[Bug]: Deprecation Warnings/Future Issues with MP json loading with new ``pymatgen``

[kavanase]

Code snippet

from pymatgen.ext.matproj import MPRester
import warnings

warnings.simplefilter("error")
with MPRester() as mpr:
    entries = mpr.get_entry_by_material_id("mp-1000")

What happened?

Note: The MWE shows the error/warnings obtained using pymatgen.ext.matproj which of course is separate to mp-api, but I believe the issue applies to both implementations (being related to the loading of MP JSONs with recently deprecated pymatgen code). I'm not entirely sure which repo is best to raise this in, so let me know if it should be moved elsewhere!

Running the code without setting warnings to 'error' runs fine, without a warning appearing, however this code will eventually break once the deprecation is enforced in 2027.1, and also causes issues with tests that track warnings.
Caused by the MP jsons using the old code structure (pymatgen.entries.computed_entries, pymatgen.entries.compatibility etc.). Can these be replaced to match the new code structure?

Version

Latest

Which OS?

• MacOS
• Windows
• Linux

Log output

---------------------------------------------------------------------------
DeprecationWarning                        Traceback (most recent call last)
File ~/Packages/pymatgen/src/pymatgen/ext/matproj.py:184, in MPRester.request(self, sub_url, payload, method, mp_decode, timeout)
    183 if response.status_code in {200, 400}:
--> 184     data = json.loads(response.text, cls=MontyDecoder) if mp_decode else orjson.loads(response.text)
    185 else:

File ~/miniconda3/lib/python3.13/json/__init__.py:359, in loads(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    358     kw['parse_constant'] = parse_constant
--> 359 return cls(**kw).decode(s)

File ~/miniconda3/lib/python3.13/site-packages/monty/json.py:900, in MontyDecoder.decode(self, s)
    899     d = json.loads(s)
--> 900 return self.process_decoded(d)

File ~/miniconda3/lib/python3.13/site-packages/monty/json.py:879, in MontyDecoder.process_decoded(self, d)
    876             return bson.objectid.ObjectId(d["oid"])
    878     return {
--> 879         self.process_decoded(k): self.process_decoded(v) for k, v in d.items()
    880     }
    882 if isinstance(d, list):

File ~/miniconda3/lib/python3.13/site-packages/monty/json.py:883, in MontyDecoder.process_decoded(self, d)
    882 if isinstance(d, list):
--> 883     return [self.process_decoded(x) for x in d]
    885 return d

File ~/miniconda3/lib/python3.13/site-packages/monty/json.py:879, in MontyDecoder.process_decoded(self, d)
    876             return bson.objectid.ObjectId(d["oid"])
    878     return {
--> 879         self.process_decoded(k): self.process_decoded(v) for k, v in d.items()
    880     }
    882 if isinstance(d, list):

File ~/miniconda3/lib/python3.13/site-packages/monty/json.py:879, in MontyDecoder.process_decoded(self, d)
    876             return bson.objectid.ObjectId(d["oid"])
    878     return {
--> 879         self.process_decoded(k): self.process_decoded(v) for k, v in d.items()
    880     }
    882 if isinstance(d, list):

File ~/miniconda3/lib/python3.13/site-packages/monty/json.py:790, in MontyDecoder.process_decoded(self, d)
    788     return Path(d["string"])
--> 790 mod = __import__(modname, globals(), locals(), [classname], 0)
    791 if hasattr(mod, classname):

File ~/Packages/pymatgen/src/pymatgen/entries/__init__.py:22
     20 import warnings
---> 22 warnings.warn(
     23     "Entry, ComputedEntry and ComputedStructureEntry have been moved to pymatgen.core.entries module. "
     24     "This stub will be removed v2027.1.",
     25     DeprecationWarning,
     26     stacklevel=2,
     27 )

DeprecationWarning: Entry, ComputedEntry and ComputedStructureEntry have been moved to pymatgen.core.entries module. This stub will be removed v2027.1.

During handling of the above exception, another exception occurred:

MPRestError                               Traceback (most recent call last)
Cell In[2], line 6
      4 warnings.simplefilter("error")
      5 with MPRester() as mpr:
----> 6     entries = mpr.get_entry_by_material_id("mp-1000")

File ~/Packages/pymatgen/src/pymatgen/ext/matproj.py:457, in MPRester.get_entry_by_material_id(self, material_id, *args, **kwargs)
    445 def get_entry_by_material_id(self, material_id: str, *args, **kwargs) -> AnyComputedEntry:
    446     r"""Get a ComputedEntry corresponding to a material_id.
    447 
    448     Args:
   (...)    455         ComputedStructureEntry object.
    456     """
--> 457     return self.get_entries(material_id, *args, **kwargs)[0]

File ~/Packages/pymatgen/src/pymatgen/ext/matproj.py:414, in MPRester.get_entries(self, criteria, compatible_only, property_data, summary_data, **kwargs)
    412 entries: list = []
    413 fields = ["entries", *property_data] if property_data is not None else ["entries"]
--> 414 response = self.request(f"materials/thermo/?_fields={','.join(fields)}&{query}")
    415 for dct in response:
    416     for entry in dct["entries"].values():

File ~/Packages/pymatgen/src/pymatgen/ext/matproj.py:193, in MPRester.request(self, sub_url, payload, method, mp_decode, timeout)
    191     except Exception as ex:
    192         msg = f"{ex}. Content: {response.content}" if hasattr(response, "content") else str(ex)
--> 193         raise MPRestError(msg)
    194 return all_data

MPRestError: Entry, ComputedEntry and ComputedStructureEntry have been moved to pymatgen.core.entries module. This stub will be removed v2027.1.. Content: b'{"data":[{"entries":{"GGA":{"@module":"pymatgen.entries.computed_entries","@class":"ComputedStructureEntry","energy":-8.64743015,"composition":{"Ba":1.0,"Te":1.0},"entry_id":"mp-1000-GGA","correction":-0.422,"energy_adjustments":[{"@module":"pymatgen.entries.computed_entries","@class":"CompositionEnergyAdjustment","@version":null,"adj_per_atom":-0.422,"n_atoms":1.0,"uncertainty_per_atom":0.0262,"name":"MP2020 anion correction (Te)","cls":{"@module":"pymatgen.entries.compatibility","@class":"MaterialsProject2020Compatibility","@version":null},"description":"Composition-based energy adjustment"}],"parameters":{"potcar_spec":[{"titel":"PAW_PBE Ba_sv 06Sep2000","hash":"c0477913afb63dfae3439f3534fbf0ed","summary_stats":null},{"titel":"PAW_PBE Te 08Apr2002","hash":"72719856e22fb1d3032df6f96d98a0f2","summary_stats":null}],"run_type":"GGA","is_hubbard":false,"hubbards":null},"data":{"oxide_type":"None","aspherical":true,"last_updated":"2024-11-21 20:16:15.215275+00:00","task_id":"mp-2299050","material_id":"mp-1000","oxidation_states":{"Ba":2.0,"Te":-2.0},"license":"BY-C","run_type":"GGA"},"structure":{"@module":"pymatgen.core.structure","@class":"Structure","charge":0,"lattice":{"matrix":[[-3.544879,-3.544879,0.0],[-3.544879,0.0,-3.544879],[0.0,-3.544879,-3.544879]],"pbc":[true,true,true],"a":5.013215958771575,"b":5.013215958771575,"c":5.013215958771575,"alpha":60.00000000000001,"beta":60.00000000000001,"gamma":60.00000000000001,"volume":89.09108390126052},"properties":{},"sites":[{"species":[{"element":"Ba","occu":1}],"abc":[0.0,0.0,0.0],"properties":{},"label":"Ba","xyz":[0.0,0.0,0.0]},{"species":[{"element":"Te","occu":1}],"abc":[0.5,0.5,0.5],"properties":{},"label":"Te","xyz":[-3.544879,-3.544879,-3.544879]}]}}}},{"entries":{"r2SCAN":{"@module":"pymatgen.entries.computed_entries","@class":"ComputedStructureEntry","energy":-56.02996258,"composition":{"Ba":1.0,"Te":1.0},"entry_id":"mp-1000-r2SCAN","correction":46.96053243,"energy_adjustments":[{"@module":"pymatgen.entries.computed_entries","@class":"ConstantEnergyAdjustment","@version":null,"value":46.96053243,"uncertainty":0.0,"name":"MP GGA(+U)/r2SCAN mixing adjustment","cls":{"@module":"pymatgen.entries.mixing_scheme","@class":"MaterialsProjectDFTMixingScheme","@version":null,"structure_matcher":{"version":"1.0","@module":"pymatgen.analysis.structure_matcher","@class":"StructureMatcher","comparator":{"version":"1.0","@module":"pymatgen.analysis.structure_matcher","@class":"SpeciesComparator"},"stol":0.30000000000000004,"ltol":0.2,"angle_tol":5,"primitive_cell":true,"scale":true,"attempt_supercell":false,"allow_subset":false,"supercell_size":"num_sites","ignored_species":[]},"run_type_1":"GGA(+U)","run_type_2":"r2SCAN","compat_1":{"@module":"pymatgen.entries.compatibility","@class":"MaterialsProject2020Compatibility","@version":null},"compat_2":null,"fuzzy_matching":false,"check_potcar":true},"description":"Place r2SCAN energy onto the GGA(+U) hull"}],"parameters":{"potcar_spec":[{"titel":"PAW_PBE Ba_sv 06Sep2000","hash":"f5e095059d44e59d56e740eec161fb74","summary_stats":null},{"titel":"PAW_PBE Te 08Apr2002","hash":"11ac22d05d08fb6be6beb8cf78b0127c","summary_stats":null}],"run_type":"r2SCAN","is_hubbard":false,"hubbards":null},"data":{"oxide_type":"None","aspherical":true,"last_updated":"2024-11-21 20:16:15.201095+00:00","task_id":"mp-1947896","material_id":"mp-1000","oxidation_states":{"Ba":2.0,"Te":-2.0},"license":"BY-C","run_type":"R2SCAN"},"structure":{"@module":"pymatgen.core.structure","@class":"Structure","charge":0,"lattice":{"matrix":[[4.34162192,0.0,2.50663673],[1.44720731,4.09332126,2.50663673],[0.0,0.0,5.01327346]],"pbc":[true,true,true],"a":5.013273241347371,"b":5.013273943429635,"c":5.01327346,"alpha":60.000003189876224,"beta":59.99999855723588,"gamma":60.00000363270144,"volume":89.09415786940792},"properties":{},"sites":[{"species":[{"element":"Ba","occu":1}],"abc":[-0.0,-0.0,-0.0],"properties":{},"label":"Ba","xyz":[0.0,0.0,0.0]},{"species":[{"element":"Te","occu":1}],"abc":[0.5,0.5,0.5],"properties":{},"label":"Te","xyz":[2.894414614999999,2.04666063,5.01327346]}]}}}},{"entries":{"r2SCAN":{"@module":"pymatgen.entries.computed_entries","@class":"ComputedStructureEntry","energy":-56.02996258,"composition":{"Ba":1.0,"Te":1.0},"entry_id":"mp-1000-r2SCAN","correction":0.0,"energy_adjustments":[],"parameters":{"potcar_spec":[{"titel":"PAW_PBE Ba_sv 06Sep2000","hash":"f5e095059d44e59d56e740eec161fb74","summary_stats":null},{"titel":"PAW_PBE Te 08Apr2002","hash":"11ac22d05d08fb6be6beb8cf78b0127c","summary_stats":null}],"run_type":"r2SCAN","is_hubbard":false,"hubbards":null},"data":{"oxide_type":"None","aspherical":true,"last_updated":"2024-11-21 20:16:15.201095+00:00","task_id":"mp-1947896","material_id":"mp-1000","oxidation_states":{"Ba":2.0,"Te":-2.0},"license":"BY-C","run_type":"R2SCAN"},"structure":{"@module":"pymatgen.core.structure","@class":"Structure","charge":0,"lattice":{"matrix":[[4.34162192,0.0,2.50663673],[1.44720731,4.09332126,2.50663673],[0.0,0.0,5.01327346]],"pbc":[true,true,true],"a":5.013273241347371,"b":5.013273943429635,"c":5.01327346,"alpha":60.000003189876224,"beta":59.99999855723588,"gamma":60.00000363270144,"volume":89.09415786940792},"properties":{},"sites":[{"species":[{"element":"Ba","occu":1}],"abc":[-0.0,-0.0,-0.0],"properties":{},"label":"Ba","xyz":[0.0,0.0,0.0]},{"species":[{"element":"Te","occu":1}],"abc":[0.5,0.5,0.5],"properties":{},"label":"Te","xyz":[2.894414614999999,2.04666063,5.01327346]}]}}}}],"meta":{"api_version":"0.86.4.dev10+g324115fa4","time_stamp":"2026-03-24T19:29:44.384628+00:00","total_doc":3,"facet":null,"max_limit":1000,"default_fields":["thermo_id","material_id","last_updated"]}}'

[esoteric-ephemera]

Thanks for the heads up @kavanase. We would have to make these across our org to reflect the pymatgen changes

I don't see a real benefit to the change in imports given how long this code has existed in pymatgen. I think better for now to push on the pymatgen side to undo that change, and instead not support newer versions of pymatgen until that can be resolved