Variables injected in doctest_namespace no longer loaded in Pytest 9.1.x

[Zeitsperre]

Description

I'm running into issues with pytest 9.1.x when running my doctests. I've been able to inject variables and functions into the namespace for doctests via a fixture so that I don't need to explicitly write these things into all my doctests, e.g.:

@pytest.fixture(scope="session", autouse=True)
def doctest_setup(doctest_namespace, nimbus, worker_id, open_dataset) -> None:  # numpydoc ignore=PR01
    """Gather testing data on doctest run."""
    testing_setup_warnings()
    gather_testing_data(worker_cache_dir=nimbus.path, worker_id=worker_id)
    doctest_namespace.update(custom_testing_data(nimbus=nimbus))

    class AttrDict(dict):  # numpydoc ignore=PR01
        """A dictionary that allows access to its keys as attributes."""

        def __init__(self, *args, **kwargs):
            super().__init__(*args, **kwargs)
            self.__dict__ = self

    xr = AttrDict()
    xr["DataArray"] = xarray.DataArray
    xr["date_range"] = xarray.date_range
    xr["open_dataset"] = custom_library.open_dataset
    doctest_namespace["xr"] = xr

    doctest_namespace.update(add_doctest_filepaths())
    doctest_namespace.update(add_example_file_paths())

This has been working well for many years, but it seems like there's been a major change in how the latest pytest collects/runs fixtures for doctests.

All my tests are now failing with NameError: name '<variable/function name injected from doctest_setup>' is not defined.

Environment Setup

Package                       Version
----------------------------- ------------
alabaster                     1.0.0
annotated-doc                 0.0.4
annotated-types               0.7.0
anyio                         4.14.1
ast_serialize                 0.6.0
astroid                       4.0.4
asttokens                     3.0.1
attrs                         26.1.0
babel                         2.18.0
beautifulsoup4                4.15.0
bleach                        6.4.0
boltons                       26.0.0
Bottleneck                    1.6.0
bracex                        3.0
bump-my-version               1.4.1
cachetools                    7.1.4
certifi                       2026.6.17
cf_xarray                     0.11.3
cfgv                          3.5.0
cftime                        1.6.5
charset-normalizer            3.4.8
click                         8.4.2
cloudpickle                   3.1.2
codespell                     2.4.2
colorama                      0.4.6
comm                          0.2.3
contourpy                     1.3.3
coverage                      7.15.0
cycler                        0.12.1
dask                          2026.6.0
debugpy                       1.8.21
decorator                     5.3.1
defusedxml                    0.7.1
deptry                        0.25.1
dill                          0.4.1
distlib                       0.4.3
docutils                      0.22.4
execnet                       2.1.2
executing                     2.2.1
fastjsonschema                2.21.2
filelock                      3.29.5
flake8                        7.3.0
flake8-rst-docstrings         0.4.0
flexcache                     0.3
flexparser                    0.4
flox                          0.11.2
fonttools                     4.63.0
fsspec                        2026.6.0
h11                           0.16.0
h5netcdf                      1.8.1
h5py                          3.16.0
httpcore2                     2.5.0
httpx2                        2.5.0
identify                      2.6.19
idna                          3.18
imagesize                     2.0.0
iniconfig                     2.3.0
ipykernel                     7.3.0
ipython                       9.15.0
ipython_pygments_lexers       1.1.1
isort                         8.0.1
jedi                          0.20.0
Jinja2                        3.1.6
joblib                        1.5.3
jsonpickle                    4.1.2
jsonschema                    4.26.0
jsonschema-specifications     2025.9.1
jupyter_client                8.9.1
jupyter_core                  5.9.1
jupyterlab_pygments           0.3.0
kiwisolver                    1.5.0
librt                         0.12.0
llvmlite                      0.48.0
lmoments3                     1.0.8
locket                        1.0.0
markdown-it-py                4.2.0
MarkupSafe                    3.0.3
matplotlib                    3.11.0
matplotlib-inline             0.2.2
mccabe                        0.7.0
mdurl                         0.1.2
mistune                       3.3.2
mypy                          2.1.0
mypy_extensions               1.1.0
narwhals                      2.23.0
nbclient                      0.11.0
nbconvert                     7.17.1
nbformat                      5.10.4
nbval                         0.11.0
nest-asyncio2                 1.7.2
nodeenv                       1.10.0
numba                         0.66.0
numbagg                       0.9.4
numpy                         2.4.6
numpy-groupies                0.11.3
numpydoc                      1.10.0
packaging                     26.2
pandas                        3.0.3
pandas-stubs                  3.0.3.260530
pandocfilters                 1.5.1
parso                         0.8.7
partd                         1.4.2
pathspec                      1.1.1
patsy                         1.0.2
pexpect                       4.9.0
pillow                        12.3.0
Pint                          0.25.3
pip                           26.1.2
platformdirs                  4.10.0
pluggy                        1.6.0
pooch                         1.9.0
pre_commit                    4.6.0
prompt_toolkit                3.0.52
psutil                        7.2.2
ptyprocess                    0.7.0
pure_eval                     0.2.3
pyarrow                       24.0.0
pycodestyle                   2.14.0
pydantic                      2.13.4
pydantic_core                 2.46.4
pydantic-settings             2.14.2
pyflakes                      3.4.0
Pygments                      2.20.0
pylint                        4.0.6
pymannkendall                 1.4.3
pyparsing                     3.3.2
pyproject-api                 1.10.1
pytest                        9.1.1
pytest-cov                    7.1.0
pytest-socket                 0.8.0
pytest-timeout                2.4.0
pytest-xdist                  3.8.0
python-dateutil               2.9.0.post0
python-discovery              1.4.3
python-dotenv                 1.2.2
PyYAML                        6.0.3
pyzmq                         27.1.0
questionary                   2.1.1
referencing                   0.37.0
requests                      2.34.2
requirements-parser           0.13.1
restructuredtext_lint         2.0.2
rich                          15.0.0
rich-click                    1.9.8
roman-numerals                4.1.0
rpds-py                       2026.6.3
ruff                          0.15.20
scikit-learn                  1.9.0
scipy                         1.18.0
shellingham                   1.5.4
six                           1.17.0
snowballstemmer               3.1.1
soupsieve                     2.8.4
Sphinx                        9.1.0
sphinxcontrib-applehelp       2.0.0
sphinxcontrib-devhelp         2.0.0
sphinxcontrib-htmlhelp        2.1.0
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-qthelp          2.0.0
sphinxcontrib-serializinghtml 2.0.0
stack-data                    0.6.3
statsmodels                   0.14.6
threadpoolctl                 3.6.0
tinycss2                      1.5.1
tokenize_rt                   6.2.0
tomli                         2.4.1
tomli_w                       1.2.0
tomlkit                       0.15.0
toolz                         1.1.0
tornado                       6.5.7
tox                           4.56.1
tox-gh                        1.7.1
traitlets                     5.15.1
truststore                    0.10.4
typer                         0.26.8
typing_extensions             4.16.0
typing-inspection             0.4.2
urllib3                       2.7.0
virtualenv                    21.5.2
vulture                       2.16
wcmatch                       10.2.1
wcwidth                       0.8.2
webencodings                  0.5.1
xarray                        2026.4.0
xclim                         0.61.2.dev1
xsdba                         0.7.0
yamale                        6.1.0
yamllint                      1.38.0

Questions

• Is this a bug or a new design direction?
• Is there a new method to set up pytest fixtures for doctests that maintains the same behaviour as before?

Possibly related: #14635

[The-Compiler]

Can you show a minimal reproducer? Without more information, assuming this is indeed just a duplicate of #14635 and the fixture simply isn't run.

Maybe you could also add an 1/0 to the fixture (or run with --setup-show for a less crude approach) to see if the fixture is getting run at all.

[Zeitsperre]

Sure thing. Here's the simplified structure of my project:

src -> xclim -> testing -> conftest.py (doctest-specific)
tests -> conftest.py (general testing)

In my project, the call to run the doctests is:

pytest --rootdir src/xclim/testing --config-file=src/xclim/testing/conftest.py --numprocesses=0 --doctest-modules src/xclim

Under pytest 9.0, I can see the following being called:

SETUP    S doctest_namespace
SETUP    S tmp_path_factory
SETUP    S threadsafe_data_dir (fixtures used: tmp_path_factory)
SETUP    S worker_id
SETUP    S nimbus (fixtures used: threadsafe_data_dir, worker_id)
SETUP    S open_dataset (fixtures used: threadsafe_data_dir, worker_id)
SETUP    S doctest_setup (fixtures used: doctest_namespace, nimbus, open_dataset, worker_id)
SETUP    S is_matplotlib_installed (fixtures used: doctest_namespace)
... (lots of passing tests with fixtures marked as loaded)
TEARDOWN S is_matplotlib_installed
TEARDOWN S doctest_setup
TEARDOWN S open_dataset
TEARDOWN S nimbus
TEARDOWN S worker_id
TEARDOWN S threadsafe_data_dir
TEARDOWN S tmp_path_factory
TEARDOWN S doctest_namespace

Under pytest 9.1, it looks like almost no fixtures are loaded (running with -x flag):

SETUP    S doctest_namespace
        core/bootstrapping.py::xclim.core.bootstrapping.percentile_bootstrap F
TEARDOWN S doctest_namespace

When adding a ZeroDivisionError to my fixture, it correctly fails in pytest v9.0 and is never reached in v9.1.

[The-Compiler]

Probably indeed a duplicate of #14635 then. @RonnyPfannschmidt wdyt?