BUG: collect methods from private superclasses #179

ev-br · 2024-12-15T16:34:19Z

ev-br · 2024-12-15T16:35:18Z

@mdhaber @steppi could you please check that this branch fixes the issue with stats docstrings?

ev-br · 2024-12-17T08:22:35Z

THere is now a little hiccup from gh-180: some things from superclasses are collected twice (Klass.__weakref__). The standard library doctest finding maintains the cache of things already collected, need to duplicate it here.

EDIT: worked around it.

ev-br · 2024-12-17T11:03:50Z

I can't say I like how __weakref__ appears depending on the strategy being 'None' or not. Not much to do about it, and it is rather unlikely to have examples in its docstring anyway, so let's just roll with how it is now.

mdhaber · 2024-12-17T17:17:51Z

Oops, missed the ping. I can't test locally, but I could create a PR to the SciPy repo with a mistake in a doctest to see whether it fails now?

ev-br · 2024-12-17T17:40:33Z

Yup, that'd be helpful if you can't test locally. OTOH, why is that. If you can build scipy locally, installing an additional pure python lib is hardly a blocker?

That said, I'm pretty confident this one works as intended, no big issues in either scipy or numpy with scipy-doctest==1.6 which contains this fix. So if you're pressed on time, it's not blocking.

mdhaber · 2024-12-17T17:43:35Z

Yup, that'd be helpful if you can't test locally. OTOH, why is that. If you can build scipy locally, installing an additional pure python lib is hardly a blocker?

If you can give me the invocation to run the refguide check without dev.py, I can try. But I use an in-place build, and when I've asked before, the answer involved dev.py.

ev-br · 2024-12-17T17:51:35Z

Ah, interesting. I think it's

pytest --doctest-modules --doctest-collect=api path/to/scipy

The --doctest-modules --doctest-collect=api part I'm sure about; whether this plays ball with selecting specific test files and/or needs explicit --ignores, is... untested.

ev-br · 2024-12-17T17:54:25Z

Also:

make sure you've updated scipy-doctest: the fix is in 1.6 only.
dev.py additionally passes --assert-plain to pytest; I think it's not needed anymore, but it's pytest magic, so hard to be sure.

mdhaber · 2024-12-17T18:01:06Z

And I use mamba. Install scipy-doctest with pip nonetheless?

ev-br · 2024-12-17T18:13:13Z

Yes, I also use mamba and have no issues with pip install scipy-doctest or pip install -e ..

mdhaber · 2024-12-17T18:22:26Z

I'm in the scipy repo. I get collection errors when the path/to/scipy is just the scipy subdirectory.

(scipy-dev) C:\Users\matth\Desktop\scipy>pytest --doctest-modules --doctest-collect=api scipy
meson-python: building scipy: meson compile
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: C:\Users\matth\miniforge3\envs\scipy-dev\Library\bin\ninja.EXE
[2/338] Generating subprojects/highs/src/HConfig.h with a custom command
================================================= test session starts =================================================
platform win32 -- Python 3.12.5, pytest-8.3.2, pluggy-1.5.0
rootdir: C:\Users\matth\Desktop\scipy
configfile: pytest.ini
plugins: anyio-4.4.0, hypothesis-6.112.0, cov-5.0.0, timeout-2.3.1, xdist-3.6.1, scipy_doctest-1.6
collected 3866 items / 20 errors

======================================================= ERRORS ========================================================
___________________________________ ERROR collecting scipy/_build_utils/tempita.py ____________________________________
import file mismatch:
imported module 'tempita' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\scipy\_build_utils\tempita
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\_build_utils\tempita.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
_____________________________________ ERROR collecting scipy/_lib/_boost_utils.py _____________________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\_boost_utils.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy._lib._boost_utils'
____________________________________ ERROR collecting scipy/_lib/_unuran_utils.py _____________________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\_unuran_utils.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy._lib._unuran_utils'
______________________________ ERROR collecting scipy/_lib/array_api_extra/docs/conf.py _______________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\array_api_extra\docs\conf.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\metadata\__init__.py:397: in from_name
    return next(cls.discover(name=name))
E   StopIteration

During handling of the above exception, another exception occurred:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
scipy\_lib\array_api_extra\docs\conf.py:5: in <module>
    version = release = importlib.metadata.version("array_api_extra")
..\..\miniforge3\envs\scipy-dev\Lib\importlib\metadata\__init__.py:889: in version
    return distribution(distribution_name).version
..\..\miniforge3\envs\scipy-dev\Lib\importlib\metadata\__init__.py:862: in distribution
    return Distribution.from_name(distribution_name)
..\..\miniforge3\envs\scipy-dev\Lib\importlib\metadata\__init__.py:399: in from_name
    raise PackageNotFoundError(name)
E   importlib.metadata.PackageNotFoundError: No package metadata was found for array_api_extra
_____________________ ERROR collecting scipy/_lib/array_api_extra/src/array_api_extra/__init__.py _____________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\array_api_extra\src\array_api_extra\__init__.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:5: in <module>
    from ..._array_api_compat_vendor import (  # pyright: ignore[reportMissingImports]
E   ImportError: attempted relative import beyond top-level package

During handling of the above exception, another exception occurred:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
scipy\_lib\array_api_extra\src\array_api_extra\__init__.py:1: in <module>
    from ._funcs import atleast_nd, cov, create_diagonal, expand_dims, kron, setdiff1d, sinc
scipy\_lib\array_api_extra\src\array_api_extra\_funcs.py:3: in <module>
    from ._lib import _compat, _utils
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:10: in <module>
    from array_api_compat import (  # pyright: ignore[reportMissingTypeStubs]
E   ModuleNotFoundError: No module named 'array_api_compat'
______________________ ERROR collecting scipy/_lib/array_api_extra/src/array_api_extra/_funcs.py ______________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\array_api_extra\src\array_api_extra\_funcs.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:5: in <module>
    from ..._array_api_compat_vendor import (  # pyright: ignore[reportMissingImports]
E   ImportError: attempted relative import beyond top-level package

During handling of the above exception, another exception occurred:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
scipy\_lib\array_api_extra\src\array_api_extra\__init__.py:1: in <module>
    from ._funcs import atleast_nd, cov, create_diagonal, expand_dims, kron, setdiff1d, sinc
scipy\_lib\array_api_extra\src\array_api_extra\_funcs.py:3: in <module>
    from ._lib import _compat, _utils
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:10: in <module>
    from array_api_compat import (  # pyright: ignore[reportMissingTypeStubs]
E   ModuleNotFoundError: No module named 'array_api_compat'
___________________ ERROR collecting scipy/_lib/array_api_extra/src/array_api_extra/_lib/_compat.py ___________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:5: in <module>
    from ..._array_api_compat_vendor import (  # pyright: ignore[reportMissingImports]
E   ImportError: attempted relative import beyond top-level package

During handling of the above exception, another exception occurred:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:10: in <module>
    from array_api_compat import (  # pyright: ignore[reportMissingTypeStubs]
E   ModuleNotFoundError: No module named 'array_api_compat'
___________________ ERROR collecting scipy/_lib/array_api_extra/src/array_api_extra/_lib/_utils.py ____________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\_lib\array_api_extra\src\array_api_extra\_lib\_utils.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:5: in <module>
    from ..._array_api_compat_vendor import (  # pyright: ignore[reportMissingImports]
E   ImportError: attempted relative import beyond top-level package

During handling of the above exception, another exception occurred:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_utils.py:1: in <module>
    from . import _compat
scipy\_lib\array_api_extra\src\array_api_extra\_lib\_compat.py:10: in <module>
    from array_api_compat import (  # pyright: ignore[reportMissingTypeStubs]
E   ModuleNotFoundError: No module named 'array_api_compat'
________________________________ ERROR collecting scipy/interpolate/_interpnd_info.py _________________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\interpolate\_interpnd_info.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy.interpolate._interpnd_info'
______________________________ ERROR collecting scipy/interpolate/_rbfinterp_pythran.py _______________________________
import file mismatch:
imported module 'scipy.interpolate._rbfinterp_pythran' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\build\cp312\scipy\interpolate\_rbfinterp_pythran.cp312-win_amd64.pyd
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\interpolate\_rbfinterp_pythran.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
____________________________ ERROR collecting scipy/linalg/_cython_signature_generator.py _____________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\linalg\_cython_signature_generator.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy.linalg._cython_signature_generator'
___________________________________ ERROR collecting scipy/linalg/_generate_pyx.py ____________________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\linalg\_generate_pyx.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy.linalg._generate_pyx'
__________________________________ ERROR collecting scipy/linalg/_linalg_pythran.py ___________________________________
import file mismatch:
imported module 'scipy.linalg._linalg_pythran' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\build\cp312\scipy\linalg\_linalg_pythran.cp312-win_amd64.pyd
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\linalg\_linalg_pythran.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
________________________________ ERROR collecting scipy/linalg/_matfuncs_sqrtm_triu.py ________________________________
import file mismatch:
imported module 'scipy.linalg._matfuncs_sqrtm_triu' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\build\cp312\scipy\linalg\_matfuncs_sqrtm_triu.cp312-win_amd64.pyd
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\linalg\_matfuncs_sqrtm_triu.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
_________________________ ERROR collecting scipy/ndimage/utils/generate_label_testvectors.py __________________________
scipy\ndimage\utils\generate_label_testvectors.py:44: in <module>
    generate_test_vecs("label_inputs.txt", "label_strels.txt", "label_results.txt")
        __builtins__ = <builtins>
        __cached__ = 'C:\\Users\\matth\\Desktop\\scipy\\scipy\\ndimage\\utils\\__pycache__\\generate_label_testvectors.cpython-312.pyc'
        __doc__    = None
        __file__   = 'C:\\Users\\matth\\Desktop\\scipy\\scipy\\ndimage\\utils\\generate_label_testvectors.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x000001D36DCEE030>
        __name__   = 'generate_label_testvectors'
        __package__ = ''
        __spec__   = ModuleSpec(name='generate_label_testvectors', loader=<_frozen_importlib_external.SourceFileLoader object at 0x000001D36DCEE030>, origin='C:\\Users\\matth\\Desktop\\scipy\\scipy\\ndimage\\utils\\generate_label_testvectors.py')
        __warningregistry__ = {'version': 4331}
        generate_test_vecs = <function generate_test_vecs at 0x000001D36DD0B1A0>
        label      = <function label at 0x000001D36B4AA0C0>
        np         = <module 'numpy' from 'C:\\Users\\matth\\miniforge3\\envs\\scipy-dev\\Lib\\site-packages\\numpy\\__init__.py'>
scipy\ndimage\utils\generate_label_testvectors.py:34: in generate_test_vecs
    strels = [np.fromstring(s, dtype=int).reshape((3, 3))
E   DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
        bitimage   = <function generate_test_vecs.<locals>.bitimage at 0x000001D36DD0B060>
        data       = [array([[1., 1., 1., 1., 1., 1., 1.],
       [1., 1., 1., 1., 1., 1., 1.],
       [1., 1., 1., 1., 1., 1., 1.],
      ...,
       [False, False, False,  True, False, False, False],
       [ True, False,  True,  True,  True, False,  True]])]
        infile     = 'label_inputs.txt'
        resultfile = 'label_results.txt'
        strelfile  = 'label_strels.txt'
        strels     = [array([[1., 1., 1.],
       [1., 1., 1.],
       [1., 1., 1.]]), array([[0., 0., 0.],
       [0., 0., 0.],
       [0....alse, False,  True]]), array([[False, False, False],
       [ True,  True,  True],
       [False, False, False]]), ...]
__________________________________ ERROR collecting scipy/optimize/_group_columns.py __________________________________
import file mismatch:
imported module 'scipy.optimize._group_columns' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\build\cp312\scipy\optimize\_group_columns.cp312-win_amd64.pyd
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\optimize\_group_columns.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
_________________________________ ERROR collecting scipy/signal/_max_len_seq_inner.py _________________________________
import file mismatch:
imported module 'scipy.signal._max_len_seq_inner' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\build\cp312\scipy\signal\_max_len_seq_inner.cp312-win_amd64.pyd
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\signal\_max_len_seq_inner.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
_______________________________ ERROR collecting scipy/sparse/_generate_sparsetools.py ________________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\sparse\_generate_sparsetools.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy.sparse._generate_sparsetools'
___________________________________ ERROR collecting scipy/special/_generate_pyx.py ___________________________________
ImportError while importing test module 'C:\Users\matth\Desktop\scipy\scipy\special\_generate_pyx.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
..\..\miniforge3\envs\scipy-dev\Lib\importlib\__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
E   ModuleNotFoundError: No module named 'scipy.special._generate_pyx'
___________________________________ ERROR collecting scipy/stats/_stats_pythran.py ____________________________________
import file mismatch:
imported module 'scipy.stats._stats_pythran' has this __file__ attribute:
  C:\Users\matth\Desktop\scipy\build\cp312\scipy\stats\_stats_pythran.cp312-win_amd64.pyd
which is not the same as the test file we want to collect:
  C:\Users\matth\Desktop\scipy\scipy\stats\_stats_pythran.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
=============================================== short test summary info ===============================================
ERROR scipy/_build_utils/tempita.py
ERROR scipy/_lib/_boost_utils.py
ERROR scipy/_lib/_unuran_utils.py
ERROR scipy/_lib/array_api_extra/docs/conf.py
ERROR scipy/_lib/array_api_extra/src/array_api_extra/__init__.py
ERROR scipy/_lib/array_api_extra/src/array_api_extra/_funcs.py
ERROR scipy/_lib/array_api_extra/src/array_api_extra/_lib/_compat.py
ERROR scipy/_lib/array_api_extra/src/array_api_extra/_lib/_utils.py
ERROR scipy/interpolate/_interpnd_info.py
ERROR scipy/interpolate/_rbfinterp_pythran.py
ERROR scipy/linalg/_cython_signature_generator.py
ERROR scipy/linalg/_generate_pyx.py
ERROR scipy/linalg/_linalg_pythran.py
ERROR scipy/linalg/_matfuncs_sqrtm_triu.py
ERROR scipy/ndimage/utils/generate_label_testvectors.py - DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use ...
ERROR scipy/optimize/_group_columns.py
ERROR scipy/signal/_max_len_seq_inner.py
ERROR scipy/sparse/_generate_sparsetools.py
ERROR scipy/special/_generate_pyx.py
ERROR scipy/stats/_stats_pythran.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 20 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
================================================= 20 errors in 6.89s ==================================================

When I specify the file, no tests run:

(scipy-dev) C:\Users\matth\Desktop\scipy>pytest --doctest-modules --doctest-collect=api scipy/stats/_probability_distribution.py
meson-python: building scipy: meson compile
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: C:\Users\matth\miniforge3\envs\scipy-dev\Library\bin\ninja.EXE
[2/338] Generating subprojects/highs/src/HConfig.h with a custom command
================================================= test session starts =================================================
platform win32 -- Python 3.12.5, pytest-8.3.2, pluggy-1.5.0
rootdir: C:\Users\matth\Desktop\scipy
configfile: pytest.ini
plugins: anyio-4.4.0, hypothesis-6.112.0, cov-5.0.0, timeout-2.3.1, xdist-3.6.1, scipy_doctest-1.6
collected 0 items

================================================ no tests ran in 1.37s ================================================

ev-br · 2024-12-17T18:34:56Z

Ugh. Can you detail how you build scipy? I'll try replicating.

mdhaber · 2024-12-17T19:05:52Z

It sounds like spin will support in-place builds, so it might not be worth the trouble?

But I follow the Windows MinGW-w64 + Conda env instructions at Building from source, with the required exceptions: I remove compilers from environment.yml before creating the environment, and instead of pip install scipy --no-build-isolation --no-binary scipy, I do python -m pip install --no-build-isolation --editable .

lucascolley · 2024-12-17T19:16:25Z

let me look at getting scipy_doctest on conda-forge

ev-br · 2024-12-17T19:36:46Z

Tried (on linux, but that won't matter, hopefully):

$ git clean -xdf
$ pip install --no-build-isolation -e .

... seems to have been built ...

$ pytest -v --doctest-modules --doctest-collect=api --pyargs scipy

Fails at collection stage, similar to #179 (comment)

$ pytest -v --doctest-modules --doctest-collect=api build/cp311/scipy/

runs but misses our configuration. Not strange because conftest.py has not been copied to build/

$ pytest -v --doctest-modules --doctest-collect=api --import-mode=importlib ./scipy --ignore=scipy/special/_generate_pyx.py --ignore=scipy/_build_utils --ignore=scipy/ndimage/utils/

Works! The list of --ignores is constructed experimentally : was adding --ignore of what it complained until it stopped.

Let me now check if --import-mode=importlib is relevant or not:

$ pytest -v --doctest-modules --doctest-collect=api ./scipy --ignore=scipy/special/_generate_pyx.py --ignore=scipy/_build_utils --ignore=scipy/ndimage/utils/

fails at collection, so yes, it's needed. So to sum up:

In the scipy directory (where you ran pip install, feed the scipy directory to pytest: pytest ./scipy
Add --doctest-modules to activate doctesting, add --doctest-collect=api to match the scipy's dev.py
Add --import-mode=importlib (no idea what it does and, yes, I read the docs and fora, and no, I still have no idea)
Add enough --ignore=path/which/fails/collection

ev-br · 2024-12-17T19:37:39Z

let me look at getting scipy_doctest on conda-forge

Wow, thank you Lucas!

mdhaber · 2024-12-17T19:42:59Z

I tried:

(scipy-dev) C:\Users\matth\Desktop\scipy>pytest -v --doctest-modules --doctest-collect=api --import-mode=importlib  ./scipy/stats/_distribution_infrastructure.py --ignore=scipy/special/_generate_pyx.py --ignore=scipy/_build_utils --ignore=s
cipy/ndimage/utils/
meson-python: building scipy: meson compile
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: C:\Users\matth\miniforge3\envs\scipy-dev\Library\bin\ninja.EXE
[2/338] Generating subprojects/highs/src/HConfig.h with a custom command
================================================= test session starts =================================================
platform win32 -- Python 3.12.5, pytest-8.3.2, pluggy-1.5.0 -- C:\Users\matth\miniforge3\envs\scipy-dev\python.exe
cachedir: .pytest_cache
hypothesis profile 'deterministic' -> database=None, deadline=None, print_blob=True, derandomize=True, suppress_health_check=[HealthCheck.data_too_large, HealthCheck.filter_too_much, HealthCheck.too_slow, HealthCheck.large_base_example, HealthCheck.function_scoped_fixture, HealthCheck.differing_executors]
rootdir: C:\Users\matth\Desktop\scipy
configfile: pytest.ini
plugins: anyio-4.4.0, hypothesis-6.112.0, cov-5.0.0, timeout-2.3.1, xdist-3.6.1, scipy_doctest-1.6
collected 28 items

================================================ no tests ran in 1.44s ================================================

which is your magic command but with the full path to the file in question, but still it doesn't run : (

ev-br · 2024-12-17T19:55:11Z

Ah, that actually has an explanation :-). TL;DR: remove --doctest-collect=api

Why on earth? This flag makes doctest collection only look at public objects. What is public is --- in this single-file case --- decided by what is __all__. Since _distribution_infrastructure.py does not have __all__, nothing happends. See how it "collected 28 tests" but then "no tests run", they all got removed by the piece of logic which filters out what's public.

This is what dev.py does (and spin check-docs does in numpy):

        if not args.tests:
            extra_argv += ['--doctest-collect=api']

Without this switch, you're back to collecting all doctests from all functions, so you may get extra failures from objects which are actually private in scipy, but the doctester does not know it.

No idea what this really does, but apparently it does something. See the discussion around #179 (comment)

mdhaber · 2024-12-17T20:10:54Z

Hah, ok. Now the problem is that the tests are passing locally (which they shouldn't). They failed as expected on CI : )

(scipy-dev) C:\Users\matth\Desktop\scipy>pytest -v --doctest-modules --import-mode=importlib  ./scipy/stats/_new_distributions.py --ignore=scipy/special/_generate_pyx.py --ignore=scipy/_build_utils --ignore=s
meson-python: building scipy: meson compile
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: C:\Users\matth\miniforge3\envs\scipy-dev\Library\bin\ninja.EXE
[2/338] Generating subprojects/highs/src/HConfig.h with a custom command
================================================= test session starts =================================================
platform win32 -- Python 3.12.5, pytest-8.3.2, pluggy-1.5.0 -- C:\Users\matth\miniforge3\envs\scipy-dev\python.exe
cachedir: .pytest_cache
hypothesis profile 'deterministic' -> database=None, deadline=None, print_blob=True, derandomize=True, suppress_health_check=[HealthCheck.data_too_large, HealthCheck.filter_too_much, HealthCheck.too_slow, HealthCheck.large_base_example, HealthCheck.function_scoped_fixture, HealthCheck.differing_executors]
rootdir: C:\Users\matth\Desktop\scipy
configfile: pytest.ini
plugins: anyio-4.4.0, hypothesis-6.112.0, cov-5.0.0, timeout-2.3.1, xdist-3.6.1, scipy_doctest-1.6
collected 2 items

scipy/stats/_new_distributions.py::scipy.stats._new_distributions.Normal PASSED                                  [ 50%]
scipy/stats/_new_distributions.py::scipy.stats._new_distributions.Uniform PASSED                                 [100%]

================================================== 2 passed in 1.87s ==================================================

ev-br · 2024-12-17T20:18:32Z

Don't know. Wrong branch?

Applied

$ git diff
diff --git a/scipy/stats/_distribution_infrastructure.py b/scipy/stats/_distribution_infrastructure.py
index 291f3d997a..be0cfce12f 100644
--- a/scipy/stats/_distribution_infrastructure.py
+++ b/scipy/stats/_distribution_infrastructure.py
@@ -211,6 +211,9 @@ class _Domain(ABC):
         Returns a text representation of the domain (e.g. ``[0, b)``).
         Used for generating documentation.
 
+    >>> 2 / 3
+    4
+
     """
     symbols = {np.inf: r"\infty", -np.inf: r"-\infty", np.pi: r"\pi", -np.pi: r"-\pi"}

to main, and it does pick a failure in _Domain for me locally.

lucascolley · 2024-12-17T20:22:15Z

https://anaconda.org/conda-forge/scipy-doctest

ev-br · 2024-12-17T20:27:27Z

How do we advertise it? Maybe add conda-forge and pypi badges to README? I personally don't care about the download counts, just that these builds are discoverable.

lucascolley · 2024-12-17T22:06:46Z

Feel free to copy from https://github.com/data-apis/array-api-extra/blob/main/README.md or https://github.com/data-apis/array-api-extra/blob/main/docs/index.md

ev-br added the bug Something isn't working label Dec 15, 2024

ev-br force-pushed the superclasses branch from fe93a74 to 37cf07d Compare December 17, 2024 08:18

ev-br force-pushed the superclasses branch from 37cf07d to 601d829 Compare December 17, 2024 10:35

ev-br mentioned this pull request Dec 17, 2024

BUG: collect doctests from docstrings of data descriptors #180

Merged

BUG: collect methods from private superclasses

1e97c50

ev-br force-pushed the superclasses branch from 601d829 to 1e97c50 Compare December 17, 2024 11:00

ev-br merged commit 7d012aa into main Dec 17, 2024
16 checks passed

ev-br deleted the superclasses branch December 17, 2024 11:14

lucascolley mentioned this pull request Dec 17, 2024

DOC: stats: check that doctests inherited by public classes from private classes are run in CI scipy/scipy#22111

Closed

ev-br added a commit that referenced this pull request Dec 17, 2024

DOC: mention --import-mode=importlib for editable installs

adea1a4

No idea what this really does, but apparently it does something. See the discussion around #179 (comment)

ev-br mentioned this pull request Dec 17, 2024

DOC: mention --import-mode=importlib for editable installs #181

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