(chore): derive CI matrix from hatch env #3607

flying-sheep · 2025-04-22T13:45:49Z

See https://github.com/scverse/cookiecutter-scverse/blob/d4bdfc5ec4c5029aebf7c0cba65609e20358144d/%7B%7Bcookiecutter.project_name%7D%7D/.github/workflows/test.yaml

This also updates the hatch env matrix to have the following jobs

stable (formerly full): run all pretty much tests except external tools
pre (unchanged): run tests with pre-release versions
min-vers (formerly min): run tests with the minimum possible versions
min-deps (new): like in anndata, tests if everything imports OK with no optional dependencies installed

The only regression is that we no longer test scanorama, because it depends on annoy, which hasn’t been updated in years and fails to build on my system.

We should probably think of a better strategy for it, but I think running the maximum set of tests that we test online also locally is a good idea.

We also need to check if codecov still works, I’m typing this while tests still run.

codecov · 2025-04-24T08:41:31Z

❌ 3 Tests Failed:

Tests completed	Failed	Passed	Skipped
2128	3	2125	104

View the top 3 failed test(s) by shortest run time

tests/test_preprocessing.py::test_regress_out_constants_equivalent

Stack Traces | 0.012s run time

#x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_regress_out_constants_equivalent#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
        #x1B[90m# Tests that constant values don't change results#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# (since support for constant values is implemented by us)#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[96msklearn#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdatasets#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m make_blobs#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        X, cat = make_blobs(#x1B[94m100#x1B[39;49;00m, #x1B[94m20#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        a = sc.AnnData(np.hstack([X, np.zeros((#x1B[94m100#x1B[39;49;00m, #x1B[94m5#x1B[39;49;00m))]), obs={#x1B[33m"#x1B[39;49;00m#x1B[33mcat#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: pd.Categorical(cat)})#x1B[90m#x1B[39;49;00m
        b = sc.AnnData(X, obs={#x1B[33m"#x1B[39;49;00m#x1B[33mcat#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: pd.Categorical(cat)})#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       sc.pp.regress_out(a, #x1B[33m"#x1B[39;49;00m#x1B[33mcat#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:439: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../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:774: 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/python3.13....../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/python3.13....../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:796: 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/python3.13.../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/python3.13.../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/python3.13.../scipy/_lib/_util.py)#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../statsmodels/distributions/discrete.py#x1B[0m:5: ImportError

tests/test_preprocessing.py::test_regress_out_constants

Stack Traces | 0.06s 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:416: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../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:774: 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/python3.13....../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/python3.13....../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:796: 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/python3.13.../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/python3.13.../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/python3.13.../scipy/_lib/_util.py)#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../statsmodels/distributions/discrete.py#x1B[0m:5: ImportError

tests/test_preprocessing.py::test_regress_out_categorical

Stack Traces | 12.1s run time

joblib.externals.loky.process_executor._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../externals/loky/process_executor.py", line 490, in _process_worker
    r = call_item()
  File "......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../externals/loky/process_executor.py", line 291, in __call__
    return self.fn(*self.args, **self.kwargs)
           ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py", line 607, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
            ~~~~^^^^^^^^^^^^^^^^^
  File ".../scanpy/preprocessing/_simple.py", line 796, in _regress_out_chunk
    import statsmodels.api as sm
  File "......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../site-packages/statsmodels/api.py", line 76, in <module>
    from . import datasets, distributions, iolib, regression, robust, tools
  File "......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../statsmodels/distributions/__init__.py", line 7, in <module>
    from .discrete import (
        genpoisson_p, zipoisson, zigenpoisson, zinegbin,
        )
  File "......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../statsmodels/distributions/discrete.py", line 5, in <module>
    from scipy._lib._util import _lazywhere
ImportError: cannot import name '_lazywhere' from 'scipy._lib._util' (......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../scipy/_lib/_util.py)
"""

#x1B[33mThe above exception was the direct cause of the following exception:#x1B[0m

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_regress_out_categorical#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
        #x1B[94mimport#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mpandas#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[96mpd#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[96msparse#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m random#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        adata = AnnData(random(#x1B[94m1000#x1B[39;49;00m, #x1B[94m100#x1B[39;49;00m, density=#x1B[94m0.6#x1B[39;49;00m, #x1B[96mformat#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33mcsr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
        #x1B[90m# create a categorical column#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mbatch#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = pd.Categorical(np.random.randint(#x1B[94m1#x1B[39;49;00m, #x1B[94m4#x1B[39;49;00m, size=adata.X.shape[#x1B[94m0#x1B[39;49;00m]))#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       multi = sc.pp.regress_out(adata, keys=#x1B[33m"#x1B[39;49;00m#x1B[33mbatch#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, n_jobs=#x1B[94m8#x1B[39;49;00m, copy=#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_preprocessing.py#x1B[0m:406: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../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:774: in regress_out
    #x1B[0mres = Parallel(n_jobs=n_jobs)(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py#x1B[0m:2072: 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../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py#x1B[0m:1682: in _get_outputs
    #x1B[0m#x1B[94myield from#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._retrieve()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py#x1B[0m:1784: in _retrieve
    #x1B[0m#x1B[96mself#x1B[39;49;00m._raise_error_fast()#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py#x1B[0m:1859: in _raise_error_fast
    #x1B[0merror_job.get_result(#x1B[96mself#x1B[39;49;00m.timeout)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py#x1B[0m:758: in get_result
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._return_or_raise()#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <joblib.parallel.BatchCompletionCallBack object at 0x7fe4c4e84680>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_return_or_raise#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.status == TASK_ERROR:#x1B[90m#x1B[39;49;00m
>               #x1B[94mraise#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._result#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               ImportError: cannot import name '_lazywhere' from 'scipy._lib._util' (......................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13.../scipy/_lib/_util.py)#x1B[0m

#x1B[1m#x1B[31m../../../.local.../scanpy/B9PcT7QG/hatch-test.pre/lib/python3.13...................../site-packages/joblib/parallel.py#x1B[0m:773: ImportError

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…tch env) (#3647)

flying-sheep added 7 commits April 22, 2025 15:45

(chore): derive CI matrix from hatch env

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fix jq

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Switch to min-vers

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(fix): check xarray installation when reading in any xarray-dependent code scverse/anndata#1991

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Merge branch 'main' into pa/derive-matrix

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remove other external tools from tests

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Backport PR #3607: (chore): derive CI matrix from hatch env

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Backport PR #3607 on branch 1.11.x ((chore): derive CI matrix from hatch env) #3647

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(chore): derive CI matrix from hatch env scverse/anndata#1998

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