importing pyenzyme fails under Python 3.13 (v2-migration branch)

[jmrohwer]

When trying to import pyenzyme from a fresh install of the v2-migration branch, the import fails due to some error with functools. Under Python 3.12 everything works without error. The traceback follows:

[1]: import pyenzyme

/home/jr/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/units/units.py:52: FutureWarning: functools.partial will be a method descriptor in future Python versions; wrap it in enum.member() if you want to preserve the old behavior
  k = partial(set_scale, scale=3.0)
/home/jr/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/units/units.py:53: FutureWarning: functools.partial will be a method descriptor in future Python versions; wrap it in enum.member() if you want to preserve the old behavior
  m = partial(set_scale, scale=-3.0)
/home/jr/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/units/units.py:54: FutureWarning: functools.partial will be a method descriptor in future Python versions; wrap it in enum.member() if you want to preserve the old behavior
  u = partial(set_scale, scale=-6.0)
/home/jr/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/units/units.py:55: FutureWarning: functools.partial will be a method descriptor in future Python versions; wrap it in enum.member() if you want to preserve the old behavior
  n = partial(set_scale, scale=-9.0)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[1], line 1
----> 1 import pyenzyme

File ~/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/__init__.py:9
      6 from rich import print
      8 from .model import *  # noqa: F403
----> 9 from .sbml import to_sbml, read_sbml  # noqa: F401
     10 from .suite import EnzymeMLSuite  # noqa: F401
     11 from .tabular import to_pandas, read_csv, read_excel, from_dataframe  # noqa: F401

File ~/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/sbml/__init__.py:3
      1 from .omex import create_sbml_omex, read_sbml_omex
      2 from .parser import read_sbml
----> 3 from .serializer import to_sbml
      5 __all__ = [
      6     "to_sbml",
      7     "read_sbml",
      8     "create_sbml_omex",
      9     "read_sbml_omex",
     10 ]

File ~/.virtualenvs/fair-nmr/lib/python3.13/site-packages/pyenzyme/sbml/serializer.py:21
     19 from pyenzyme.tabular import to_pandas
     20 from pyenzyme.tools import to_dict_wo_json_ld
---> 21 from pyenzyme.units.units import UnitDefinition
     23 MAPPINGS = tools.read_static_file("pyenzyme.sbml", "mappings.toml")
     24 NSMAP = {"enzymeml": "https://www.enzymeml.org/v2"}

File ~/.virtualenvs/fair-nmr[/](http://localhost:8888/lab/tree/Data/Python/NMRPy/EnzymeML_datamodel/EnzymeMLxNMRpy.ipynb)lib/python3.13/site-packages/pyenzyme[/](http://localhost:8888/lab/tree/Data/Python/NMRPy/EnzymeML_datamodel/EnzymeMLxNMRpy.ipynb)units/__init__.py:1
----> 1 from .predefined import *  # noqa: F403

File ~[/](http://localhost:8888/lab/tree/Data/Python/NMRPy/EnzymeML_datamodel/EnzymeMLxNMRpy.ipynb).virtualenvs/fair-nmr/lib/python3.13[/](http://localhost:8888/lab/tree/Data/Python/NMRPy/EnzymeML_datamodel/EnzymeMLxNMRpy.ipynb)site-packages/pyenzyme/units/predefined.py:70
     68 # Molarity
     69 M = Unit.mol() / Unit.litre()
---> 70 mM = m * Unit.mol() / Unit.litre()
     71 uM = u * Unit.mol() / Unit.litre()
     72 nM = n * Unit.mol() / Unit.litre()

TypeError: unsupported operand type(s) for *: 'functools.partial' and 'BaseUnit'

[JR-1991]

@jmrohwer thanks for raising awareness of this! The issue seems to be tied to a breaking change in functool.partial which does not allow closures outside non-context (@partial) environments. I have opened a PR to fix this:

• Fix 313 enum variants #73

[JR-1991]

We are also switching to a less hacky implementation based on string variants, as implemented here. It's much more embedded and safer to use since astropy is supporting the unit extraction.

Example

data = MeasurementData(data_unit="mmol")
data.data_unit # Will be the fully compatible SBML unit definition