TypeError: deprecated() got an unexpected keyword argument 'deadline'

[hongyi-zhao]

Python version

Python 3.11.1

Pymatgen version

2024.5.31

Operating system version

Ubuntu 22.04.4 LTS

Current behavior

Description: When trying to import MPRester from mp_api.client, I encountered a TypeError related to the deprecated decorator in the pymatgen library. The error message indicates that the deprecated() function received an unexpected keyword argument 'deadline'.

Error Traceback:

TypeError: deprecated() got an unexpected keyword argument 'deadline'

In [3]: from mp_api.client import MPRester
   ...: from pymatgen.io.vasp.sets import MPRelaxSet
   ...: 
   ...: # Replace with your Materials Project API Key
   ...: # api_key = "YOUR_API_KEY"
   ...: 
   ...: # Use MPRester to fetch data
   ...: with MPRester() as mpr:
   ...:     # Search for materials with chemical system "Au" and space group "Fm-3m"
   ...:     results = mpr.materials.search(chemsys="Au", spacegroup_symbol="Fm-3m")
   ...: 
   ...:     # Print results
   ...:     for result in results:
   ...:         material_id = result.material_id
   ...:         print(f"Material ID: {material_id}, Formula: {result.formula_pretty}")
   ...: 
   ...:         # Get material structure
   ...:         structure = mpr.materials.get_structure_by_material_id(material_id)
   ...: 
   ...:         # Generate VASP input files using MPRelaxSet
   ...:         vasp_input_set = MPRelaxSet(structure)
   ...:         incar = vasp_input_set.incar
   ...: 
   ...:         # Print INCAR file content
   ...:         print(incar)
   ...: 
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[3], line 1
----> 1 from mp_api.client import MPRester
      2 from pymatgen.io.vasp.sets import MPRelaxSet
      4 # Replace with your Materials Project API Key
      5 # api_key = "YOUR_API_KEY"
      6 
      7 # Use MPRester to fetch data

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/mp_api/client/__init__.py:7
      4 import os
      5 from importlib.metadata import PackageNotFoundError, version
----> 7 from .core import MPRestError
      8 from .mprester import MPRester
     10 try:

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/mp_api/client/core/__init__.py:3
      1 from __future__ import annotations
----> 3 from .client import BaseRester, MPRestError
      4 from .settings import MAPIClientSettings

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/mp_api/client/core/client.py:24
     21 from urllib.parse import quote, urljoin
     23 import requests
---> 24 from emmet.core.utils import jsanitize
     25 from monty.json import MontyDecoder
     26 from pydantic import BaseModel, create_model

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/emmet/core/utils.py:10
      8 from monty.json import MSONable
      9 from pydantic import BaseModel
---> 10 from pymatgen.analysis.graphs import MoleculeGraph
     11 from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender
     12 from pymatgen.analysis.molecule_matcher import MoleculeMatcher

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/analysis/graphs.py:26
     23 from scipy.spatial import KDTree
     24 from scipy.stats import describe
---> 26 from pymatgen.core import Lattice, Molecule, PeriodicSite, Structure
     27 from pymatgen.core.structure import FunctionalGroups
     28 from pymatgen.util.coord import lattice_points_in_supercell

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/__init__.py:12
      8 from typing import Any
     10 from ruamel.yaml import YAML
---> 12 from pymatgen.core.composition import Composition
     13 from pymatgen.core.lattice import Lattice
     14 from pymatgen.core.operations import SymmOp

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/composition.py:22
     19 from monty.json import MSONable
     20 from monty.serialization import loadfn
---> 22 from pymatgen.core.periodic_table import DummySpecies, Element, ElementType, Species, get_el_sp
     23 from pymatgen.core.units import Mass
     24 from pymatgen.util.string import Stringify, formula_double_format

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/periodic_table.py:39
     32     _pt_data = json.load(ptable_json)
     34 _pt_row_sizes = (2, 8, 8, 18, 18, 32, 32)
     37 @functools.total_ordering
     38 @unique
---> 39 class ElementBase(Enum):
     40     """Element class defined without any enum values so it can be subclassed.
     41 
     42     This class is needed to get nested (as|from)_dict to work properly. All emmet classes that had
   (...)
     45     only when they were top level. See https://github.com/materialsproject/pymatgen/issues/2999.
     46     """
     48     def __init__(self, symbol: SpeciesLike) -> None:

File ~/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/core/periodic_table.py:700, in ElementBase()
    696     """True if element is a post-transition or poor metal."""
    697     return self.symbol in ("Al", "Ga", "In", "Tl", "Sn", "Pb", "Bi")
    699 @property
--> 700 @deprecated(
    701     message="Please use is_rare_earth instead, which is corrected to include Y and Sc.", deadline=(2025, 1, 1)
    702 )
    703 def is_rare_earth_metal(self) -> bool:
    704     """True if element is a rare earth metal, Lanthanides (La) series and Actinides (Ac) series.
    705 
    706     This property is Deprecated, and scheduled for removal after 2025-01-01.
    707     """
    708     return self.is_lanthanoid or self.is_actinoid

TypeError: deprecated() got an unexpected keyword argument 'deadline'

Expected Behavior

The code should execute without errors, fetching materials data and generating VASP input files.

Actual Behavior:

The code execution is halted by a TypeError due to an unexpected keyword argument 'deadline' in the deprecated decorator.

Environment:

(datasci) werner@x13dai-t:~$ python --version
Python 3.11.1
(datasci) werner@x13dai-t:~$ pip list | grep mp-api
mp-api                        0.41.2
(datasci) werner@x13dai-t:~$ pip list | grep 'pymatgen[ ]'
pymatgen                      2024.5.31
(datasci) werner@x13dai-t:~$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 22.04.4 LTS
Release:	22.04
Codename:	jammy

Additional Information:

The issue seems to be related to the deprecated decorator in the pymatgen library, specifically in the ElementBase class in periodic_table.py.

Possible Solution:

Check the implementation of the deprecated decorator and ensure it handles the 'deadline' keyword argument correctly.

This issue affects the usage of both mp-api and pymatgen libraries. Please investigate and provide a fix or workaround.

Minimal example

from mp_api.client import MPRester
from pymatgen.io.vasp.sets import MPRelaxSet

# Replace with your Materials Project API Key
# api_key = "YOUR_API_KEY"

# Use MPRester to fetch data
with MPRester() as mpr:
    # Search for materials with chemical system "Au" and space group "Fm-3m"
    results = mpr.materials.search(chemsys="Au", spacegroup_symbol="Fm-3m")

    # Print results
    for result in results:
        material_id = result.material_id
        print(f"Material ID: {material_id}, Formula: {result.formula_pretty}")

        # Get material structure
        structure = mpr.materials.get_structure_by_material_id(material_id)

        # Generate VASP input files using MPRelaxSet
        vasp_input_set = MPRelaxSet(structure)
        incar = vasp_input_set.incar

        # Print INCAR file content
        print(incar)

Relevant files to reproduce this bug

No response

Regards,
Zhao

[DanielYang59]

Yes we already noticed this #3752 (comment), please try to update monty version to latest with pip install -U monty

[hongyi-zhao]

@DanielYang59 Yes. Your tip does the trick.

But, should the deadline=(2025, 1, 1) in the following line be removed or fixed?

pymatgen/pymatgen/core/periodic_table.py

Line 701 in 2982968

message="Please use is_rare_earth instead, which is corrected to include Y and Sc.", deadline=(2025, 1, 1)

[DanielYang59]

@DanielYang59 Yes. Your tip does the trick.

Great to know. Sorry I forgot to update the monty in setup.py which caused this issue:

pymatgen/setup.py

Line 32 in 2982968

"monty>=2024.2.2",

But, should the deadline=(2025, 1, 1) in the following line be removed or fixed?

pymatgen/pymatgen/core/periodic_table.py

Line 701 in 2982968

message="Please use is_rare_earth instead, which is corrected to include Y and Sc.", deadline=(2025, 1, 1)

Sorry I don't quite understand your question, this property is scheduled for removal after 2025-01-01. Is there anything wrong with the decorator?

[hongyi-zhao]

Sorry I don't quite understand your question, this property is scheduled for removal after 2025-01-01. Is there anything wrong with the decorator?

I mean, why wait until 2025-01-01, and not remove it immediately?

[DanielYang59]

We decided to schedule it for removal after 2025-01-01 in #3817 to minimize potential impact to other's code base.

If we were to remove it immediately, all code relying on this would be broken without a grace period.