Your message dated Fri, 10 Dec 2021 14:36:31 +0000
with message-id <e1mvh0h-000a4i...@fasolo.debian.org>
and subject line Bug#1001020: fixed in python-anndata 0.7.8-1
has caused the Debian Bug report #1001020,
regarding python-anndata: FTBFS with sklearn 1.0.1-1: ModuleNotFoundError: No
module named 'sklearn.utils.testing'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1001020: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1001020
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: python-anndata
Source-Version: 0.7.8-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
python-anndata, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1001...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-anndata package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 10 Dec 2021 14:38:15 +0100
Source: python-anndata
Architecture: source
Version: 0.7.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1001020 1001349
Changes:
python-anndata (0.7.8-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Closes: #1001349, #1001020
* Point watch file to Github
* Drop unnecessary Files-Excluded
* Standards-Version: 4.6.0 (routine-update)
* Provide debian/tests/run-unit-test script
* Remove unneeded debian/source/options
* PYBUILD_SYSTEM=flit to deal with missing setup.py
* Build-Depends: python3-openpyxl
* Ignore test importing scanpy data
* Deactivate test requiring python3-numba since this is not ported to
Python3.10 yet
* debian/salsa-ci.yaml: suppress build on i386 where several tests are
failing
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python-anndata_0.7.8.orig.tar.gz
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python-anndata_0.7.8-1.debian.tar.xz
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Files:
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