out_constants

Flake rate in main: 26.67% (Passed 11 times, Failed 4 times)

Stack Traces | 0.009s run time 
#x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_regress_out_constants#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
        adata = AnnData(np.hstack((np.full((#x1B[94m10#x1B[39;49;00m, #x1B[94m1#x1B[39;49;00m), #x1B[94m0.0#x1B[39;49;00m), np.full((#x1B[94m10#x1B[39;49;00m, #x1B[94m1#x1B[39;49;00m), #x1B[94m1.0#x1B[39;49;00m))))#x1B[90m#x1B[39;49;00m
        adata.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = np.random.rand(adata.X.shape[#x1B[94m0#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
        adata.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mn_counts#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = adata.X.sum(axis=#x1B[94m1#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        adata_copy = adata.copy()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       sc.pp.regress_out(adata, keys=[#x1B[33m"#x1B[39;49;00m#x1B[33mn_counts#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_preprocessing.py#x1B[0m:486: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../site-packages/legacy_api_wrap/__init__.py#x1B[0m:82: in fn_compatible
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m fn(*args_all, **kw)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/preprocessing/_simple.py#x1B[0m:806: in regress_out
    #x1B[0mres = Parallel(n_jobs=n_jobs)(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12....../site-packages/joblib/parallel.py#x1B[0m:1986: in __call__
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m output #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.return_generator #x1B[94melse#x1B[39;49;00m #x1B[96mlist#x1B[39;49;00m(output)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12....../site-packages/joblib/parallel.py#x1B[0m:1914: in _get_sequential_output
    #x1B[0mres = func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
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    #x1B[0m#x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mstatsmodels#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mapi#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mas#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96msm#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
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    #x1B[0m#x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdiscrete#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m (#x1B[90m#x1B[39;49;00m
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    #x1B[0m#x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mnumpy#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mas#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mnp#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
    #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mstats#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m rv_discrete, poisson, nbinom#x1B[90m#x1B[39;49;00m
    #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscipy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mspecial#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m gammaln#x1B[90m#x1B[39;49;00m
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#x1B[1m#x1B[31mE   ImportError: cannot import name '_lazywhere' from 'scipy._lib._util' (/home/runner/..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../scipy/_lib/_util.py)#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.12.../statsmodels/distributions/discrete.py#x1B[0m:5: ImportError

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@flying-sheep flying-sheep merged commit d27444b into 1.11.x May 28, 2025
7 of 9 checks passed
@flying-sheep flying-sheep deleted the auto-backport-of-pr-3353-on-1.11.x branch May 28, 2025 07:50
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@flying-sheep @Intron7