[Debian-med-packaging] Bug#1001020: python-anndata: FTBFS with sklearn 1.0.1-1: ModuleNotFoundError: No module named 'sklearn.utils.testing'

[Nilesh Patra]

Source: python-anndata
Version: 0.7.5+ds-3
Severity: serious

Dear Maintainer,

python-anndata FTBFS, it probably needs changes with new sklearn.
Log pasted below.

Regards,
Nilesh

copying anndata/tests/data/excel.xlsx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build/anndata/tests/data
   dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:285: cp -R /<<PKGBUILDDIR>>/anndata.egg-info /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_anndata/build
I: pybuild base:237: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_anndata/build; python3.10 -m pytest -v
============================= test session starts ==============================
platform linux -- Python 3.10.0+, pytest-6.2.5, py-1.10.0, pluggy-0.13.0 -- /usr/bin/python3.10
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>, configfile: pyproject.toml
plugins: cov-3.0.0
collecting ... collected 1449 items / 2 errors / 1447 selected

==================================== ERRORS ====================================
_ ERROR collecting .pybuild/cpython3_3.10_anndata/build/anndata/tests/test_inplace_subset.py _
anndata/tests/test_inplace_subset.py:3: in <module>
    from sklearn.utils.testing import assert_array_equal
E   ModuleNotFoundError: No module named 'sklearn.utils.testing'
_ ERROR collecting .pybuild/cpython3_3.10_anndata/build/anndata/tests/test_inplace_subset.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_anndata/build/anndata/tests/test_inplace_subset.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
anndata/tests/test_inplace_subset.py:3: in <module>
    from sklearn.utils.testing import assert_array_equal
E   ModuleNotFoundError: No module named 'sklearn.utils.testing'
=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/natsort/compat/fastnumbers.py:7
  /usr/lib/python3/dist-packages/natsort/compat/fastnumbers.py:7: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
    from distutils.version import StrictVersion

anndata/core.py:3
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_anndata/build/anndata/core.py:3: DeprecationWarning: Please only import from anndata, not anndata.core
    warn("Please only import from anndata, not anndata.core", DeprecationWarning)

anndata/readwrite.py:3
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_anndata/build/anndata/readwrite.py:3: DeprecationWarning: Please only import from anndata, not anndata.readwrite
    warn("Please only import from anndata, not anndata.readwrite", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
ERROR anndata/tests/test_inplace_subset.py - ModuleNotFoundError: No module n...
ERROR anndata/tests/test_inplace_subset.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
======================== 3 warnings, 2 errors in 1.71s =========================
E: pybuild pybuild:354: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_anndata/build; python3.10 -m pytest -v
I: pybuild pybuild:285: cp -R /<<PKGBUILDDIR>>/anndata.egg-info /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build
I: pybuild base:237: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build; python3.9 -m pytest -v
============================= test session starts ==============================
platform linux -- Python 3.9.9, pytest-6.2.5, py-1.10.0, pluggy-0.13.0 -- /usr/bin/python3.9
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>, configfile: pyproject.toml
plugins: cov-3.0.0
collecting ... collected 1449 items / 2 errors / 1447 selected

==================================== ERRORS ====================================
_ ERROR collecting .pybuild/cpython3_3.9_anndata/build/anndata/tests/test_inplace_subset.py _
anndata/tests/test_inplace_subset.py:3: in <module>
    from sklearn.utils.testing import assert_array_equal
E   ModuleNotFoundError: No module named 'sklearn.utils.testing'
_ ERROR collecting .pybuild/cpython3_3.9_anndata/build/anndata/tests/test_inplace_subset.py _
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build/anndata/tests/test_inplace_subset.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
anndata/tests/test_inplace_subset.py:3: in <module>
    from sklearn.utils.testing import assert_array_equal
E   ModuleNotFoundError: No module named 'sklearn.utils.testing'
=============================== warnings summary ===============================
anndata/core.py:3
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build/anndata/core.py:3: DeprecationWarning: Please only import from anndata, not anndata.core
    warn("Please only import from anndata, not anndata.core", DeprecationWarning)

anndata/readwrite.py:3
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build/anndata/readwrite.py:3: DeprecationWarning: Please only import from anndata, not anndata.readwrite
    warn("Please only import from anndata, not anndata.readwrite", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
ERROR anndata/tests/test_inplace_subset.py - ModuleNotFoundError: No module n...
ERROR anndata/tests/test_inplace_subset.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
======================== 2 warnings, 2 errors in 1.89s =========================
E: pybuild pybuild:354: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_anndata/build; python3.9 -m pytest -v
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13


-- System Information:
Debian Release: bookworm/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 5.14.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled