pytest 8 compatibility

[ivirshup]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the master branch of scanpy.

What happened?

When running the tests with pytest<=8, the doctest for scanpy.preprocessing._simple.filter_cells errors in a way I can't quite figure out how to fix.

I think what's happening is that the "error on warning" isn't being overridden correctly when we expect the test to warn. Possibly related to pytest-dev/pytest#11759

@flying-sheep any ideas how to fix? I will just pin pytest for now.

Minimal code sample

Examples
    --------
    >>> import scanpy as sc
    >>> adata = sc.datasets.krumsiek11()
    UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
        utils.warn_names_duplicates("obs")

Error output

======================================================================================================================= FAILURES =======================================================================================================================
_________________________________________________________________________________________________ [doctest] scanpy.preprocessing._simple.filter_cells __________________________________________________________________________________________________
081         Boolean index mask that does filtering. `True` means that the
082         cell is kept. `False` means the cell is removed.
083     number_per_cell
084         Depending on what was thresholded (`counts` or `genes`),
085         the array stores `n_counts` or `n_cells` per gene.
086 
087     Examples
088     --------
089     >>> import scanpy as sc
090     >>> adata = sc.datasets.krumsiek11()
UNEXPECTED EXCEPTION: UserWarning('Observation names are not unique. To make them unique, call `.obs_names_make_unique`.')
Traceback (most recent call last):
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/doctest.py", line 1353, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest scanpy.preprocessing._simple.filter_cells[1]>", line 1, in <module>
  File "/mnt/workspace/repos/scanpy/scanpy/datasets/_datasets.py", line 109, in krumsiek11
    adata = read(filename, first_column_names=True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/mnt/workspace/repos/scanpy/scanpy/readwrite.py", line 124, in read
    return _read(
           ^^^^^^
  File "/mnt/workspace/repos/scanpy/scanpy/readwrite.py", line 801, in _read
    adata = read_text(filename, delimiter, first_column_names)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/anndata/_io/read.py", line 360, in read_text
    return _read_text(f, delimiter, first_column_names, dtype)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/anndata/_io/read.py", line 471, in _read_text
    return AnnData(
           ^^^^^^^^
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/anndata/_core/anndata.py", line 362, in __init__
    self._init_as_actual(
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/anndata/_core/anndata.py", line 574, in _init_as_actual
    self._check_uniqueness()
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/anndata/_core/anndata.py", line 1906, in _check_uniqueness
    utils.warn_names_duplicates("obs")
  File "/mnt/workspace/mambaforge/envs/scanpy-dev/lib/python3.11/site-packages/anndata/utils.py", line 275, in warn_names_duplicates
    warnings.warn(
UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
/mnt/workspace/repos/scanpy/scanpy/preprocessing/_simple.py:90: UnexpectedException

Versions

-----
anndata     0.10.5.post1
scanpy      1.10.0.dev197+g96e19540
-----
IPython             8.20.0
PIL                 10.2.0
asciitree           NA
asttokens           NA
cloudpickle         3.0.0
cycler              0.12.1
cython_runtime      NA
dask                2024.1.1
dateutil            2.8.2
decorator           5.1.1
executing           2.0.1
fasteners           0.19
h5py                3.10.0
igraph              0.11.3
iniconfig           NA
jedi                0.19.1
jinja2              3.1.3
joblib              1.3.2
kiwisolver          1.4.5
legacy_api_wrap     NA
leidenalg           0.10.2
llvmlite            0.41.1
markupsafe          2.1.4
matplotlib          3.8.2
mpl_toolkits        NA
msgpack             1.0.7
natsort             8.4.0
numba               0.58.1
numcodecs           0.12.1
numpy               1.26.3
packaging           23.2
pandas              2.2.0
parso               0.8.3
pexpect             4.9.0
pluggy              1.4.0
prompt_toolkit      3.0.43
psutil              5.9.8
ptyprocess          0.7.0
pure_eval           0.2.2
py                  NA
pygments            2.17.2
pyparsing           3.1.1
pytest              8.0.0
pytz                2023.4
scipy               1.12.0
session_info        1.0.0
six                 1.16.0
sklearn             1.4.0
sparse              0.15.1
stack_data          0.6.3
tblib               3.0.0
texttable           1.7.0
threadpoolctl       3.2.0
tlz                 0.12.1
toolz               0.12.1
traitlets           5.14.1
wcwidth             0.2.13
yaml                6.0.1
zarr                2.16.1
zipp                NA
-----
Python 3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:43:09) [GCC 12.3.0]
Linux-5.15.0-87-generic-x86_64-with-glibc2.35
-----
Session information updated at 2024-01-29 14:16

[flying-sheep]

Same way as in anndata: We use an autouse fixture and directly execute the effects instead of adding marks.

[flying-sheep]

OK, that’s weird: Now there’s a bunch of ImageComparisonFailures in the minimal tests job. are they unrelated? A fluke?

https://dev.azure.com/scverse/scanpy/_build/results?buildId=5487&view=logs&j=50ff7263-9206-5a84-1219-938c9ee7fde7&t=2e49bd34-47bd-5a56-3183-6247e293d44d