--- Begin Message ---
Source: python-pybedtools
Version: 0.10.0-1
Severity: normal
User: debian-pyt...@lists.debian.org
Usertags: python3.13
Forwarded: https://github.com/daler/pybedtools/issues/413
This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.
To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.
What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html
Log snippet:
Finished processing dependencies for pybedtools==0.10.0
I: pybuild base:311: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest
-k "not test_chromsizes"
============================= test session starts ==============================
platform linux -- Python 3.13.0rc2, pytest-8.3.2, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build
configfile: pyproject.toml
plugins: typeguard-4.3.0
collected 511 items / 2 deselected / 509 selected
pybedtools/test/test_1.py .............................................. [ 9%]
.......................x..x.x...... [ 15%]
pybedtools/test/test_cbedtools.py ...................................... [ 23%]
. [ 23%]
pybedtools/test/test_contrib.py .. [ 23%]
pybedtools/test/test_gzip_support.py ........ [ 25%]
pybedtools/test/test_helpers.py ...... [ 26%]
pybedtools/test/test_issues.py ......................................... [ 34%]
.F [ 35%]
pybedtools/test/test_iter.py ........................................... [ 43%]
........................................................................ [ 57%]
........................................................................ [ 71%]
........................................................................ [ 86%]
.................................................................... [ 99%]
pybedtools/test/test_pathlib.py FFF [100%]
=================================== FAILURES ===================================
________________________________ test_issue_405 ________________________________
self =
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
others =
(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'),)
kwargs = {}
other_beds =
[<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>]
other =
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>
postmerge = True, force_truncate = False, stream_merge = False
@_log_to_history
def cat(self, *others, **kwargs):
"""
Concatenate interval files together.
Concatenates two BedTool objects (or an object and a file) and does an
optional post-merge of the features.
*postmerge=True* by default; use *postmerge=False* if you want to keep
features separate.
*force_truncate=False* by default; *force_truncate=True* to truncate
all files to chrom, start, stop.
When *force_truncate=False* and *postmerge=False*, the output will
contain the smallest number of fields observed across all inputs. This
maintains compatibility with BEDTools programs, which assume constant
number of fields in all lines of a file.
Other kwargs are sent to :meth:`BedTool.merge` (and assuming that
*postmerge=True*).
Example usage:
>>> a = pybedtools.example_bedtool('a.bed')
>>> b = pybedtools.example_bedtool('b.bed')
>>> print(a.cat(b)) #doctest: +NORMALIZE_WHITESPACE
chr1 1 500
chr1 800 950
<BLANKLINE>
>>> print(a.cat(*[b,b],
... postmerge=False)) #doctest: +NORMALIZE_WHITESPACE
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -
chr1 900 950 feature4 0 +
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
<BLANKLINE>
"""
assert len(others) > 0, "You must specify at least one other bedfile!"
other_beds = []
for other in others:
if isinstance(other, (str, Path)):
other = BedTool(other)
else:
assert isinstance(
other, BedTool
), "Either filename or another BedTool instance required"
other_beds.append(other)
# postmerge and force_trucate don't get passed on to merge
postmerge = kwargs.pop("postmerge", True)
force_truncate = kwargs.pop("force_truncate", False)
stream_merge = kwargs.get("stream", False)
if stream_merge and postmerge:
raise ValueError(
"The post-merge step in the `cat()` method "
"perfoms a sort, which uses stream=True. Using "
"stream=True for the merge as well will result in a "
"deadlock!"
)
# if filetypes and field counts are the same, don't truncate
if not force_truncate:
try:
> a_type = self.file_type
pybedtools/bedtool.py:3240:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self =
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
@property
def file_type(self):
"""
Return the type of the current file. One of ('bed','vcf','gff', 'bam',
'sam', 'empty').
>>> a = pybedtools.example_bedtool('a.bed')
>>> print(a.file_type)
bed
"""
if not isinstance(self.fn, str):
> raise ValueError(
"Checking file_type not supported for "
"non-file BedTools. Use .saveas() to "
"save as a temp file first."
)
E ValueError: Checking file_type not supported for non-file BedTools.
Use .saveas() to save as a temp file first.
pybedtools/bedtool.py:1106: ValueError
During handling of the above exception, another exception occurred:
def test_issue_405():
a = Path(pybedtools.example_filename('a.bed'))
b = Path(pybedtools.example_filename('b.bed'))
a = pybedtools.BedTool(a)
> a.cat(b)
pybedtools/test/test_issues.py:921:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pybedtools/bedtool.py:907: in decorated
result = method(self, *args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self =
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
others =
(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'),)
kwargs = {}
other_beds =
[<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>]
other =
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>
postmerge = True, force_truncate = False, stream_merge = False
@_log_to_history
def cat(self, *others, **kwargs):
"""
Concatenate interval files together.
Concatenates two BedTool objects (or an object and a file) and does an
optional post-merge of the features.
*postmerge=True* by default; use *postmerge=False* if you want to keep
features separate.
*force_truncate=False* by default; *force_truncate=True* to truncate
all files to chrom, start, stop.
When *force_truncate=False* and *postmerge=False*, the output will
contain the smallest number of fields observed across all inputs. This
maintains compatibility with BEDTools programs, which assume constant
number of fields in all lines of a file.
Other kwargs are sent to :meth:`BedTool.merge` (and assuming that
*postmerge=True*).
Example usage:
>>> a = pybedtools.example_bedtool('a.bed')
>>> b = pybedtools.example_bedtool('b.bed')
>>> print(a.cat(b)) #doctest: +NORMALIZE_WHITESPACE
chr1 1 500
chr1 800 950
<BLANKLINE>
>>> print(a.cat(*[b,b],
... postmerge=False)) #doctest: +NORMALIZE_WHITESPACE
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -
chr1 900 950 feature4 0 +
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
<BLANKLINE>
"""
assert len(others) > 0, "You must specify at least one other bedfile!"
other_beds = []
for other in others:
if isinstance(other, (str, Path)):
other = BedTool(other)
else:
assert isinstance(
other, BedTool
), "Either filename or another BedTool instance required"
other_beds.append(other)
# postmerge and force_trucate don't get passed on to merge
postmerge = kwargs.pop("postmerge", True)
force_truncate = kwargs.pop("force_truncate", False)
stream_merge = kwargs.get("stream", False)
if stream_merge and postmerge:
raise ValueError(
"The post-merge step in the `cat()` method "
"perfoms a sort, which uses stream=True. Using "
"stream=True for the merge as well will result in a "
"deadlock!"
)
# if filetypes and field counts are the same, don't truncate
if not force_truncate:
try:
a_type = self.file_type
files = [self] + other_beds
filetypes = set(
[self.file_type] + [i.file_type for i in other_beds]
).difference(["empty"])
field_nums = (
set([self.field_count()] + [i.field_count() for i in
other_beds])
.difference([None])
.difference([0])
)
same_field_num = len(field_nums) == 1
same_type = len(set(filetypes)) == 1
except ValueError:
> raise ValueError(
"Can't check filetype or field count -- "
"is one of the files you're merging a 'streaming' "
"BedTool? If so, use .saveas() to save to file first"
)
E ValueError: Can't check filetype or field count -- is one of
the files you're merging a 'streaming' BedTool? If so, use .saveas() to save
to file first
pybedtools/bedtool.py:3254: ValueError
______________________________ test_pathlib_base _______________________________
def test_pathlib_base():
file = "a.bed"
fn = os.path.join(pybedtools.filenames.data_dir(), file)
path = pathlib.PurePath(fn)
> assert pybedtools.BedTool(path).fn == fn
E AssertionError: assert
PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed')
==
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'
E + where
PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed')
=
<BedTool(PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>.fn
E + where
<BedTool(PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
= <class
'pybedtools.bedtool.BedTool'>(PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))
E + where <class 'pybedtools.bedtool.BedTool'> = pybedtools.BedTool
pybedtools/test/test_pathlib.py:12: AssertionError
_____________________________ test_pathlib_derived _____________________________
def test_pathlib_derived():
file = "a.bed"
fn = os.path.join(pybedtools.filenames.data_dir(), file)
path = pathlib.Path(fn)
> assert pybedtools.BedTool(path).fn == fn
E AssertionError: assert
PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed')
==
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'
E + where
PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed')
=
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>.fn
E + where
<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
= <class
'pybedtools.bedtool.BedTool'>(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))
E + where <class 'pybedtools.bedtool.BedTool'> = pybedtools.BedTool
pybedtools/test/test_pathlib.py:19: AssertionError
________________________ test_pathlib_nonexistent_file _________________________
def test_pathlib_nonexistent_file():
fn = os.path.join(pybedtools.filenames.data_dir(),
"this_file_is_missing")
path = pathlib.Path(fn)
> with pytest.raises(FileNotFoundError):
E Failed: DID NOT RAISE <class 'FileNotFoundError'>
pybedtools/test/test_pathlib.py:26: Failed
=========================== short test summary info ============================
FAILED pybedtools/test/test_issues.py::test_issue_405 - ValueError: Can't che...
FAILED pybedtools/test/test_pathlib.py::test_pathlib_base - AssertionError: a...
FAILED pybedtools/test/test_pathlib.py::test_pathlib_derived - AssertionError...
FAILED pybedtools/test/test_pathlib.py::test_pathlib_nonexistent_file - Faile...
=========== 4 failed, 502 passed, 2 deselected, 3 xfailed in 18.82s ============
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest
-k "not test_chromsizes"
I: pybuild pybuild:308: cp /<<PKGBUILDDIR>>/debian/mpl-expected.png
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/ ;
python3 /<<PKGBUILDDIR>>/setup.py install --user ; export
HOME=/<<PKGBUILDDIR>>/fakehome
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated
as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning:
Unknown distribution option: 'language_level'
warnings.warn(msg)
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66:
SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html
for details.
********************************************************************************
!!
self.initialize_options()
error: can't combine user with prefix, exec_prefix/home, or install_(plat)base
I: pybuild base:311: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build; python3.12 -m pytest
-k "not test_chromsizes"
============================= test session starts ==============================
platform linux -- Python 3.12.6, pytest-8.3.2, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build
configfile: pyproject.toml
plugins: typeguard-4.3.0
collected 511 items / 2 deselected / 509 selected
pybedtools/test/test_1.py .............................................. [ 9%]
.......................x..x.x...... [ 15%]
pybedtools/test/test_cbedtools.py ...................................... [ 23%]
. [ 23%]
pybedtools/test/test_contrib.py .. [ 23%]
pybedtools/test/test_gzip_support.py ........ [ 25%]
pybedtools/test/test_helpers.py ...... [ 26%]
pybedtools/test/test_issues.py ......................................... [ 34%]
.. [ 35%]
pybedtools/test/test_iter.py ........................................... [ 43%]
........................................................................ [ 57%]
........................................................................ [ 71%]
........................................................................ [ 86%]
.................................................................... [ 99%]
pybedtools/test/test_pathlib.py ... [100%]
================ 506 passed, 2 deselected, 3 xfailed in 18.70s =================
I: pybuild pybuild:334: cd /<<PKGBUILDDIR>>/docs ; make clean doctest
make[1]: Entering directory '/<<PKGBUILDDIR>>/docs'
rm -rf build/* source/autodocs/*.rst
sphinx-build -b doctest -d build/doctrees source build/doctest
Running Sphinx v7.4.7
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst':
'restructuredtext'}`.
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst,
autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst,
default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst,
history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst,
topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst,
topical-low-level-ops.rst, topical-random.rst, topical-saving.rst,
topical-wrapping.rst, tutorial-contents.rst
[autosummary] generating autosummary for:
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst,
...,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.filenames.example_filename.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.filenames.list_example_files.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.chromsizes.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.chromsizes_to_file.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.cleanup.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.get_chromsizes_from_ucsc.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst,
/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst
building [mo]: targets for 0 po files that are out of date
writing output...
building [doctest]: targets for 48 source files that are out of date
updating environment: [new config] 157 added, 0 changed, 0 removed
reading sources... [ 1%] 3-brief-examples
reading sources... [ 1%] FAQs
reading sources... [ 2%] autodoc_source
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown
section Example in the docstring of decorated in
/<<PKGBUILDDIR>>/pybedtools/bedtool.py.
warn(msg)
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown
section Example in the docstring of tag_bedpe in
/<<PKGBUILDDIR>>/pybedtools/contrib/long_range_interaction.py.
warn(msg)
reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown
section Example in the docstring of decorated in
/<<PKGBUILDDIR>>/pybedtools/bedtool.py.
warn(msg)
reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance
reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits
reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate
reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits
reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile
reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at
reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed
reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq
reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6
reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster
reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.count
reading sources... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut
reading sources... [ 16%] autodocs/pybedtools.bedtool.BedTool.each
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter
reading sources... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby
reading sources... [ 21%] autodocs/pybedtools.bedtool.BedTool.head
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect
reading sources... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.links
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.map
reading sources... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto
reading sources... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content
reading sources... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence
reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op
reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown
section Example in the docstring of decorated in
/<<PKGBUILDDIR>>/pybedtools/bedtool.py.
warn(msg)
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection
reading sources... [ 36%]
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1 items passed all tests:
8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.
Document: topical-bam
---------------------
1 items passed all tests:
15 tests in default
15 tests in 1 items.
15 passed and 0 failed.
Test passed.
Document: topical-random
------------------------
1 items passed all tests:
10 tests in default
10 tests in 1 items.
10 passed and 0 failed.
Test passed.
Document: intervals
-------------------
1 items passed all tests:
50 tests in default
50 tests in 1 items.
50 passed and 0 failed.
Test passed.
Document: topical-low-level-ops
-------------------------------
1 items passed all tests:
6 tests in default
6 tests in 1 items.
6 passed and 0 failed.
Test passed.
Document: piping
----------------
1 items passed all tests:
17 tests in default
17 tests in 1 items.
17 passed and 0 failed.
Test passed.
Document: topical-create-a-bedtool
----------------------------------
1 items passed all tests:
10 tests in default
10 tests in 1 items.
10 passed and 0 failed.
Test passed.
Document: default-arguments
---------------------------
1 items passed all tests:
13 tests in default
13 tests in 1 items.
13 passed and 0 failed.
Test passed.
Document: save-results
----------------------
1 items passed all tests:
8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.
Doctest summary
===============
223 tests
0 failures in tests
0 failures in setup code
0 failures in cleanup code
build succeeded, 126 warnings.
Testing of doctests in the sources finished, look at the results in
build/doctest/output.txt.
Testing of doctests in the sources finished, look at the results in
build/doctest/output.txt.
make[1]: Leaving directory '/<<PKGBUILDDIR>>/docs'
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13
3.12" returned exit code 13
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/712382/
This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.
Thanks,
Stefano
--- End Message ---
pgpTTiWNYFpCJ.pgp
