Merge remote-tracking branch 'materialsproject/main'

.github/dependabot.yml

@@ -7,4 +7,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "weekly"

emmet-core/emmet/core/electrode.py

@@ -10,6 +10,7 @@
 from pymatgen.core.periodic_table import Element
 from pymatgen.entries.computed_entries import ComputedEntry
 
+from emmet.core.mpid import MPID
 from emmet.core.utils import jsanitize
 
 
@@ -126,7 +127,7 @@ def from_entries(
         cls,
         grouped_entries: List[ComputedEntry],
         working_ion_entry: ComputedEntry,
-        task_id: str,
+        task_id: Union[MPID, int],
         host_structure: Structure,
     ) -> Union["InsertionElectrodeDoc", None]:
         try:
@@ -196,7 +197,7 @@ def from_composition_and_entries(
         composition: Composition,
         entries: List[ComputedEntry],
         working_ion_symbol: str,
-        task_id: str,
+        task_id: Union[MPID, int],
     ):
         ce = ConversionElectrode.from_composition_and_entries(
             comp=composition,

emmet-core/emmet/core/material.py

@@ -9,6 +9,7 @@
 from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering
 from pymatgen.core import Structure
 
+from emmet.core.mpid import MPID
 from emmet.core.structure import StructureMetadata
 
 
@@ -18,7 +19,9 @@ class PropertyOrigin(BaseModel):
     """
 
     name: str = Field(..., description="The property name")
-    task_id: str = Field(..., description="The calculation ID this property comes from")
+    task_id: Union[MPID, int] = Field(
+        ..., description="The calculation ID this property comes from"
+    )
     last_updated: datetime = Field(
         description="The timestamp when this calculation was last updated",
         default_factory=datetime.utcnow,
@@ -34,10 +37,10 @@ class MaterialsDoc(StructureMetadata):
     """
 
     # Only material_id is required for all documents
-    material_id: str = Field(
+    material_id: Union[MPID, int] = Field(
         ...,
         description="The ID of this material, used as a universal reference across proeprty documents."
-        "This comes in the form: mp-******",
+        "This comes in the form and MPID or int",
     )
 
     structure: Structure = Field(
@@ -54,7 +57,7 @@ class MaterialsDoc(StructureMetadata):
         description="Initial structures used in the DFT optimizations corresponding to this material",
     )
 
-    task_ids: Sequence[str] = Field(
+    task_ids: Sequence[Union[MPID, int]] = Field(
         [],
         title="Calculation IDs",
         description="List of Calculations IDs used to make this Materials Document",
@@ -87,7 +90,7 @@ class MaterialsDoc(StructureMetadata):
 
     @classmethod
     def from_structure(  # type: ignore[override]
-        cls: Type[T], structure: Structure, material_id: str, **kwargs
+        cls: Type[T], structure: Structure, material_id: Union[MPID, int], **kwargs
     ) -> T:
         """
         Builds a materials document using the minimal amount of information

emmet-core/emmet/core/material_property.py

@@ -10,6 +10,7 @@
 from pymatgen.core import Structure
 
 from emmet.core.material import PropertyOrigin
+from emmet.core.mpid import MPID
 from emmet.core.structure import StructureMetadata
 
 S = TypeVar("S", bound="PropertyDoc")
@@ -23,10 +24,10 @@ class PropertyDoc(StructureMetadata):
     """
 
     property_name: ClassVar[str]
-    material_id: str = Field(
+    material_id: Union[MPID, int] = Field(
         ...,
         description="The ID of the material, used as a universal reference across proeprty documents."
-        "This comes in the form: mp-******",
+        "This comes in the form of an MPID or int",
     )
 
     last_updated: datetime = Field(
@@ -44,7 +45,7 @@ class PropertyDoc(StructureMetadata):
 
     @classmethod
     def from_structure(  # type: ignore[override]
-        cls: Type[S], structure: Structure, material_id: str, **kwargs
+        cls: Type[S], structure: Structure, material_id: Union[MPID, int], **kwargs
     ) -> S:
         """
         Builds a materials document using the minimal amount of information

emmet-core/emmet/core/mpid.py

@@ -0,0 +1,24 @@
+from dataclasses import dataclass
+from typing import Union
+
+NOTHING = object()
+
+
+class MPID(str):
+    """
+    A Materials Project type ID with a prefix and an integer
+    This class enables seemlessly mixing MPIDs and regular integer IDs
+    Prefixed IDs are considered less than non-prefixed IDs to enable proper
+    mixing with the Materials Project
+    """
+
+    def __lt__(self, other: Union["MPID", int, str]):
+
+        # Always sort MPIDs before pure integer IDs
+        if isinstance(other, int):
+            return True
+
+        self_parts = self.split("-")
+        other_parts = other.split("-")
+
+        return self_parts < other_parts

emmet-core/emmet/core/spectrum.py

@@ -5,6 +5,7 @@
 
 from pydantic import Field
 
+from emmet.core.mpid import MPID
 from emmet.core.structure import StructureMetadata
 
 
@@ -14,7 +15,7 @@ class SpectrumDoc(StructureMetadata):
     metadata on the structure the spectra pertains to
     """
 
-    material_id: str = Field(
+    material_id: Union[MPID, int] = Field(
         ...,
         description="The ID of the material, used as a universal reference across proeprty documents."
         "This comes in the form: mp-******",

emmet-core/emmet/core/structure_group.py

@@ -10,6 +10,8 @@
 from pymatgen.core import Composition, Structure
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
+from emmet.core.mpid import MPID
+
 logger = logging.getLogger(__name__)
 
 
@@ -48,7 +50,7 @@ class StructureGroupDoc(BaseModel):
     Group of structure
     """
 
-    material_id: str = Field(
+    material_id: Union[MPID, int] = Field(
         None,
         description="The combined material_id of the grouped document is given by the numerically smallest task id ",
     )

emmet-core/emmet/core/stubs.py

@@ -4,9 +4,10 @@
 outside the standard MSONable model
 """
 from typing import Dict
+
 import pymatgen.core.structure
-from pymatgen.core.periodic_table import Element
 from pydantic import BaseModel
+from pymatgen.core.periodic_table import Element
 
 """
 The stub names are kept in sync with the actual classes so they

emmet-core/emmet/core/thermo.py

@@ -10,6 +10,7 @@
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
 from emmet.core.material_property import PropertyDoc
+from emmet.core.mpid import MPID
 from emmet.core.structure import StructureMetadata
 
 
@@ -18,7 +19,7 @@ class DecompositionProduct(BaseModel):
     Entry metadata for a decomposition process
     """
 
-    material_id: str = Field(
+    material_id: Union[MPID, int] = Field(
         None, description="The material this decomposition points to"
     )
     formula: str = Field(

emmet-core/emmet/core/vasp/material.py

@@ -71,7 +71,7 @@ def from_tasks(
 
         # Material ID
         possible_mat_ids = [task.task_id for task in structure_optimizations]
-        possible_mat_ids = sorted(possible_mat_ids, key=ID_to_int)
+        possible_mat_ids = sorted(possible_mat_ids)
 
         if len(possible_mat_ids) == 0:
             raise Exception(f"Could not find a material ID for {task_ids}")
@@ -157,17 +157,3 @@ def _structure_eval(task: TaskDocument):
             origins=origins,
             entries=entries,
         )
-
-
-def ID_to_int(s_id: str) -> Tuple[str, int]:
-    """
-    Converts a string id to tuple
-    falls back to assuming ID is an Int if it can't process
-    Assumes string IDs are of form "[chars]-[int]" such as mp-234
-    """
-    if isinstance(s_id, str):
-        return (s_id.split("-")[0], int(str(s_id).split("-")[-1]))
-    elif isinstance(s_id, (int, float)):
-        return ("", s_id)
-    else:
-        return None

emmet-core/emmet/core/vasp/task.py

@@ -11,6 +11,7 @@
 
 from emmet.core import SETTINGS
 from emmet.core.math import Matrix3D, Vector3D
+from emmet.core.mpid import MPID
 from emmet.core.structure import StructureMetadata
 from emmet.core.utils import ValueEnum
 from emmet.core.vasp.calc_types import (
@@ -122,7 +123,7 @@ class TaskDocument(StructureMetadata):
     orig_inputs: Dict[str, Dict] = Field(
         None, description="Summary of the original VASP inputs"
     )
-    task_id: str = Field(None, description="the Task ID For this document")
+    task_id: Union[MPID, int] = Field(None, description="the Task ID For this document")
     tags: List[str] = Field([], description="Metadata tags for this task document")
 
     @property

emmet-core/emmet/core/vasp/validation.py

@@ -6,6 +6,7 @@
 from pymatgen.core import Structure
 
 from emmet.core import SETTINGS
+from emmet.core.mpid import MPID
 from emmet.core.utils import DocEnum
 from emmet.core.vasp.task import TaskDocument
 
@@ -24,7 +25,9 @@ class ValidationDoc(BaseModel):
     Validation document for a VASP calculation
     """
 
-    task_id: str = Field(..., description="The task_id for this validation document")
+    task_id: Union[MPID, int] = Field(
+        ..., description="The task_id for this validation document"
+    )
     valid: bool = Field(False, description="Whether this task is valid or not")
     last_updated: datetime = Field(
         description="Last updated date for this document",

emmet-core/emmet/core/xas.py

@@ -1,11 +1,12 @@
 from datetime import datetime
-from typing import List, Optional
+from typing import List, Optional, Union
 
 from pydantic import BaseModel, Field, root_validator
 from pymatgen.analysis.xas.spectrum import XAS
 from pymatgen.core import Structure
 from pymatgen.core.periodic_table import Element
 
+from emmet.core.mpid import MPID
 from emmet.core.spectrum import SpectrumDoc
 from emmet.core.utils import ValueEnum
 
@@ -62,7 +63,7 @@ class XASDoc(SpectrumDoc):
     def from_spectrum(
         cls,
         xas_spectrum: XAS,
-        material_id: str,
+        material_id: Union[MPID, int],
         **kwargs,
     ):
         spectrum_type = xas_spectrum.spectrum_type

emmet-core/emmet/core/xrd.py

@@ -1,5 +1,5 @@
 from enum import Enum
-from typing import Dict, List, Optional, Tuple
+from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np
 from pydantic import BaseModel, Field, root_validator
@@ -11,6 +11,7 @@
 from pymatgen.core import Structure
 from pymatgen.core.periodic_table import Element
 
+from emmet.core.mpid import MPID
 from emmet.core.spectrum import SpectrumDoc
 from emmet.core.utils import ValueEnum, jsanitize
 
@@ -60,7 +61,7 @@ def get_target_and_edge(cls, values: Dict):
     @classmethod
     def from_structure(  # type: ignore[override]
         cls,
-        material_id: str,
+        material_id: Union[MPID, int],
         spectrum_id: str,
         structure: Structure,
         wavelength: float,
@@ -88,7 +89,7 @@ def from_structure(  # type: ignore[override]
     @classmethod
     def from_target(
         cls,
-        material_id: str,
+        material_id: Union[MPID, int],
         structure: Structure,
         target: Element,
         edge: Edge,

emmet-core/requirements.txt

@@ -1,4 +1,4 @@
-pymatgen==2021.2.14
+pymatgen==2021.2.16
 https://github.com/materialsvirtuallab/monty/archive/8d67c335bd5d8bb71ecc8ac732c82a53e0def4a1.zip
 pydantic==1.7.3
 pybtex==0.24.0

tests/emmet-core/test_mpid.py

@@ -0,0 +1,10 @@
+from emmet.core.mpid import MPID
+
+
+def test_mpid():
+
+    assert MPID("mp-3") == MPID("mp-3")
+    assert MPID("mp-3") < 3
+    assert MPID("mp-3") < MPID("np-3")
+    assert MPID("mp-3") > MPID("mp-2")
+    assert 3 > MPID("mp-3")