Fedora is preparing for the next Python release and currently testing packages with Python 3.13.0b1. It turns out one of the tests is failing with Python 3.13. I'm not entirely sure if this is an issue with bioframe or with pandas. I'm reporting it here as a starting point and for awareness. We are using version 2.2.1 of pandas.
______________________________ test_assembly_info ______________________________
def test_assembly_info():
> hg38 = assembly_info("hg38")
tests/test_assembly_info.py:15:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../BUILDROOT/python-bioframe-0.6.4-1.fc41.x86_64/usr/lib/python3.13/site-packages/bioframe/io/assembly.py:144: in assembly_info
result = assemblies.query(q)
/usr/lib64/python3.13/site-packages/pandas/core/frame.py:4811: in query
res = self.eval(expr, **kwargs)
/usr/lib64/python3.13/site-packages/pandas/core/frame.py:4937: in eval
return _eval(expr, inplace=inplace, **kwargs)
/usr/lib64/python3.13/site-packages/pandas/core/computation/eval.py:328: in eval
env = ensure_scope(
/usr/lib64/python3.13/site-packages/pandas/core/computation/scope.py:58: in ensure_scope
return Scope(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'Scope' object has no attribute 'resolvers'") raised in repr()] Scope object at 0x7f3716c1aa70>
level = 4, global_dict = None, local_dict = None
resolvers = ({'cytobands': 0 hg19.cytoband.tsv
1 hg19.cytoband.tsv
2 hg38.cytoband.tsv
3 hg38.cytoband.tsv
4 ... 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
dtype: int64})
target = None
def __init__(
self, level: int, global_dict=None, local_dict=None, resolvers=(), target=None
) -> None:
self.level = level + 1
# shallow copy because we don't want to keep filling this up with what
# was there before if there are multiple calls to Scope/_ensure_scope
self.scope = DeepChainMap(DEFAULT_GLOBALS.copy())
self.target = target
if isinstance(local_dict, Scope):
self.scope.update(local_dict.scope)
if local_dict.target is not None:
self.target = local_dict.target
self._update(local_dict.level)
frame = sys._getframe(self.level)
try:
# shallow copy here because we don't want to replace what's in
# scope when we align terms (alignment accesses the underlying
# numpy array of pandas objects)
scope_global = self.scope.new_child(
(global_dict if global_dict is not None else frame.f_globals).copy()
)
self.scope = DeepChainMap(scope_global)
if not isinstance(local_dict, Scope):
scope_local = self.scope.new_child(
> (local_dict if local_dict is not None else frame.f_locals).copy()
)
E AttributeError: 'FrameLocalsProxy' object has no attribute 'copy'
/usr/lib64/python3.13/site-packages/pandas/core/computation/scope.py:176: AttributeError
Fedora is preparing for the next Python release and currently testing packages with Python 3.13.0b1. It turns out one of the tests is failing with Python 3.13. I'm not entirely sure if this is an issue with
bioframeor withpandas. I'm reporting it here as a starting point and for awareness. We are using version 2.2.1 ofpandas.