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Deprecate save parameter of plots #3675

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@Zethson Zethson commented Jun 7, 2025 •
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TODO

  • Discuss what to do with settings.figdir
  • Deprecate there or in savefig_or_show

@Zethson
Deprecate save parameter of plots
58d7161 
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
@Zethson Zethson added this to the 1.12.0 milestone Jun 7, 2025
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codecov bot commented Jun 7, 2025 •
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❌ 10 Tests Failed:

Tests completed Failed Passed Skipped
2118 10 2108 105
View the top 3 failed test(s) by shortest run time 
tests/test_ingest.py::test_ingest_map_embedding_umap
Stack Traces | 0.015s run time 
#x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_ingest_map_embedding_umap#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
        adata_ref = sc.AnnData(X)#x1B[90m#x1B[39;49;00m
        adata_new = sc.AnnData(T)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        sc.pp.neighbors(#x1B[90m#x1B[39;49;00m
            adata_ref, method=#x1B[33m"#x1B[39;49;00m#x1B[33mumap#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, use_rep=#x1B[33m"#x1B[39;49;00m#x1B[33mX#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, n_neighbors=#x1B[94m4#x1B[39;49;00m, random_state=#x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        sc.tl.umap(adata_ref, random_state=#x1B[94m0#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       ing = sc.tl.Ingest(adata_ref)#x1B[90m#x1B[39;49;00m
              ^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_ingest.py#x1B[0m:148: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/tools/_ingest.py#x1B[0m:342: in __init__
    #x1B[0m#x1B[96mself#x1B[39;49;00m._init_neighbors(adata, neighbors_key)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/tools/_ingest.py#x1B[0m:309: in _init_neighbors
    #x1B[0m#x1B[96mself#x1B[39;49;00m._init_pynndescent(neighbors[#x1B[33m"#x1B[39;49;00m#x1B[33mdistances#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/tools/_ingest.py#x1B[0m:264: in _init_pynndescent
    #x1B[0m#x1B[96mself#x1B[39;49;00m._nnd_idx = NNDescent(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py#x1B[0m:923: in __init__
    #x1B[0m#x1B[96mself#x1B[39;49;00m._neighbor_graph = nn_descent(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../numba/core/dispatcher.py#x1B[0m:424: in _compile_for_args
    #x1B[0merror_rewrite(e, #x1B[33m'#x1B[39;49;00m#x1B[33mtyping#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...           init_rp_tree(data, dist, current_graph, leaf_array)\n            ^\n\nDuring: Pass nopython_type_inference')
issue_type = 'typing'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92merror_rewrite#x1B[39;49;00m(e, issue_type):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""#x1B[39;49;00m
    #x1B[33m    Rewrite and raise Exception `e` with help supplied based on the#x1B[39;49;00m
    #x1B[33m    specified issue_type.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m config.SHOW_HELP:#x1B[90m#x1B[39;49;00m
            help_msg = errors.error_extras[issue_type]#x1B[90m#x1B[39;49;00m
            e.patch_message(#x1B[33m'#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m.join((#x1B[96mstr#x1B[39;49;00m(e).rstrip(), help_msg)))#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m config.FULL_TRACEBACKS:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m e#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m e.with_traceback(#x1B[94mNone#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Invalid use of iternext with parameters (range_state_int64)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: typing of intrinsic-call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (77)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py", line 77:#x1B[0m
#x1B[1m#x1B[31mE           def generate_leaf_updates(leaf_block, dist_thresholds, data, dist):#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE               updates = [[(-1, -1, np.inf)] for i in range(leaf_block.shape[0])]#x1B[0m
#x1B[1m#x1B[31mE               ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function generate_leaf_updates at 0x7fbe396262a0>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (111)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function generate_leaf_updates at 0x7fbe396262a0>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (111)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py", line 111:#x1B[0m
#x1B[1m#x1B[31mE           def init_rp_tree(data, dist, current_graph, leaf_array):#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE                   updates = generate_leaf_updates(leaf_block, dist_thresholds, data, dist)#x1B[0m
#x1B[1m#x1B[31mE                   ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function init_rp_tree at 0x7fbe39626480>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (347)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function init_rp_tree at 0x7fbe39626480>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (347)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py", line 347:#x1B[0m
#x1B[1m#x1B[31mE           def nn_descent(#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE                   if rp_tree_init:#x1B[0m
#x1B[1m#x1B[31mE                       init_rp_tree(data, dist, current_graph, leaf_array)#x1B[0m
#x1B[1m#x1B[31mE                       ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../numba/core/dispatcher.py#x1B[0m:365: TypingError
tests/test_scrublet.py::test_scrublet[True-sparse]
Stack Traces | 0.142s run time 
mk_data = <function pbmc200 at 0x7f43e3a849a0>, expected_idx = [13, 138]
expected_scores = [0.149254, 0.149254], use_approx_neighbors = True

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mmk_data#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mexpected_idx#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mexpected_scores#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            pytest.param(pbmc200, [#x1B[94m13#x1B[39;49;00m, #x1B[94m138#x1B[39;49;00m], [#x1B[94m0.149254#x1B[39;49;00m] * #x1B[94m2#x1B[39;49;00m, #x1B[96mid#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33msparse#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            pytest.param(paul500, [#x1B[94m180#x1B[39;49;00m], [#x1B[94m0.219178#x1B[39;49;00m], #x1B[96mid#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33mdense#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        ],#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33muse_approx_neighbors#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[94mTrue#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m, #x1B[94mNone#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_scrublet#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        mk_data: Callable[[], AnnData],#x1B[90m#x1B[39;49;00m
        expected_idx: #x1B[96mlist#x1B[39;49;00m[#x1B[96mint#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        expected_scores: #x1B[96mlist#x1B[39;49;00m[#x1B[96mfloat#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        use_approx_neighbors: #x1B[96mbool#x1B[39;49;00m | #x1B[94mNone#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
    ):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Check that scrublet runs and detects some doublets."""#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata = mk_data()#x1B[90m#x1B[39;49;00m
>       sc.pp.scrublet(adata, use_approx_neighbors=use_approx_neighbors)#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_scrublet.py#x1B[0m:51: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/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[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_scrublet/__init__.py#x1B[0m:291: in scrublet
    #x1B[0mscrubbed = _run_scrublet(adata_obs, adata_sim)#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_scrublet/__init__.py#x1B[0m:234: in _run_scrublet
    #x1B[0mad_obs = _scrublet_call_doublets(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_scrublet/__init__.py#x1B[0m:450: in _scrublet_call_doublets
    #x1B[0mscrub.calculate_doublet_scores(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_scrublet/core.py#x1B[0m:302: in calculate_doublet_scores
    #x1B[0m#x1B[96mself#x1B[39;49;00m._nearest_neighbor_classifier(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_scrublet/core.py#x1B[0m:345: in _nearest_neighbor_classifier
    #x1B[0mknn.compute_neighbors(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/neighbors/__init__.py#x1B[0m:587: in compute_neighbors
    #x1B[0m#x1B[96mself#x1B[39;49;00m._distances = transformer.fit_transform(X)#x1B[90m#x1B[39;49;00m
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../sklearn/utils/_set_output.py#x1B[0m:316: in wrapped
    #x1B[0mdata_to_wrap = f(#x1B[96mself#x1B[39;49;00m, X, *args, **kwargs)#x1B[90m#x1B[39;49;00m
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py#x1B[0m:2256: in fit_transform
    #x1B[0m#x1B[96mself#x1B[39;49;00m.fit(X, compress_index=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py#x1B[0m:2174: in fit
    #x1B[0m#x1B[96mself#x1B[39;49;00m.index_ = NNDescent(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py#x1B[0m:923: in __init__
    #x1B[0m#x1B[96mself#x1B[39;49;00m._neighbor_graph = nn_descent(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../numba/core/dispatcher.py#x1B[0m:424: in _compile_for_args
    #x1B[0merror_rewrite(e, #x1B[33m'#x1B[39;49;00m#x1B[33mtyping#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...           init_rp_tree(data, dist, current_graph, leaf_array)\n            ^\n\nDuring: Pass nopython_type_inference')
issue_type = 'typing'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92merror_rewrite#x1B[39;49;00m(e, issue_type):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""#x1B[39;49;00m
    #x1B[33m    Rewrite and raise Exception `e` with help supplied based on the#x1B[39;49;00m
    #x1B[33m    specified issue_type.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m config.SHOW_HELP:#x1B[90m#x1B[39;49;00m
            help_msg = errors.error_extras[issue_type]#x1B[90m#x1B[39;49;00m
            e.patch_message(#x1B[33m'#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m.join((#x1B[96mstr#x1B[39;49;00m(e).rstrip(), help_msg)))#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m config.FULL_TRACEBACKS:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m e#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m e.with_traceback(#x1B[94mNone#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Invalid use of iternext with parameters (range_state_int64)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: typing of intrinsic-call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py (77)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py", line 77:#x1B[0m
#x1B[1m#x1B[31mE           def generate_leaf_updates(leaf_block, dist_thresholds, data, dist):#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE               updates = [[(-1, -1, np.inf)] for i in range(leaf_block.shape[0])]#x1B[0m
#x1B[1m#x1B[31mE               ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function generate_leaf_updates at 0x7f43e40fd260>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py (111)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function generate_leaf_updates at 0x7f43e40fd260>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py (111)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py", line 111:#x1B[0m
#x1B[1m#x1B[31mE           def init_rp_tree(data, dist, current_graph, leaf_array):#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE                   updates = generate_leaf_updates(leaf_block, dist_thresholds, data, dist)#x1B[0m
#x1B[1m#x1B[31mE                   ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function init_rp_tree at 0x7f43e40fc900>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py (347)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function init_rp_tree at 0x7f43e40fc900>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py (347)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13................................./site-packages/pynndescent/pynndescent_.py", line 347:#x1B[0m
#x1B[1m#x1B[31mE           def nn_descent(#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE                   if rp_tree_init:#x1B[0m
#x1B[1m#x1B[31mE                       init_rp_tree(data, dist, current_graph, leaf_array)#x1B[0m
#x1B[1m#x1B[31mE                       ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../numba/core/dispatcher.py#x1B[0m:365: TypingError
tests/test_ingest.py::test_neighbors
Stack Traces | 0.609s run time 
adatas = (AnnData object with n_obs × n_vars = 500 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_scor...pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities', AnnData object with n_obs × n_vars = 200 × 765)

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_neighbors#x1B[39;49;00m(adatas):#x1B[90m#x1B[39;49;00m
        adata_ref = adatas[#x1B[94m0#x1B[39;49;00m].copy()#x1B[90m#x1B[39;49;00m
        adata_new = adatas[#x1B[94m1#x1B[39;49;00m].copy()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       ing = sc.tl.Ingest(adata_ref)#x1B[90m#x1B[39;49;00m
              ^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_ingest.py#x1B[0m:77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/tools/_ingest.py#x1B[0m:342: in __init__
    #x1B[0m#x1B[96mself#x1B[39;49;00m._init_neighbors(adata, neighbors_key)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/tools/_ingest.py#x1B[0m:309: in _init_neighbors
    #x1B[0m#x1B[96mself#x1B[39;49;00m._init_pynndescent(neighbors[#x1B[33m"#x1B[39;49;00m#x1B[33mdistances#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/tools/_ingest.py#x1B[0m:264: in _init_pynndescent
    #x1B[0m#x1B[96mself#x1B[39;49;00m._nnd_idx = NNDescent(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py#x1B[0m:923: in __init__
    #x1B[0m#x1B[96mself#x1B[39;49;00m._neighbor_graph = nn_descent(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../numba/core/dispatcher.py#x1B[0m:424: in _compile_for_args
    #x1B[0merror_rewrite(e, #x1B[33m'#x1B[39;49;00m#x1B[33mtyping#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

e = TypingError('Failed in nopython mode pipeline (step: nopython frontend)\nFailed in nopython mode pipeline (step: nopyt...           init_rp_tree(data, dist, current_graph, leaf_array)\n            ^\n\nDuring: Pass nopython_type_inference')
issue_type = 'typing'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92merror_rewrite#x1B[39;49;00m(e, issue_type):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""#x1B[39;49;00m
    #x1B[33m    Rewrite and raise Exception `e` with help supplied based on the#x1B[39;49;00m
    #x1B[33m    specified issue_type.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m config.SHOW_HELP:#x1B[90m#x1B[39;49;00m
            help_msg = errors.error_extras[issue_type]#x1B[90m#x1B[39;49;00m
            e.patch_message(#x1B[33m'#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m.join((#x1B[96mstr#x1B[39;49;00m(e).rstrip(), help_msg)))#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m config.FULL_TRACEBACKS:#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m e#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m e.with_traceback(#x1B[94mNone#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Failed in nopython mode pipeline (step: nopython frontend)#x1B[0m
#x1B[1m#x1B[31mE           Invalid use of iternext with parameters (range_state_int64)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: typing of intrinsic-call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (77)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py", line 77:#x1B[0m
#x1B[1m#x1B[31mE           def generate_leaf_updates(leaf_block, dist_thresholds, data, dist):#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE               updates = [[(-1, -1, np.inf)] for i in range(leaf_block.shape[0])]#x1B[0m
#x1B[1m#x1B[31mE               ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function generate_leaf_updates at 0x7fbe396262a0>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (111)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function generate_leaf_updates at 0x7fbe396262a0>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (111)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py", line 111:#x1B[0m
#x1B[1m#x1B[31mE           def init_rp_tree(data, dist, current_graph, leaf_array):#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE                   updates = generate_leaf_updates(leaf_block, dist_thresholds, data, dist)#x1B[0m
#x1B[1m#x1B[31mE                   ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function init_rp_tree at 0x7fbe39626480>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (347)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: resolving callee type: type(CPUDispatcher(<function init_rp_tree at 0x7fbe39626480>))#x1B[0m
#x1B[1m#x1B[31mE           During: typing of call at /home/runner/..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py (347)#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           File "../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.........................../site-packages/pynndescent/pynndescent_.py", line 347:#x1B[0m
#x1B[1m#x1B[31mE           def nn_descent(#x1B[0m
#x1B[1m#x1B[31mE               <source elided>#x1B[0m
#x1B[1m#x1B[31mE                   if rp_tree_init:#x1B[0m
#x1B[1m#x1B[31mE                       init_rp_tree(data, dist, current_graph, leaf_array)#x1B[0m
#x1B[1m#x1B[31mE                       ^#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           During: Pass nopython_type_inference#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.13.../numba/core/dispatcher.py#x1B[0m:365: TypingError

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@Zethson
Use correct PR number
f8a75c0 
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
@Zethson Zethson mentioned this pull request Jun 7, 2025
Open
Zethson added 2 commits June 7, 2025 09:51
@Zethson
Update submodule
0e94942 
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
@Zethson
fix tests
d08451e 
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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Saving plots results in a prefixed filename, regardless of sc.settings.figdir
1 participant
@Zethson