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levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
http://pyteomics.readthedocs.io
Apache License 2.0
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Unimod doesn't work with SQLAlchemy 1.4.2 #31

Closed levitsky closed 3 years ago

levitsky commented 3 years ago

The unimod test fails to start with this error on latest SQLAlchemy 1.4.2:

ERROR: setUpClass (__main__.UnimodTests)
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Traceback (most recent call last):
  File "/home/lev/py/pyteomics/tests/test_unimod.py", line 12, in setUpClass
    cls.handle = unimod.Unimod()
  File "/home/lev/py/pyteomics/pyteomics/mass/unimod.py", line 688, in __init__
    self.session = load(_unimod_xml_download_url)
  File "/home/lev/py/pyteomics/pyteomics/mass/unimod.py", line 655, in load
    for model in Base._decl_class_registry.values():
AttributeError: type object 'Base' has no attribute '_decl_class_registry'
mobiusklein commented 3 years ago

SQLAlchemy is starting to migrate to a new architecture. I just started seeing breakages on CI for 1.4 on other projects. I'll get started on this at least, it should be easier to fix.