maximum recursion error

[hliu56]

Hi,

Could you help me see how to resolve this issue?

Describe the bug
when import pymzml, it encountered maximum recursion issure.

To Reproduce
Steps to reproduce the behavior:
import pymzml

Error information
File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/mss/mssmain.py:1
----> 1 import pymzml
2 from tqdm import tqdm
3 import numpy as np

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/pymzml/init.py:41
38 version = version_file.read().strip()
40 # Imports of individual modules
---> 41 import pymzml.run
42 import pymzml.spec
43 from pymzml.spec import MSDecoder

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/pymzml/run.py:48
45 from io import BytesIO
46 from pathlib import Path
---> 48 from . import spec
49 from . import obo
50 from . import regex_patterns

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/pymzml/spec.py:60
58 try:
59 DECON_DEP = True
---> 60 from ms_deisotope.deconvolution import deconvolute_peaks
61 from ms_peak_picker import simple_peak
62 except (ImportError, ModuleNotFoundError) as e:

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/ms_deisotope/init.py:14
10 pass
12 from .version import version
---> 14 from .averagine import (
15 Averagine, AveragineCache,
16 peptide, glycan, glycopeptide, heparin,
17 heparan_sulfate, permethylated_glycan,
18 mass_charge_ratio, neutral_mass,
19 calculate_mass, isotopic_shift)
20 from .deconvolution import (
21 AveragineDeconvoluter, CompositionListDeconvoluter,
22 AveraginePeakDependenceGraphDeconvoluter,
23 CompositionListPeakDependenceGraphDeconvoluter,
24 deconvolute_peaks)
25 from .scoring import MSDeconVFitter, PenalizedMSDeconVFitter, DistinctPatternFitter, IsotopicFitRecord

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/ms_deisotope/averagine.py:477
475 _Averagine = Averagine
476 _TheoreticalIsotopicPattern = TheoreticalIsotopicPattern
--> 477 from ms_deisotope._c.averagine import Averagine, TheoreticalIsotopicPattern
478 except ImportError as e:
479 _has_c = False

File src/ms_deisotope/_c/averagine.pyx:1, in init ms_deisotope._c.averagine()

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/ms_peak_picker/init.py:2
1 import os
----> 2 from .peak_picker import PeakProcessor, pick_peaks, fit_type_map, peak_mode_map
3 from .peak_set import PeakSet, FittedPeak, is_peak, simple_peak
4 from .peak_index import PeakIndex

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/ms_peak_picker/peak_picker.py:14
12 from .search import get_nearest_binary, get_nearest
13 from .peak_set import FittedPeak, PeakSet
---> 14 from .peak_index import PeakIndex
15 from .scan_filter import transform
16 from .utils import Base

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/ms_peak_picker/peak_index.py:3
1 import numpy as np
2 from .search import get_nearest
----> 3 from .fft_patterson_charge_state import fft_patterson_charge_state
4 from .peak_statistics import peak_area
7 class PeakIndex(object):

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/ms_peak_picker/fft_patterson_charge_state.py:8
2 '''
3 This module contains a simple translation of Gordon Slyz's implementation of Senko's
4 Fourier Patterson Charge State determination algorithm.
5 '''
7 import numpy as np
----> 8 from scipy import interpolate
10 from ms_peak_picker.peak_set import FittedPeak
13 def autocorr(inp):

File :1229, in handle_fromlist(module, fromlist, import, recursive)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/scipy/init.py:134, in getattr(name)
132 def getattr(name):
133 if name in submodules:
--> 134 return _importlib.import_module(f'scipy.{name}')
135 else:
136 try:

File ~/anaconda3/envs/HPLC/lib/python3.11/importlib/init.py:126, in import_module(name, package)
124 break
125 level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/scipy/interpolate/init.py:167
1 """
2 ========================================
3 Interpolation (:mod:scipy.interpolate)
(...)
165 (should not be used in new code).
166 """
--> 167 from ._interpolate import *
168 from ._fitpack_py import *
170 # New interface to fitpack library:

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/scipy/interpolate/_interpolate.py:12
9 from scipy._lib._util import copy_if_needed
10 from scipy.special import comb
---> 12 from . import _fitpack_py
13 from ._polyint import _Interpolator1D
14 from . import _ppoly

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/scipy/interpolate/_fitpack_py.py:8
5 import numpy as np
7 # These are in the API for fitpack even if not used in fitpack.py itself.
----> 8 from ._fitpack_impl import bisplrep, bisplev, dblint # noqa: F401
9 from . import _fitpack_impl as _impl
10 from ._bsplines import BSpline

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/scipy/interpolate/_fitpack_impl.py:103
52 _iermess = {
53 0: ["The spline has a residual sum of squares fp such that "
54 "abs(fp-s)/s<=0.001", None],
(...)
68 'unknown': ["An error occurred", TypeError]
69 }
71 _iermess2 = {
72 0: ["The spline has a residual sum of squares fp such that "
73 "abs(fp-s)/s<=0.001", None],
(...)
99 'unknown': ["An error occurred", TypeError]
100 }
102 _parcur_cache = {'t': array([], float), 'wrk': array([], float),
--> 103 'iwrk': array([], dfitpack_int), 'u': array([], float),
104 'ub': 0, 'ue': 1}
107 def splprep(x, w=None, u=None, ub=None, ue=None, k=3, task=0, s=None, t=None,
108 full_output=0, nest=None, per=0, quiet=1):
109 # see the docstring of _fitpack_py/splprep
110 if task <= 0:

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:46, in repr(dtype)
45 def repr(dtype):
---> 46 arg_str = _construction_repr(dtype, include_align=False)
47 if dtype.isalignedstruct:
48 arg_str = arg_str + ", align=True"

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:100, in _construction_repr(dtype, include_align, short)
98 return _subarray_str(dtype)
99 else:
--> 100 return _scalar_str(dtype, short=short)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:143, in _scalar_str(dtype, short)
140 elif dtype.type == np.timedelta64:
141 return "'%sm8%s'" % (byteorder, _datetime_metadata_str(dtype))
--> 143 elif np.issubdtype(dtype, np.number):
144 # Short repr with endianness, like '<f8'
145 if short or dtype.byteorder not in ('=', '|'):
146 return "'%s%c%d'" % (byteorder, dtype.kind, dtype.itemsize)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/numerictypes.py:417, in issubdtype(arg1, arg2)
359 r"""
360 Returns True if first argument is a typecode lower/equal in type hierarchy.
361
(...)
414
415 """
416 if not issubclass_(arg1, generic):
--> 417 arg1 = dtype(arg1).type
418 if not issubclass_(arg2, generic):
419 arg2 = dtype(arg2).type

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:46, in repr(dtype)
45 def repr(dtype):
---> 46 arg_str = _construction_repr(dtype, include_align=False)
47 if dtype.isalignedstruct:
48 arg_str = arg_str + ", align=True"

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:100, in _construction_repr(dtype, include_align, short)
98 return _subarray_str(dtype)
99 else:
--> 100 return _scalar_str(dtype, short=short)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:143, in _scalar_str(dtype, short)
140 elif dtype.type == np.timedelta64:
141 return "'%sm8%s'" % (byteorder, _datetime_metadata_str(dtype))
--> 143 elif np.issubdtype(dtype, np.number):
144 # Short repr with endianness, like '<f8'
145 if short or dtype.byteorder not in ('=', '|'):
146 return "'%s%c%d'" % (byteorder, dtype.kind, dtype.itemsize)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/numerictypes.py:417, in issubdtype(arg1, arg2)
359 r"""
360 Returns True if first argument is a typecode lower/equal in type hierarchy.
361
(...)
414
415 """
416 if not issubclass_(arg1, generic):
--> 417 arg1 = dtype(arg1).type
418 if not issubclass_(arg2, generic):
419 arg2 = dtype(arg2).type

[... skipping similar frames: __repr__ at line 46 (471 times), _construction_repr at line 100 (471 times), _scalar_str at line 143 (470 times), issubdtype at line 417 (470 times)]

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:143, in _scalar_str(dtype, short)
140 elif dtype.type == np.timedelta64:
141 return "'%sm8%s'" % (byteorder, _datetime_metadata_str(dtype))
--> 143 elif np.issubdtype(dtype, np.number):
144 # Short repr with endianness, like '<f8'
145 if short or dtype.byteorder not in ('=', '|'):
146 return "'%s%c%d'" % (byteorder, dtype.kind, dtype.itemsize)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/numerictypes.py:417, in issubdtype(arg1, arg2)
359 r"""
360 Returns True if first argument is a typecode lower/equal in type hierarchy.
361
(...)
414
415 """
416 if not issubclass_(arg1, generic):
--> 417 arg1 = dtype(arg1).type
418 if not issubclass_(arg2, generic):
419 arg2 = dtype(arg2).type

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:46, in repr(dtype)
45 def repr(dtype):
---> 46 arg_str = _construction_repr(dtype, include_align=False)
47 if dtype.isalignedstruct:
48 arg_str = arg_str + ", align=True"

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:100, in _construction_repr(dtype, include_align, short)
98 return _subarray_str(dtype)
99 else:
--> 100 return _scalar_str(dtype, short=short)

File ~/anaconda3/envs/HPLC/lib/python3.11/site-packages/numpy/core/_dtype.py:104, in _scalar_str(dtype, short)
103 def _scalar_str(dtype, short):
--> 104 byteorder = byte_order_str(dtype)
106 if dtype.type == np.bool:
107 if short:

RecursionError: maximum recursion depth exceeded

Desktop (please complete the following information):

• OS: macOS
• Version 14.1 (23B2073)

Thank you!