Control: clone -1 -2
Control: reassign -2 python3-sorted-nearest 0.0.41+dfsg-1
On Sat, Nov 29, 2025 at 02:59:26PM +0100, Alexandre Detiste wrote:
reassign 1120469 python-ncls
I'm in the process of uploading 0.0.70+ds-1 to fix the parts of this
that were due to python3-ncls, but there are also similar problems in
python3-sorted-nearest (even with your upload of 0.0.41+dfsg-1 today - I
built that locally to check). Here's the remaining test failure, since
it can be a bit hard to pick out from the build log:
root@sbuild:/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build#
python3.13 -m pytest tests/test_unary.py::test_windows
============================= test session starts
==============================
platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0
rootdir: /build/reproducible-path/pyranges-0.0.111+ds
plugins: hypothesis-6.148.2, xdist-3.8.0, typeguard-4.4.4
collected 1 item
tests/test_unary.py F
[100%]
=================================== FAILURES
===================================
_________________________________ test_windows
_________________________________
@pytest.mark.bedtools
> @settings(
max_examples=max_examples,
print_blob=True,
deadline=deadline,
suppress_health_check=HealthCheck.all())
tests/test_unary.py:230:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_
tests/test_unary.py:259: in test_windows
result = gr.window(10)["Chromosome Start End".split()].unstrand()
^^^^^^^^^^^^^
pyranges/pyranges.py:5485: in window
df = pyrange_apply_single(_windows, self, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pyranges/multithreaded.py:347: in pyrange_apply_single
result = call_f_single(function, nparams, df, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pyranges/multithreaded.py:30: in call_f_single
return f.remote(df, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
pyranges/methods/windows.py:11: in _windows
idxs, starts, ends = makewindows(df.index.values, df.Start.values,
sorted_nearest/src/windows.pyx:16: in sorted_nearest.src.windows.makewindows
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_
> ???
E NameError: name 'long' is not defined
E Falsifying example: test_windows(
E
gr=+--------------+-----------+-----------+------------+-----------+--------------+
E | Chromosome | Start | End | Name | Score |
Strand |
E | (category) | (int64) | (int64) | (object) | (int64) |
(category) |
E
|--------------+-----------+-----------+------------+-----------+--------------|
E | chr1 | 1 | 2 | a | 0 | +
|
E
+--------------+-----------+-----------+------------+-----------+--------------+
E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes.
E For printing, the PyRanges was sorted on Chromosome and Strand.,
E )
E
E You can reproduce this example by temporarily adding
@reproduce_failure('6.148.2', b'AAFBAQAAQQEAQQEAQQEAQQA=') as a decorator on
your test case
sorted_nearest/src/windows.pyx:87: NameError
----------------------------- Captured stdout call
-----------------------------
bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpz4g2xuc7/f1.bed)
bedtools_df
Chromosome Start End
0 chr1 1 2
bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpkbwfyzdx/f1.bed)
bedtools_df
Chromosome Start End
0 chr1 1 2
=============================== warnings summary
===============================
pyranges/__init__.py:18
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/__init__.py:18:
DeprecationWarning: pkg_resources is deprecated as an API. See
https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
tests/test_unary.py:35
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:35:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
tests/test_unary.py:100
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:100:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
tests/test_unary.py:163
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:163:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
tests/test_unary.py:205
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:205:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
tests/test_unary.py:234
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:234:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
tests/test_unary.py:272
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:272:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
pyranges/methods/init.py:60
.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py::test_windows
.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py::test_windows
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/pyranges/methods/init.py:60:
FutureWarning: The default of observed=False is deprecated and will be changed
to True in a future version of pandas. Pass observed=False to retain current
behavior or observed=True to adopt the future default and silence this warning.
return {k: v for k, v in df.groupby(grpby_key)}
tests/test_unary.py:287
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:287:
HypothesisDeprecationWarning: The return_value health check is deprecated,
because this is always an error.
@settings(
tests/test_unary.py:315
/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.13_pyranges/build/tests/test_unary.py:315:
HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use
`list(HealthCheck)` instead.
The `hypothesis codemod` command-line tool can automatically refactor
your code to fix this warning.
suppress_health_check=HealthCheck.all())
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info
============================
FAILED tests/test_unary.py::test_windows - NameError: name 'long' is not
defined
======================== 1 failed, 12 warnings in 0.20s
========================
Thanks,
--
Colin Watson (he/him) [[email protected]]
