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Backport PR #4385 on branch 1.12.x (fix: multi-column groupby crashing on non-string observations) - #4517

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Backport PR #4385 on branch 1.12.x (fix: multi-column groupby crashing on non-string observations)#4517
flying-sheep merged 1 commit into
scverse:1.12.xfrom
meeseeksmachine:auto-backport-of-pr-4385-on-1.12.x

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@meeseeksmachine meeseeksmachine commented Nov 12, 2026

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Backport PR #4385: fix: multi-column groupby crashing on non-string observations

@lumberbot-app lumberbot-app Bot added this to the 1.12.7 milestone Nov 12, 2026
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Documentation build overview

📚 scanpy | 🛠️ Build #4721177 | 📁 Comparing 0b675b0 against latest (386ce0a)

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454 files changed · + 141 added · ± 137 modified · - 176 deleted

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❌ 1 Tests Failed:

Tests completed Failed Passed Skipped
3024 1 3023 175
View the top 1 failed test(s) by shortest run time 
tests/test_datasets.py::test_ebi_expression_atlas
Stack Traces | 389s run time 
self = <http.client.HTTPResponse object at 0x795ff3c35720>, amt = 8192

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_read_chunked#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, amt=#x1B[94mNone#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.chunked != _UNKNOWN#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m amt #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m #x1B[95mand#x1B[39;49;00m amt < #x1B[94m0#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            amt = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        value = []#x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           #x1B[94mwhile#x1B[39;49;00m (chunk_left := #x1B[96mself#x1B[39;49;00m._get_chunk_left()) #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                                 ^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31m../................./_temp/uv-python-dir/cpython-3.14.10-linux-x86_64-gnu/lib/python3.14/http/client.py#x1B[0m:621: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../................./_temp/uv-python-dir/cpython-3.14.10-linux-x86_64-gnu/lib/python3.14/http/client.py#x1B[0m:601: in _get_chunk_left
    #x1B[0m#x1B[96mself#x1B[39;49;00m._safe_read(#x1B[94m2#x1B[39;49;00m)  #x1B[90m# toss the CRLF at the end of the chunk#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    ^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <http.client.HTTPResponse object at 0x795ff3c35720>, amt = 2

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_safe_read#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, amt):#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Read the number of bytes requested.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    This function should be used when <amt> bytes "should" be present for#x1B[39;49;00m
    #x1B[33m    reading. If the bytes are truly not available (due to EOF), then the#x1B[39;49;00m
    #x1B[33m    IncompleteRead exception can be used to detect the problem.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        cursize = #x1B[96mmin#x1B[39;49;00m(amt, _MIN_READ_BUF_SIZE)#x1B[90m#x1B[39;49;00m
        data = #x1B[96mself#x1B[39;49;00m.fp.read(cursize)#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96mlen#x1B[39;49;00m(data) >= amt:#x1B[90m#x1B[39;49;00m
            #x1B[94mreturn#x1B[39;49;00m data#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96mlen#x1B[39;49;00m(data) < cursize:#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m IncompleteRead(data, amt - #x1B[96mlen#x1B[39;49;00m(data))#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           http.client.IncompleteRead: IncompleteRead(0 bytes read, 2 more expected)#x1B[0m

#x1B[1m#x1B[31m../................./_temp/uv-python-dir/cpython-3.14.10-linux-x86_64-gnu/lib/python3.14/http/client.py#x1B[0m:671: IncompleteRead

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

monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x795fad63b1e0>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.internet#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_ebi_expression_atlas#x1B[39;49;00m(monkeypatch: pytest.MonkeyPatch):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscanpy#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 _ebi_expression_atlas #x1B[94mas#x1B[39;49;00m ea_mod#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# make sure we use chunks when testing.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# This dataset has <8M entries, so 4M entries/chunk = 2 chunks#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m #x1B[96mhasattr#x1B[39;49;00m(ea_mod, #x1B[33m"#x1B[39;49;00m#x1B[33mCHUNK_SIZE#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        monkeypatch.setattr(ea_mod, #x1B[33m"#x1B[39;49;00m#x1B[33mCHUNK_SIZE#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[96mint#x1B[39;49;00m(#x1B[94m4e6#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       adata = sc.datasets.ebi_expression_atlas(#x1B[33m"#x1B[39;49;00m#x1B[33mE-MTAB-4888#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_datasets.py#x1B[0m:85: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/datasets/_ebi_expression_atlas.py#x1B[0m:159: in ebi_expression_atlas
    #x1B[0mdownload_experiment(accession)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_utils.py#x1B[0m:16: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m f(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_ebi_expression_atlas.py#x1B[0m:58: in download_experiment
    #x1B[0m_download(mtx_url, experiment_dir / #x1B[33m"#x1B[39;49;00m#x1B[33mexpression_archive.zip#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/scanpy/readwrite.py#x1B[0m:1102: in _download
    #x1B[0mblock = resp.read(blocksize)#x1B[90m#x1B[39;49;00m
            ^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../................./_temp/uv-python-dir/cpython-3.14.10-linux-x86_64-gnu/lib/python3.14/http/client.py#x1B[0m:488: in read
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._read_chunked(amt)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <http.client.HTTPResponse object at 0x795ff3c35720>, amt = 8192

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_read_chunked#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, amt=#x1B[94mNone#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m.chunked != _UNKNOWN#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m amt #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m #x1B[95mand#x1B[39;49;00m amt < #x1B[94m0#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            amt = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        value = []#x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mwhile#x1B[39;49;00m (chunk_left := #x1B[96mself#x1B[39;49;00m._get_chunk_left()) #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m amt #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m #x1B[95mand#x1B[39;49;00m amt <= chunk_left:#x1B[90m#x1B[39;49;00m
                    value.append(#x1B[96mself#x1B[39;49;00m._safe_read(amt))#x1B[90m#x1B[39;49;00m
                    #x1B[96mself#x1B[39;49;00m.chunk_left = chunk_left - amt#x1B[90m#x1B[39;49;00m
                    #x1B[94mbreak#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
                value.append(#x1B[96mself#x1B[39;49;00m._safe_read(chunk_left))#x1B[90m#x1B[39;49;00m
                #x1B[94mif#x1B[39;49;00m amt #x1B[95mis#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                    amt -= chunk_left#x1B[90m#x1B[39;49;00m
                #x1B[96mself#x1B[39;49;00m.chunk_left = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mreturn#x1B[39;49;00m #x1B[33mb#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m.join(value)#x1B[90m#x1B[39;49;00m
        #x1B[94mexcept#x1B[39;49;00m IncompleteRead #x1B[94mas#x1B[39;49;00m exc:#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m IncompleteRead(#x1B[33mb#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m.join(value)) #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mexc#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           http.client.IncompleteRead: IncompleteRead(0 bytes read)#x1B[0m

#x1B[1m#x1B[31m../................./_temp/uv-python-dir/cpython-3.14.10-linux-x86_64-gnu/lib/python3.14/http/client.py#x1B[0m:633: IncompleteRead

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@flying-sheep
flying-sheep merged commit 4064e4f into scverse:1.12.x Nov 13, 2026
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@meeseeksmachine @flying-sheep @barlowa124