add Deprecated entry checking, update dependencies

examples/1_enumerators.ipynb

@@ -1790,7 +1790,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.11.5"
   },
   "vscode": {
    "interpreter": {

pyproject.toml

@@ -37,10 +37,9 @@ requires-python = ">=3.9"
 dependencies = [
     "pymatgen>=2023.11.12",
     "numba>=0.58.1",
-    "jobflow>=0.1.14",
-    "ray>=2.8.0",
+    "jobflow>=0.1.15",
+    "ray>=2.9.0",
     "rustworkx>=0.13.2",
-    "pydantic<2.5"  # ray not supporting pydantic 2.5 yet
 ]
 
 [project.optional-dependencies]
@@ -54,16 +53,16 @@ docs = [
     "sphinx==7.2.6",
 ]
 tests = [
-    "mp-api==0.37.5",  # required for testing get_entry_set job
+    "mp-api==0.39.4",  # required for testing get_entry_set job
     "pytest==7.4.3",
     "pytest-cov==4.1.0",
-    "pytest-xdist==3.3.1",
+    "pytest-xdist==3.5.0",
 ]
 strict = [
-    "pymatgen==2023.11.12",
+    "pymatgen==2023.12.18",
     "numba==0.58.1",
     "jobflow==0.1.14",
-    "ray==2.8.0",
+    "ray==2.9.0",
     "rustworkx==0.13.2",
 ]
 

src/rxn_network/data/nist/deprecated_compounds.json

@@ -0,0 +1,3 @@
+[
+    "NaCO3"
+]

src/rxn_network/entries/experimental.py

@@ -10,6 +10,10 @@
 from scipy.interpolate import interp1d
 
 from rxn_network.core import Composition
+from rxn_network.utils.funcs import get_logger
+
+logger = get_logger(__name__)
+
 
 if TYPE_CHECKING:
     from pymatgen.core.periodic_table import Element
@@ -22,6 +26,7 @@ class ExperimentalReferenceEntry(ComputedEntry):
     """
 
     REFERENCES: dict = {}
+    DEPRECATED: list = []
 
     def __init__(
         self,
@@ -30,19 +35,23 @@ def __init__(
         energy_adjustments: list[EnergyAdjustment] | None = None,
         data: dict | None = None,
     ):
-        """Args:
-        composition: Composition object
-        temperature: Temperature in Kelvin. If temperature is not selected within
-        the range of the reference  data (see self._validate_temperature), then
-        this will raise an error.
-        energy_adjustments: A list of EnergyAdjustments to apply to the entry.
-        data: Optional dictionary containing entry data.
         """
+        Args:
+            composition: Composition object
+            temperature: Temperature in Kelvin. If temperature is not selected within
+                the range of the reference  data (see self._validate_temperature), then
+                this will raise an error.
+            energy_adjustments: A list of EnergyAdjustments to apply to the entry.
+            data: Optional dictionary containing entry data.
+        """
+        self.is_deprecated = composition.reduced_formula in self.DEPRECATED
+
         formula = composition.reduced_formula
+
         entry_id = f"{self.__class__.__name__}-{formula}_{temperature}"
 
-        self._temperature = temperature
         self._validate_temperature(formula, temperature)
+        self._temperature = temperature
 
         energy = self._get_energy(formula, temperature)
 
@@ -54,8 +63,9 @@ def __init__(
             entry_id=entry_id,
         )
         self._composition = composition
-
         self.name = formula
+        if self.is_deprecated:
+            self.name += " (deprecated)"
 
     def get_new_temperature(self, new_temperature: float) -> ExperimentalReferenceEntry:
         """Return a copy of the NISTReferenceEntry at the new specified temperature.
@@ -82,19 +92,20 @@ def to_grand_entry(self, chempots: dict[Element, float]):
         """
         return GrandPotPDEntry(self, chempots)
 
-    @classmethod
-    def _validate_temperature(cls, formula: str, temperature: float) -> None:
+    def _validate_temperature(self, formula: str, temperature: float) -> None:
         """Ensure that the temperature is from a valid range."""
-        if formula not in cls.REFERENCES:
-            raise ValueError(f"{formula} not in reference data!")
+        if self.is_deprecated:
+            logger.warning(f"{formula} is deprecated! Using a formation energy of 0.0 eV.")
+            return  # skip validation
 
-        g = cls.REFERENCES[formula]
+        if formula not in self.REFERENCES:
+            raise ValueError(f"{formula} not in reference data!")
 
+        g = self.REFERENCES[formula]
         if temperature < min(g) or temperature > max(g):
             raise ValueError(f"Temperature must be selected from range: {min(g)} K to {max(g)} K")
 
-    @classmethod
-    def _get_energy(cls, formula: str, temperature: float) -> float:
+    def _get_energy(self, formula: str, temperature: float) -> float:
         """Convenience method for accessing and interpolating experimental data.
 
         Args:
@@ -104,7 +115,10 @@ def _get_energy(cls, formula: str, temperature: float) -> float:
         Returns:
             Gibbs free energy of formation of formula at specified temperature [eV]
         """
-        data = cls.REFERENCES[formula]
+        if self.is_deprecated:
+            return 0.0
+
+        data = self.REFERENCES[formula]
 
         if temperature % 100 > 0:
             g_interp = interp1d(list(data.keys()), list(data.values()))
@@ -169,10 +183,16 @@ def from_dict(cls, d: dict) -> ExperimentalReferenceEntry:
         )
 
     def __repr__(self) -> str:
-        output = [
-            f"{self.__class__.__name__} | {self.composition.reduced_formula}",
-            f"Gibbs Energy ({self.temperature} K) = {self.energy:.4f}",
-        ]
+        output = []
+        if self.is_deprecated:
+            output.append("DEPRECATED")
+
+        output.extend(
+            [
+                f"{self.__class__.__name__} | {self.composition.reduced_formula}",
+                f"Gibbs Energy ({self.temperature} K) = {self.energy:.4f}",
+            ]
+        )
         return "\n".join(output)
 
     def __eq__(self, other) -> bool:

src/rxn_network/entries/nist.py

@@ -5,6 +5,8 @@
 
 from typing import TYPE_CHECKING
 
+from monty.serialization import loadfn
+
 from rxn_network.data import PATH_TO_NIST, load_experimental_data
 from rxn_network.entries.experimental import ExperimentalReferenceEntry
 
@@ -14,6 +16,7 @@
     from rxn_network.core import Composition
 
 G_COMPOUNDS = load_experimental_data(PATH_TO_NIST / "compounds.json.gz")
+DEPRECATED_COMPOUNDS = loadfn(PATH_TO_NIST / "deprecated_compounds.json")
 
 
 class NISTReferenceEntry(ExperimentalReferenceEntry):
@@ -28,6 +31,7 @@ class NISTReferenceEntry(ExperimentalReferenceEntry):
     """
 
     REFERENCES = G_COMPOUNDS
+    DEPRECATED = DEPRECATED_COMPOUNDS
 
     def __init__(
         self,

tests/entries/test_nist.py

@@ -26,6 +26,11 @@ def test_invalid_temperature():
         NISTReferenceEntry(Composition("K2CO3"), temperature=2300)
 
 
+def test_deprecated():
+    entry = NISTReferenceEntry(Composition("NaCO3"), temperature=300)
+    assert entry.is_deprecated
+
+
 def test_energy(entries):
     expected_energies = [
         -4.087606831162386,