Support python3.13

[DanielYang59]

Summary

• Support python 3.13, to close Python 3.13 support #4284
• Make pybtex optional dependency (doesn't work on MacOS Python 3.13)
• Need to fix the EOS test failure on Ubuntu 3.13 (seemingly related to numerical precision but cannot recreate locally)
• Revert all platforms tested on Python 3.13 (c9cc898)

Optional dependencies that miss Python 3.13 support:

• openff-toolkit (conda source)
• chgnet

[DanielYang59]

might close this one now as too many packages don't support python 3.13, feel free to take over this

[DanielYang59]

I don't think this would be breaking, this just re-raise the exception from requires to provide more context, otherwise the error message when pybtex is not available would be:

tests/analysis/test_prototypes.py:6: in <module>
    from pymatgen.analysis.prototypes import AflowPrototypeMatcher
src/pymatgen/analysis/prototypes.py:28: in <module>
    AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{MODULE_DIR}/aflow_prototypes.json")
venv312/lib/python3.12/site-packages/monty/serialization.py:79: in loadfn
    return json.load(fp, *args, **kwargs)
../../opt/miniconda3/envs/pmg/lib/python3.12/json/__init__.py:293: in load
    return loads(fp.read(),
../../opt/miniconda3/envs/pmg/lib/python3.12/json/__init__.py:359: in loads
    return cls(**kw).decode(s)
venv312/lib/python3.12/site-packages/monty/json.py:879: in decode
    return self.process_decoded(d)
venv312/lib/python3.12/site-packages/monty/json.py:857: in process_decoded
    return [self.process_decoded(x) for x in d]
venv312/lib/python3.12/site-packages/monty/json.py:853: in process_decoded
    self.process_decoded(k): self.process_decoded(v) for k, v in d.items()
venv312/lib/python3.12/site-packages/monty/json.py:777: in process_decoded
    return cls_.from_dict(data)
src/pymatgen/util/provenance.py:340: in from_dict
    return cls(
src/pymatgen/util/provenance.py:229: in __init__
    if references and not is_valid_bibtex(references):
venv312/lib/python3.12/site-packages/monty/dev.py:167: in decorated
    raise self.err_cls(self.message)
E   RuntimeError: pybtex is not available

---

Before adding the requires decorator to is_valid_bibtex:

tests/analysis/test_prototypes.py:6: in <module>
    from pymatgen.analysis.prototypes import AflowPrototypeMatcher
src/pymatgen/analysis/prototypes.py:29: in <module>
    AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{MODULE_DIR}/aflow_prototypes.json")
venv312/lib/python3.12/site-packages/monty/serialization.py:79: in loadfn
    return json.load(fp, *args, **kwargs)
../../opt/miniconda3/envs/pmg/lib/python3.12/json/__init__.py:293: in load
    return loads(fp.read(),
../../opt/miniconda3/envs/pmg/lib/python3.12/json/__init__.py:359: in loads
    return cls(**kw).decode(s)
venv312/lib/python3.12/site-packages/monty/json.py:879: in decode
    return self.process_decoded(d)
venv312/lib/python3.12/site-packages/monty/json.py:857: in process_decoded
    return [self.process_decoded(x) for x in d]
venv312/lib/python3.12/site-packages/monty/json.py:853: in process_decoded
    self.process_decoded(k): self.process_decoded(v) for k, v in d.items()
venv312/lib/python3.12/site-packages/monty/json.py:777: in process_decoded
    return cls_.from_dict(data)
src/pymatgen/util/provenance.py:340: in from_dict
    return cls(
src/pymatgen/util/provenance.py:229: in __init__
    if references and not is_valid_bibtex(references):
src/pymatgen/util/provenance.py:53: in is_valid_bibtex
    parser = bibtex.Parser()
E   AttributeError: 'NoneType' object has no attribute 'Parser'

Update: I just realized pybtex is not an optional dependency, need to put more thoughts into this:

pymatgen/pyproject.toml

Lines 56 to 64 in 5b997f7

	dependencies = [
	"joblib>=1",
	"matplotlib>=3.8",
	"monty>=2025.1.9",
	"networkx>=2.7", # PR4116
	"palettable>=3.3.3",
	"pandas>=2",
	"plotly>=4.5.0,<6.0.0",
	"pybtex>=0.24.0",

[DanielYang59]

Weird, pybtex is installed successfully in MacOS CI but some or all parts of pybtex is still not available, need to look into the reason later as I don't have a MacOS machine at hand right now

---

Update:

On MacOS, from pybtex.database.input import bibtex gives:

Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/debug/test_pybtex_install.py", line 8, in <module>
    from pybtex.database.input import bibtex
  File "/Users/yang/developer/pymatgen/venv313/lib/python3.13/site-packages/pybtex/database/__init__.py", line 44, in <module>
    from pybtex.plugin import find_plugin
  File "/Users/yang/developer/pymatgen/venv313/lib/python3.13/site-packages/pybtex/plugin/__init__.py", line 26, in <module>
    import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'

Which is an already fixed issue from pybtex's side but they haven't got a release with this patch yet. In fact they haven't released any issue since Jan 2021

[DanielYang59]

Also cannot recreate the Windows fatal exception: access violation failure on my Windows machine (pytest-dev/pytest#7634)

[DanielYang59]

I'm pretty much stuck with the Windows runner failure, help needed

• Cannot recreate locally with pytest --splits 10 --group 1 --durations-path tests/files/.pytest-split-durations tests

• Cannot find much useful info, according to: Running pytest on a file importing pandas and torch.onnx leads to access violation pytest-dev/pytest#12728

  this is certain to be a bug in one (or several) other libraries.

  As there're too many dependencies in pymatgen, it's super hard to identify which "may" have caused this failure