Source: python-pybedtools Version: 0.10.0-1 Severity: normal User: [email protected] 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... 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[ 94%] topical-create-a-bedtool reading sources... [ 95%] topical-design-principles reading sources... [ 96%] topical-documentation-contents reading sources... [ 96%] topical-genome reading sources... [ 97%] topical-iterators reading sources... [ 97%] topical-low-level-ops reading sources... [ 98%] topical-random reading sources... [ 99%] topical-saving reading sources... [ 99%] topical-wrapping reading sources... [100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.filter' with 'bedtool.BedTool.filter'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.split' with 'bedtool.BedTool.split'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.midpoint' with 'featurefuncs.midpoint'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.greater_than' with 'featurefuncs.greater_than'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.less_than' with 'featurefuncs.less_than'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bedgraph_scale' with 'featurefuncs.bedgraph_scale'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.add_color' with 'featurefuncs.add_color'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.gff2bed' with 'featurefuncs.gff2bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bed2gff' with 'featurefuncs.bed2gff'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.all_hits' with 'bedtool.BedTool.all_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.any_hits' with 'bedtool.BedTool.any_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_jaccard' with 'bedtool.BedTool.random_jaccard'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_op' with 'bedtool.BedTool.random_op'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.saveas' with 'bedtool.BedTool.saveas'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.moveto' with 'bedtool.BedTool.moveto'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cat' with 'bedtool.BedTool.cat'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.at' with 'bedtool.BedTool.at'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.absolute_distance' with 'bedtool.BedTool.absolute_distance'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cut' with 'bedtool.BedTool.cut'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.total_coverage' with 'bedtool.BedTool.total_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.with_attrs' with 'bedtool.BedTool.with_attrs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.as_intervalfile' with 'bedtool.BedTool.as_intervalfile'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.introns' with 'bedtool.BedTool.introns'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.set_chromsizes' with 'bedtool.BedTool.set_chromsizes'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.print_sequence' with 'bedtool.BedTool.print_sequence'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. /<<PKGBUILDDIR>>/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>". looking for now-outdated files... none found pickling environment... done checking consistency... done running tests... Document: filtering ------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: topical-design-principles ----------------------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 passed and 0 failed. Test passed. Document: history ----------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 passed and 0 failed. Test passed. Document: topical-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: each -------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: intersections ----------------------- 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
