Test failures on 3.13 test_pathlib

[stefanor]

I haven't dug into this at all, but I saw these test failures when test-building on Python 3.13:

https://docs.python.org/3.13/whatsnew/3.13.html

============================= 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

    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 ============

[daler]

Thanks, fixed in #416. Turns out this was due to legacy support for Python 3.4 which we don't need any more!