feat: pydantic settings by flying-sheep · Pull Request #4081 · scverse/scanpy

flying-sheep · 2026-04-21T15:05:29Z

TODO: simplify logging stuff. settings.logpath can probably just be a deprecated alias to Path(settings..logfile.name), and all the side effects can happen in model validators

Closes #
Tests included or not required because:

Release notes not necessary because:

Co-authored-by: Copilot <copilot@github.com>

codecov · 2026-04-23T08:39:46Z

❌ 8 Tests Failed:

Tests completed	Failed	Passed	Skipped
1834	8	1826	908

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

tests/test_logging.py::test_deep

Stack Traces | 0.003s run time

capsys = <_pytest.capture.CaptureFixture object at 0x7ff040ddc7c0>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_deep#x1B[39;49;00m(capsys: pytest.CaptureFixture):#x1B[90m#x1B[39;49;00m
        s.logfile = sys.stderr#x1B[90m#x1B[39;49;00m
        s.verbosity = Verbosity.hint#x1B[90m#x1B[39;49;00m
        log.hint(#x1B[33m"#x1B[39;49;00m#x1B[33m0#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m capsys.readouterr().err == #x1B[33m"#x1B[39;49;00m#x1B[33m--> 0#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: assert '' == '--> 0\n'#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m#x1B[91m- --> 0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m

#x1B[1m#x1B[31mtests/test_logging.py#x1B[0m:73: AssertionError

tests/test_logging.py::test_defaults

Stack Traces | 0.003s run time

caplog = <_pytest.logging.LogCaptureFixture object at 0x7ff03e012e40>
original_settings = mappingproxy({'preset': <Preset.ScanpyV1: 'scanpy-v1'>, 'verbosity': <Verbosity.warning: 1>, 'logfile': <EncodedFile n...che_compression': 'lzf', 'max_memory': 15.0, 'n_jobs': 1, 'categories_to_ignore': ['N/A', 'dontknow', 'no_gate', '?']})

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_defaults#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        caplog: pytest.LogCaptureFixture, original_settings: Mapping[#x1B[96mstr#x1B[39;49;00m, #x1B[96mobject#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
    ) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m s.logpath #x1B[95mis#x1B[39;49;00m original_settings[#x1B[33m"#x1B[39;49;00m#x1B[33m_logpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] #x1B[95mis#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[31mE       KeyError: '_logpath'#x1B[0m

#x1B[1m#x1B[31mtests/test_logging.py#x1B[0m:26: KeyError

tests/test_logging.py::test_timing

Stack Traces | 0.003s run time

monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7ff050f671d0>
capsys = <_pytest.capture.CaptureFixture object at 0x7ff0509a5ae0>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_timing#x1B[39;49;00m(monkeypatch, capsys: pytest.CaptureFixture):#x1B[90m#x1B[39;49;00m
        counter = #x1B[94m0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mclass#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[92mIncTime#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[37m@staticmethod#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mnow#x1B[39;49;00m(tz):#x1B[90m#x1B[39;49;00m
                #x1B[94mnonlocal#x1B[39;49;00m counter#x1B[90m#x1B[39;49;00m
                counter += #x1B[94m1#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mreturn#x1B[39;49;00m datetime(#x1B[94m2000#x1B[39;49;00m, #x1B[94m1#x1B[39;49;00m, #x1B[94m1#x1B[39;49;00m, second=counter, microsecond=counter, tzinfo=tz)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        monkeypatch.setattr(log, #x1B[33m"#x1B[39;49;00m#x1B[33mdatetime#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, IncTime)#x1B[90m#x1B[39;49;00m
        s.logfile = sys.stderr#x1B[90m#x1B[39;49;00m
        s.verbosity = Verbosity.debug#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        log.hint(#x1B[33m"#x1B[39;49;00m#x1B[33m1#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m counter == #x1B[94m1#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m capsys.readouterr().err == #x1B[33m"#x1B[39;49;00m#x1B[33m--> 1#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: assert '' == '--> 1\n'#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m#x1B[91m- --> 1#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m

#x1B[1m#x1B[31mtests/test_logging.py#x1B[0m:127: AssertionError

tests/test_logging.py::test_formats

Stack Traces | 0.004s run time

capsys = <_pytest.capture.CaptureFixture object at 0x7ff0504ad250>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_formats#x1B[39;49;00m(capsys: pytest.CaptureFixture):#x1B[90m#x1B[39;49;00m
        s.logfile = sys.stderr#x1B[90m#x1B[39;49;00m
        s.verbosity = Verbosity.debug#x1B[90m#x1B[39;49;00m
        log.error(#x1B[33m"#x1B[39;49;00m#x1B[33m0#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m capsys.readouterr().err == #x1B[33m"#x1B[39;49;00m#x1B[33mERROR: 0#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: assert '' == 'ERROR: 0\n'#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m#x1B[91m- ERROR: 0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m

#x1B[1m#x1B[31mtests/test_logging.py#x1B[0m:58: AssertionError

tests/test_logging.py::test_logfile

Stack Traces | 0.004s run time

tmp_path = PosixPath('.../pytest-0/popen-gw1/test_logfile0')
caplog = <_pytest.logging.LogCaptureFixture object at 0x7ff03dc81320>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_logfile#x1B[39;49;00m(tmp_path: Path, caplog: pytest.LogCaptureFixture):#x1B[90m#x1B[39;49;00m
        s.verbosity = Verbosity.hint#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        io = StringIO()#x1B[90m#x1B[39;49;00m
        s.logfile = io#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m s.logfile #x1B[95mis#x1B[39;49;00m io#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m s.logpath #x1B[95mis#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        log.error(#x1B[33m"#x1B[39;49;00m#x1B[33mtest!#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m io.getvalue() == #x1B[33m"#x1B[39;49;00m#x1B[33mERROR: test!#x1B[39;49;00m#x1B[33m\n#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: assert '' == 'ERROR: test!\n'#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m#x1B[91m- ERROR: test!#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m

#x1B[1m#x1B[31mtests/test_logging.py#x1B[0m:91: AssertionError

tests/test_readwrite.py::test_write[default-csv]

Stack Traces | 0.004s run time

monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7ff0519239b0>
tmp_path = PosixPath('.../pytest-0/popen-gw1/test_write_default_csv_0')
ext = 'csv', style = 'default'

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, pytest.param(#x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, marks=needs.zarr), #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#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[33mstyle#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mdefault#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_write#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        monkeypatch: pytest.MonkeyPatch,#x1B[90m#x1B[39;49;00m
        tmp_path: Path,#x1B[90m#x1B[39;49;00m
        ext: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        style: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mdefault#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
    ) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        monkeypatch.chdir(tmp_path)#x1B[90m#x1B[39;49;00m
        adata = AnnData(np.array([[#x1B[94m1#x1B[39;49;00m, #x1B[94m2#x1B[39;49;00m], [#x1B[94m3#x1B[39;49;00m, #x1B[94m4#x1B[39;49;00m]]))#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# test that writing works (except style="default" and ext="csv")#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ctx = (#x1B[90m#x1B[39;49;00m
            pytest.warns(#x1B[96mFutureWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mremoved from this function#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m ext == #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94melse#x1B[39;49;00m nullcontext()#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        #x1B[94mmatch#x1B[39;49;00m style, ext:#x1B[90m#x1B[39;49;00m
            #x1B[94mcase#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m_#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mwith#x1B[39;49;00m ctx:#x1B[90m#x1B[39;49;00m
                    sc.write(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mtest.#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mext#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, adata)#x1B[90m#x1B[39;49;00m
                d = tmp_path#x1B[90m#x1B[39;49;00m
            #x1B[94mcase#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m_#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mwith#x1B[39;49;00m ctx:#x1B[90m#x1B[39;49;00m
                    sc.write(#x1B[33m"#x1B[39;49;00m#x1B[33mtest#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, adata, ext=ext)#x1B[90m#x1B[39;49;00m
                d = sc.settings.writedir#x1B[90m#x1B[39;49;00m
            #x1B[94mcase#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mdefault#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[90m# check that it throws an error instead#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                ff = sc.settings.file_format_data#x1B[90m#x1B[39;49;00m
                #x1B[94mwith#x1B[39;49;00m pytest.raises(#x1B[96mValueError#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mCannot set file_format_data to csv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
>                   sc.settings.file_format_data = ext  #x1B[90m# type: ignore[assignment]#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[.../scanpy/tests/test_readwrite.py#x1B[0m:77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.few-extras/lib/python3.14....../site-packages/pydantic/main.py#x1B[0m:1046: in __setattr__
    #x1B[0msetattr_handler(#x1B[96mself#x1B[39;49;00m, name, value)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

model = Settings(preset=<Preset.ScanpyV1: 'scanpy-v1'>, verbosity=<Verbosity.hint: 3>, logfile=<EncodedFile name="<_io.FileIO ...ories_to_ignore=['N/A', 'dontknow', 'no_gate', '?'], logpath=PosixPath("<_io.FileIO name=12 mode='rb+' closefd=True>"))
name = 'file_format_data', val = 'csv'

>   #x1B[0m    #x1B[33m'#x1B[39;49;00m#x1B[33mvalidate_assignment#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m: #x1B[94mlambda#x1B[39;49;00m model, name, val: model.__pydantic_validator__.validate_assignment(model, name, val),  #x1B[90m# pyright: ignore[reportAssignmentType]#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
        #x1B[33m'#x1B[39;49;00m#x1B[33mprivate#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m: _private_setattr_handler,#x1B[90m#x1B[39;49;00m
        #x1B[33m'#x1B[39;49;00m#x1B[33mcached_property#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m: #x1B[94mlambda#x1B[39;49;00m model, name, val: model.#x1B[91m__dict__#x1B[39;49;00m.#x1B[92m__setitem__#x1B[39;49;00m(name, val),#x1B[90m#x1B[39;49;00m
        #x1B[33m'#x1B[39;49;00m#x1B[33mextra_known#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m: #x1B[94mlambda#x1B[39;49;00m model, name, val: _object_setattr(model, name, val),#x1B[90m#x1B[39;49;00m
    }#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE   pydantic_core._pydantic_core.ValidationError: 1 validation error for Settings#x1B[0m
#x1B[1m#x1B[31mE   file_format_data#x1B[0m
#x1B[1m#x1B[31mE     Input should be 'h5ad' or 'zarr' [type=literal_error, input_value='csv', input_type=str]#x1B[0m
#x1B[1m#x1B[31mE       For further information visit https://errors.pydantic.dev/2.13/v/literal_error#x1B[0m

#x1B[1m#x1B[.../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.few-extras/lib/python3.14....../site-packages/pydantic/main.py#x1B[0m:112: ValidationError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7ff0519239b0>
tmp_path = PosixPath('.../pytest-0/popen-gw1/test_write_default_csv_0')
ext = 'csv', style = 'default'

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, pytest.param(#x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, marks=needs.zarr), #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#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[33mstyle#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mdefault#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_write#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        monkeypatch: pytest.MonkeyPatch,#x1B[90m#x1B[39;49;00m
        tmp_path: Path,#x1B[90m#x1B[39;49;00m
        ext: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        style: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mdefault#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
    ) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        monkeypatch.chdir(tmp_path)#x1B[90m#x1B[39;49;00m
        adata = AnnData(np.array([[#x1B[94m1#x1B[39;49;00m, #x1B[94m2#x1B[39;49;00m], [#x1B[94m3#x1B[39;49;00m, #x1B[94m4#x1B[39;49;00m]]))#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# test that writing works (except style="default" and ext="csv")#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ctx = (#x1B[90m#x1B[39;49;00m
            pytest.warns(#x1B[96mFutureWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mremoved from this function#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m ext == #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94melse#x1B[39;49;00m nullcontext()#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        #x1B[94mmatch#x1B[39;49;00m style, ext:#x1B[90m#x1B[39;49;00m
            #x1B[94mcase#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mpath#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m_#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mwith#x1B[39;49;00m ctx:#x1B[90m#x1B[39;49;00m
                    sc.write(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mtest.#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mext#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, adata)#x1B[90m#x1B[39;49;00m
                d = tmp_path#x1B[90m#x1B[39;49;00m
            #x1B[94mcase#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mext#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m_#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mwith#x1B[39;49;00m ctx:#x1B[90m#x1B[39;49;00m
                    sc.write(#x1B[33m"#x1B[39;49;00m#x1B[33mtest#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, adata, ext=ext)#x1B[90m#x1B[39;49;00m
                d = sc.settings.writedir#x1B[90m#x1B[39;49;00m
            #x1B[94mcase#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mdefault#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mcsv#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[90m# check that it throws an error instead#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                ff = sc.settings.file_format_data#x1B[90m#x1B[39;49;00m
>               #x1B[94mwith#x1B[39;49;00m pytest.raises(#x1B[96mValueError#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mCannot set file_format_data to csv#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[31mE               AssertionError: Regex pattern did not match.#x1B[0m
#x1B[1m#x1B[31mE                 Expected regex: 'Cannot set file_format_data to csv'#x1B[0m
#x1B[1m#x1B[31mE                 Actual message: "1 validation error for Settings\nfile_format_data\n  Input should be 'h5ad' or 'zarr' [type=literal_error, input_value='csv', input_type=str]\n    For further information visit https://errors.pydantic.dev/2.13/v/literal_error"#x1B[0m

#x1B[1m#x1B[.../scanpy/tests/test_readwrite.py#x1B[0m:76: AssertionError

src/scanpy/preprocessing/_normalization.py::scanpy.preprocessing._normalization.normalize_total

Stack Traces | 0.005s run time

212 ...             [1, 22, 1, 2, 2],
213 ...         ],
214 ...         dtype="float32",
215 ...     )
216 ... )
217 >>> adata.X
218 array([[ 3.,  3.,  3.,  6.,  6.],
219        [ 1.,  1.,  1.,  2.,  2.],
220        [ 1., 22.,  1.,  2.,  2.]], dtype=float32)
221 >>> X_norm = sc.pp.normalize_total(adata, target_sum=1, inplace=False)["X"]
Expected:
    normalizing counts per cell
        finished (0:00:00)
Got nothing

#x1B[1m#x1B[.../scanpy/preprocessing/_normalization.py#x1B[0m:221: DocTestFailure

tests/test_logging.py::test_records

Stack Traces | 0.022s run time

caplog = <_pytest.logging.LogCaptureFixture object at 0x7ff03dc80750>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_records#x1B[39;49;00m(caplog: pytest.LogCaptureFixture) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        s.verbosity = Verbosity.debug#x1B[90m#x1B[39;49;00m
        log.error(#x1B[33m"#x1B[39;49;00m#x1B[33m0#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        log.warning(#x1B[33m"#x1B[39;49;00m#x1B[33m1#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        log.info(#x1B[33m"#x1B[39;49;00m#x1B[33m2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        log.hint(#x1B[33m"#x1B[39;49;00m#x1B[33m3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        log.debug(#x1B[33m"#x1B[39;49;00m#x1B[33m4#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m caplog.record_tuples == [#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mroot#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m40#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33m0#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mroot#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m30#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33m1#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mroot#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m20#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33m2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mroot#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m15#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33m3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            (#x1B[33m"#x1B[39;49;00m#x1B[33mroot#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m10#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33m4#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[31mE       AssertionError: assert [('root', 40,...ot', 30, '1')] == [('root', 40,...ot', 10, '4')]#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m
#x1B[1m#x1B[31mE         Right contains 3 more items, first extra item: #x1B[0m(#x1B[33m'#x1B[39;49;00m#x1B[33mroot#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m, #x1B[94m20#x1B[39;49;00m, #x1B[33m'#x1B[39;49;00m#x1B[33m2#x1B[39;49;00m#x1B[33m'#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m
#x1B[1m#x1B[31mE         Full diff:#x1B[0m
#x1B[1m#x1B[31mE         #x1B[0m#x1B[90m #x1B[39;49;00m [#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m     (#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m         'root',#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m         40,#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m         '0',#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m     ),#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m     (#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m         'root',#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m         30,#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m         '1',#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m     ),#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-     (#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         'root',#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         20,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         '2',#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-     ),#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-     (#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         'root',#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         15,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         '3',#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-     ),#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-     (#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         'root',#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         10,#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-         '4',#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[91m-     ),#x1B[39;49;00m#x1B[90m#x1B[39;49;00m#x1B[0m
#x1B[1m#x1B[31mE         #x1B[90m #x1B[39;49;00m ]#x1B[90m#x1B[39;49;00m#x1B[0m

#x1B[1m#x1B[31mtests/test_logging.py#x1B[0m:45: AssertionError

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flying-sheep and others added 3 commits April 21, 2026 17:05

feat: pydantic settings

28af1cc

prevent crash

8c3c25c

cleanup

23adaa7

Co-authored-by: Copilot <copilot@github.com>

flying-sheep mentioned this pull request Apr 23, 2026

settings class scverse/scverse-misc#8

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feat: pydantic settings#4081

feat: pydantic settings#4081
flying-sheep wants to merge 3 commits intomainfrom
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flying-sheep commented Apr 21, 2026 •

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flying-sheep commented Apr 21, 2026 •

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