From 7e499adf6e6446446f9a12eaf55c8a772c16fcd6 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 13:09:34 -0700
Subject: [PATCH 01/27] thermo - improved type hints for sort func

---
 emmet-core/emmet/core/thermo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/thermo.py b/emmet-core/emmet/core/thermo.py
index e1ff775da3..1e8dcf225d 100644
--- a/emmet-core/emmet/core/thermo.py
+++ b/emmet-core/emmet/core/thermo.py
@@ -152,7 +152,7 @@ def from_entries(
 
         entry_quality_scores = {"GGA": 1, "GGA+U": 2, "SCAN": 3, "R2SCAN": 4}
 
-        def _energy_eval(entry: ComputedStructureEntry):
+        def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
             """
             Helper function to order entries for thermo energy data selection
             - Run type

From 68cd333be2fc1d7868e3b4ffc0c01dddf63cfebd Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 13:14:14 -0700
Subject: [PATCH 02/27] thero mypy ignore directives

---
 emmet-core/emmet/core/thermo.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/emmet-core/emmet/core/thermo.py b/emmet-core/emmet/core/thermo.py
index 1e8dcf225d..f3cef9fbd3 100644
--- a/emmet-core/emmet/core/thermo.py
+++ b/emmet-core/emmet/core/thermo.py
@@ -177,7 +177,7 @@ def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
 
             blessed_entry = sorted_entries[0]
 
-            (decomp, ehull) = pd.get_decomp_and_e_above_hull(blessed_entry)
+            (decomp, ehull) = pd.get_decomp_and_e_above_hull(blessed_entry)  # type: ignore[arg-type]
 
             builder_meta = EmmetMeta(license=blessed_entry.data.get("license"))
 
@@ -189,7 +189,7 @@ def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
                 / blessed_entry.composition.num_atoms,
                 "energy_per_atom": blessed_entry.energy
                 / blessed_entry.composition.num_atoms,
-                "formation_energy_per_atom": pd.get_form_energy_per_atom(blessed_entry),
+                "formation_energy_per_atom": pd.get_form_energy_per_atom(blessed_entry),  # type: ignore[arg-type]
                 "energy_above_hull": ehull,
                 "is_stable": blessed_entry in pd.stable_entries,
                 "builder_meta": builder_meta.model_dump(),
@@ -201,31 +201,31 @@ def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
 
             # Store different info if stable vs decomposes
             if d["is_stable"]:
-                d[
-                    "equilibrium_reaction_energy_per_atom"
-                ] = pd.get_equilibrium_reaction_energy(blessed_entry)
+                d["equilibrium_reaction_energy_per_atom"] = (
+                    pd.get_equilibrium_reaction_energy(blessed_entry)  # type: ignore[arg-type]
+                )
             else:
                 d["decomposes_to"] = [
                     {
-                        "material_id": de.data["material_id"],
+                        "material_id": de.data["material_id"],  # type: ignore[union-attr]
                         "formula": de.composition.formula,
                         "amount": amt,
                     }
-                    for de, amt in decomp.items()
+                    for de, amt in decomp.items()  # type: ignore[union-attr]
                 ]
 
             try:
                 decomp, energy = pd.get_decomp_and_phase_separation_energy(
-                    blessed_entry
+                    blessed_entry  # type: ignore[arg-type]
                 )
                 d["decomposition_enthalpy"] = energy
                 d["decomposition_enthalpy_decomposes_to"] = [
                     {
-                        "material_id": de.data["material_id"],
+                        "material_id": de.data["material_id"],  # type: ignore[union-attr]
                         "formula": de.composition.formula,
                         "amount": amt,
                     }
-                    for de, amt in decomp.items()
+                    for de, amt in decomp.items()  # type: ignore[union-attr]
                 ]
             except ValueError:
                 # try/except so this quantity does not take down the builder if it fails:
@@ -254,7 +254,7 @@ def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
 
             docs.append(
                 ThermoDoc.from_structure(
-                    meta_structure=blessed_entry.structure, **d, **kwargs
+                    meta_structure=blessed_entry.structure, **d, **kwargs  # type: ignore[attr-defined]
                 )
             )
 

From 378b60b2019fd6d2fd08cf1a83f238c4f09ac7d5 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 13:18:16 -0700
Subject: [PATCH 03/27] return type hinting for feff/task.py

---
 emmet-core/emmet/core/feff/task.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/emmet-core/emmet/core/feff/task.py b/emmet-core/emmet/core/feff/task.py
index ab9881ab02..ab94ae5b6d 100644
--- a/emmet-core/emmet/core/feff/task.py
+++ b/emmet-core/emmet/core/feff/task.py
@@ -4,7 +4,7 @@
 from pydantic import Field
 from pymatgen.analysis.xas.spectrum import XAS
 from pymatgen.core import Structure
-from pymatgen.core.periodic_table import Element
+from pymatgen.core.periodic_table import Element, Species
 
 from emmet.core.structure import StructureMetadata
 from emmet.core.vasp.task_valid import TaskDocument as BaseTaskDocument
@@ -48,7 +48,7 @@ class TaskDocument(BaseTaskDocument, StructureMetadata):
     # TEMP Stub properties for compatibility with atomate drone
 
     @property
-    def absorbing_element(self) -> Element:
+    def absorbing_element(self) -> Element | Species:
         if isinstance(self.structure[self.absorbing_atom].specie, Element):
             return self.structure[self.absorbing_atom].specie
         return self.structure[self.absorbing_atom].specie.element

From 2cba3f3c7ae2bf016e85837ddeb111c646eeee52 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 14:53:47 -0700
Subject: [PATCH 04/27] return type hinting for structure_group

---
 emmet-core/emmet/core/structure_group.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/structure_group.py b/emmet-core/emmet/core/structure_group.py
index 5f62b048cc..ee4b774e75 100644
--- a/emmet-core/emmet/core/structure_group.py
+++ b/emmet-core/emmet/core/structure_group.py
@@ -248,7 +248,7 @@ def group_entries_with_structure_matcher(
     g,
     struct_matcher: StructureMatcher,
     working_ion: Optional[str] = None,
-) -> Iterable[List[Union[ComputedStructureEntry]]]:
+) -> Iterable[List[Union[ComputedStructureEntry, ComputedEntry]]]:
     """
     Group the entries together based on similarity of the  primitive cells
     Args:

From ef76822ea949d065925960d54e63c190e0b02465 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:09:56 -0700
Subject: [PATCH 05/27] type hinting for migrationgraph

---
 emmet-core/emmet/core/mobility/migrationgraph.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/emmet-core/emmet/core/mobility/migrationgraph.py b/emmet-core/emmet/core/mobility/migrationgraph.py
index ad968501a3..6305a1e786 100644
--- a/emmet-core/emmet/core/mobility/migrationgraph.py
+++ b/emmet-core/emmet/core/mobility/migrationgraph.py
@@ -193,7 +193,7 @@ def generate_sc_fields(
             min_length=min_length_sc,
         )
 
-        sc_mat = sc_mat.tolist()
+        sc_mat = sc_mat.tolist()  # type: ignore[attr-defined]
         host_sc = mg.host_structure * sc_mat
         working_ion = mg.only_sites[0].species_string
 
@@ -205,9 +205,7 @@ def generate_sc_fields(
         return host_sc, sc_mat, min_length_sc, minmax_num_atoms, coords_list, combo
 
     @staticmethod
-    def ordered_sc_site_list(
-        uc_sites_only: Structure, sc_mat: List[List[Union[int, float]]]
-    ):
+    def ordered_sc_site_list(uc_sites_only: Structure, sc_mat: List[List[int]]):
         uc_no_site = uc_sites_only.copy()
         uc_no_site.remove_sites(range(len(uc_sites_only)))
         working_ion = uc_sites_only[0].species_string
@@ -238,7 +236,7 @@ def ordered_sc_site_list(
     @staticmethod
     def get_hop_sc_combo(
         unique_hops: Dict,
-        sc_mat: List[List[Union[int, float]]],
+        sc_mat: List[List[int]],
         sm: StructureMatcher,
         host_sc: Structure,
         working_ion: str,
@@ -321,7 +319,7 @@ def append_new_site(
         host_sc: Structure,
         ordered_sc_site_list: list,
         one_hop: Dict,
-        sc_mat: List[List[Union[int, float]]],
+        sc_mat: List[List[int]],
         working_ion: str,
     ):
         sc_mat_inv = np.linalg.inv(sc_mat)

From 17e28ac9a5bed3ee9d08e69c635857896c3bdecb Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:23:44 -0700
Subject: [PATCH 06/27] mypy ignore directive for alloy_pairs assignment

---
 emmet-core/emmet/core/alloys.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/alloys.py b/emmet-core/emmet/core/alloys.py
index b9b333a1c7..06063ce226 100644
--- a/emmet-core/emmet/core/alloys.py
+++ b/emmet-core/emmet/core/alloys.py
@@ -33,5 +33,5 @@ class AlloySystemDoc(EmmetBaseModel):
     @classmethod
     def from_pair(cls, alloy_system: AlloySystem):
         # Too large to duplicate alloy pairs here.
-        alloy_system.alloy_pairs = None
+        alloy_system.alloy_pairs = None  # type: ignore[assignment]
         return cls(alloy_system=alloy_system, alloy_id=alloy_system.alloy_id)

From 329456507fed25ec419a8a39e80532006f23e971 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:33:19 -0700
Subject: [PATCH 07/27] mypy ignore directive for chemenv

---
 emmet-core/emmet/core/chemenv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/chemenv.py b/emmet-core/emmet/core/chemenv.py
index daf11967ea..b70baf7194 100644
--- a/emmet-core/emmet/core/chemenv.py
+++ b/emmet-core/emmet/core/chemenv.py
@@ -442,7 +442,7 @@ def from_structure(
             inequivalent_indices_cations = [
                 indices[0]
                 for indices in symm_struct.equivalent_indices
-                if valences[indices[0]] > 0.0
+                if valences[indices[0]] > 0.0  # type: ignore[operator]
             ]
 
             se = lgf.compute_structure_environments(

From 1f653296cb5ca41b4edeba96b5f806161e8fd11f Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:45:05 -0700
Subject: [PATCH 08/27] mypy directive for xas

see comment on line 110 for explanation of attr assignment hack
---
 emmet-core/emmet/core/xas.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/emmet-core/emmet/core/xas.py b/emmet-core/emmet/core/xas.py
index f9f0bc54f0..7a4b63cb97 100644
--- a/emmet-core/emmet/core/xas.py
+++ b/emmet-core/emmet/core/xas.py
@@ -152,7 +152,7 @@ def from_task_docs(
                 try:
                     total_spectrum = xanes.stitch(exafs, mode="XAFS")
                     total_spectrum.absorbing_index = site
-                    total_spectrum.task_ids = xanes.task_ids + exafs.task_ids
+                    total_spectrum.task_ids = xanes.task_ids + exafs.task_ids  # type: ignore[attr-defined]
                     all_spectra.append(total_spectrum)
                 except ValueError as e:
                     warnings.warn(f"Warning during spectral merging in XASDoC: {e}")
@@ -167,7 +167,7 @@ def from_task_docs(
                 try:
                     total_spectrum = l2.stitch(l3, mode="L23")
                     total_spectrum.absorbing_index = site
-                    total_spectrum.task_ids = l2.task_ids + l3.task_ids
+                    total_spectrum.task_ids = l2.task_ids + l3.task_ids  # type: ignore[attr-defined]
                     all_spectra.append(total_spectrum)
                 except ValueError as e:
                     warnings.warn(f"Warning during spectral merging in XASDoC: {e}")
@@ -193,12 +193,12 @@ def from_task_docs(
                         avg_spectrum = site_weighted_spectrum(
                             relevant_spectra, num_samples=num_samples
                         )
-                        avg_spectrum.task_ids = [
+                        avg_spectrum.task_ids = [  # type: ignore[attr-defined]
                             id
                             for spectrum in relevant_spectra
                             for id in spectrum.task_ids
                         ]
-                        avg_spectrum.last_updated = max(
+                        avg_spectrum.last_updated = max(  # type: ignore[attr-defined, type-var]
                             [spectrum.last_updated for spectrum in relevant_spectra]
                         )
                         averaged_spectra.append(avg_spectrum)

From e3e769b9ebbb69fc8496e1810bfab76382f25dfd Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:57:17 -0700
Subject: [PATCH 09/27] type hint + mypy directive for piezodoc

---
 emmet-core/emmet/core/polar.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/polar.py b/emmet-core/emmet/core/polar.py
index fa3263cf14..be99914828 100644
--- a/emmet-core/emmet/core/polar.py
+++ b/emmet-core/emmet/core/polar.py
@@ -106,7 +106,7 @@ def from_ionic_and_electronic(
     ):
         ionic_tensor = BasePiezoTensor.from_vasp_voigt(ionic)
         electronic_tensor = BasePiezoTensor.from_vasp_voigt(electronic)
-        total = ionic_tensor + electronic_tensor
+        total: BasePiezoTensor = ionic_tensor + electronic_tensor  # type: ignore[assignment]
 
         # Symmeterize Convert to IEEE orientation
         total = total.convert_to_ieee(structure)

From d5524ce05a8990dff42c9fa1ed9a0a4ff7373f0a Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 17:14:42 -0700
Subject: [PATCH 10/27] mypy type hinting + ignore directives for elasticity

---
 emmet-core/emmet/core/elasticity.py | 46 ++++++++++++++---------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/emmet-core/emmet/core/elasticity.py b/emmet-core/emmet/core/elasticity.py
index 06edc63d3f..646f78f84a 100644
--- a/emmet-core/emmet/core/elasticity.py
+++ b/emmet-core/emmet/core/elasticity.py
@@ -493,7 +493,7 @@ def generate_derived_fitting_data(
     derived_2nd_pk_stresses = []
 
     for d_strain, op_set in mapping.items():
-        symmops, p_indices = zip(*op_set)
+        symmops, p_indices = zip(*op_set)  # type: ignore[assignment]
 
         p_stresses = [stresses[i] for i in p_indices]
         d_stresses = [s.transform(op) for s, op in zip(p_stresses, symmops)]
@@ -551,7 +551,7 @@ def symmetrize_stresses(
 def fit_elastic_tensor(
     strains: List[Strain],
     stresses: List[Stress],
-    eq_stress: Stress,
+    eq_stress: Stress | None,
     fitting_method: str = "finite_difference",
     order: int = 2,
 ) -> ElasticTensor:
@@ -575,17 +575,17 @@ def fit_elastic_tensor(
             strains, stresses, eq_stress=eq_stress, order=order
         )
         if order == 2:
-            result = ElasticTensor(result[0])
+            result: ElasticTensor = ElasticTensor(result[0])  # type: ignore[no-redef]
     elif fitting_method == "pseudoinverse":
-        result = ElasticTensor.from_pseudoinverse(strains, stresses)
+        result: ElasticTensor = ElasticTensor.from_pseudoinverse(strains, stresses)  # type: ignore[no-redef]
     elif fitting_method == "independent":
-        result = ElasticTensor.from_independent_strains(
+        result: ElasticTensor = ElasticTensor.from_independent_strains(  # type: ignore[no-redef]
             strains, stresses, eq_stress=eq_stress
         )
     else:
         raise ValueError(f"Unsupported elastic fitting method {fitting_method}")
 
-    return result
+    return result  # type: ignore[return-value]
 
 
 def get_derived_properties(
@@ -613,35 +613,35 @@ def get_derived_properties(
     decimals = 3
     derived_prop = {
         "bulk_modulus": BulkModulus(
-            voigt=np.round(prop_dict["k_voigt"], decimals),
-            reuss=np.round(prop_dict["k_reuss"], decimals),
-            vrh=np.round(prop_dict["k_vrh"], decimals),
+            voigt=np.round(prop_dict["k_voigt"], decimals),  # type: ignore[arg-type]
+            reuss=np.round(prop_dict["k_reuss"], decimals),  # type: ignore[arg-type]
+            vrh=np.round(prop_dict["k_vrh"], decimals),  # type: ignore[arg-type]
         ),
         "shear_modulus": ShearModulus(
-            voigt=np.round(prop_dict["g_voigt"], decimals),
-            reuss=np.round(prop_dict["g_reuss"], decimals),
-            vrh=np.round(prop_dict["g_vrh"], decimals),
+            voigt=np.round(prop_dict["g_voigt"], decimals),  # type: ignore[arg-type]
+            reuss=np.round(prop_dict["g_reuss"], decimals),  # type: ignore[arg-type]
+            vrh=np.round(prop_dict["g_vrh"], decimals),  # type: ignore[arg-type]
         ),
-        "young_modulus": np.round(prop_dict["y_mod"], 0),
-        "homogeneous_poisson": np.round(prop_dict["homogeneous_poisson"], decimals),
-        "universal_anisotropy": np.round(prop_dict["universal_anisotropy"], decimals),
+        "young_modulus": np.round(prop_dict["y_mod"], 0),  # type: ignore[arg-type]
+        "homogeneous_poisson": np.round(prop_dict["homogeneous_poisson"], decimals),  # type: ignore[arg-type]
+        "universal_anisotropy": np.round(prop_dict["universal_anisotropy"], decimals),  # type: ignore[arg-type]
     }
 
     if structure_prop_computed:
         derived_prop.update(
             {
                 "sound_velocity": SoundVelocity(
-                    transverse=prop_dict["trans_v"],
-                    longitudinal=prop_dict["long_v"],
-                    snyder_acoustic=prop_dict["snyder_ac"],
-                    snyder_optical=prop_dict["snyder_opt"],
-                    snyder_total=prop_dict["snyder_total"],
+                    transverse=prop_dict["trans_v"],  # type: ignore[arg-type]
+                    longitudinal=prop_dict["long_v"],  # type: ignore[arg-type]
+                    snyder_acoustic=prop_dict["snyder_ac"],  # type: ignore[arg-type]
+                    snyder_optical=prop_dict["snyder_opt"],  # type: ignore[arg-type]
+                    snyder_total=prop_dict["snyder_total"],  # type: ignore[arg-type]
                 ),
                 "thermal_conductivity": ThermalConductivity(
-                    clarke=prop_dict["clarke_thermalcond"],
-                    cahill=prop_dict["cahill_thermalcond"],
+                    clarke=prop_dict["clarke_thermalcond"],  # type: ignore[arg-type]
+                    cahill=prop_dict["cahill_thermalcond"],  # type: ignore[arg-type]
                 ),
-                "debye_temperature": prop_dict["debye_temperature"],
+                "debye_temperature": prop_dict["debye_temperature"],  # type: ignore[arg-type]
             }
         )
 

From e3819cb9f59a7cf0dbd47d6362ae7d5e47a58e08 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 17:20:58 -0700
Subject: [PATCH 11/27] mypy fix for stubs

---
 emmet-core/emmet/core/stubs.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/emmet-core/emmet/core/stubs.py b/emmet-core/emmet/core/stubs.py
index b302d1a588..2b542a92de 100644
--- a/emmet-core/emmet/core/stubs.py
+++ b/emmet-core/emmet/core/stubs.py
@@ -1,3 +1,4 @@
+# mypy: ignore-errors
 # isort: off
 """
 This module stubs some pymatgen classes that implement custom behavior

From 58ab43f3c63f126131c1f72ee451d4f07393fff0 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 17:21:25 -0700
Subject: [PATCH 12/27] mypy fix for molecules metal_binding

---
 emmet-core/emmet/core/molecules/metal_binding.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/molecules/metal_binding.py b/emmet-core/emmet/core/molecules/metal_binding.py
index 4cd0a25cfc..95b3b81b2b 100644
--- a/emmet-core/emmet/core/molecules/metal_binding.py
+++ b/emmet-core/emmet/core/molecules/metal_binding.py
@@ -67,7 +67,7 @@ class MetalBindingData(BaseModel):
         description="The number of atoms neighboring the metal atom or ion of interest",
     )
 
-    coordinating_atoms: Optional[List[Union[str, Species]]] = Field(
+    coordinating_atoms: Optional[List[str]] = Field(
         None, description="The elements/species coordinating the metal."
     )
 

From 127e398dccb8f25da9a9a6e688202bcdab02c7cc Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 17:24:00 -0700
Subject: [PATCH 13/27] mypy directives for qchem/molecule.py

---
 emmet-core/emmet/core/qchem/molecule.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/emmet-core/emmet/core/qchem/molecule.py b/emmet-core/emmet/core/qchem/molecule.py
index c93344b156..7b8b1fb2e6 100644
--- a/emmet-core/emmet/core/qchem/molecule.py
+++ b/emmet-core/emmet/core/qchem/molecule.py
@@ -405,8 +405,8 @@ def from_tasks(
         ad = BabelMolAdaptor(molecule)
         openbabel.StereoFrom3D(ad.openbabel_mol)
 
-        inchi = ad.pybel_mol.write("inchi").strip()
-        inchikey = ad.pybel_mol.write("inchikey").strip()
+        inchi = ad.pybel_mol.write("inchi").strip()  # type: ignore[attr-defined]
+        inchikey = ad.pybel_mol.write("inchikey").strip()  # type: ignore[attr-defined]
 
         return cls.from_molecule(
             molecule=molecule,
@@ -484,8 +484,8 @@ def construct_deprecated_molecule(
         ad = BabelMolAdaptor(molecule)
         openbabel.StereoFrom3D(ad.openbabel_mol)
 
-        inchi = ad.pybel_mol.write("inchi").strip()
-        inchikey = ad.pybel_mol.write("inchikey").strip()
+        inchi = ad.pybel_mol.write("inchi").strip()  # type: ignore[attr-defined]
+        inchikey = ad.pybel_mol.write("inchikey").strip()  # type: ignore[attr-defined]
 
         return cls.from_molecule(
             molecule=molecule,

From 3cea285c11a78fd27b749ced37dd291bb6fc0492 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Fri, 19 Jul 2024 17:46:00 -0700
Subject: [PATCH 14/27] mypy fixes for electrodes.py

---
 emmet-core/emmet/core/electrode.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/emmet-core/emmet/core/electrode.py b/emmet-core/emmet/core/electrode.py
index 3db8db395b..46982256a4 100644
--- a/emmet-core/emmet/core/electrode.py
+++ b/emmet-core/emmet/core/electrode.py
@@ -12,7 +12,7 @@
 from pymatgen.apps.battery.insertion_battery import InsertionElectrode
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.core import Composition, Structure
-from pymatgen.core.periodic_table import Element
+from pymatgen.core.periodic_table import DummySpecies, Element, Species
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
 from emmet.core.mpid import MPID
@@ -138,7 +138,7 @@ class EntriesCompositionSummary(BaseModel):
         description="Anonymous formulas for material entries across all voltage pairs.",
     )
 
-    all_elements: Optional[List[Element]] = Field(
+    all_elements: Optional[List[Element | Species | DummySpecies]] = Field(
         None,
         description="Elements in material entries across all voltage pairs.",
     )
@@ -348,7 +348,7 @@ def from_entries(
             host_structure=stripped_host.as_dict(),
             framework=framework,
             battery_formula=battery_formula,
-            electrode_object=ie.as_dict(),
+            electrode_object=ie,
             elements=elements,
             nelements=len(elements),
             chemsys=chemsys,
@@ -465,7 +465,7 @@ def from_composition_and_entries(
             entries_in_chemsys=entries,
             working_ion_symbol=working_ion_symbol,
         )
-        d = cls.get_conversion_elec_doc(ce)
+        d = cls.get_conversion_elec_doc(ce)  # type: ignore[arg-type]
         return cls(battery_id=battery_id, thermo_type=thermo_type, **d)
 
     @classmethod
@@ -480,7 +480,7 @@ def from_composition_and_pd(
         ce = ConversionElectrode.from_composition_and_pd(
             comp=comp, pd=pd, working_ion_symbol=working_ion_symbol
         )
-        d = cls.get_conversion_elec_doc(ce)
+        d = cls.get_conversion_elec_doc(ce)  # type: ignore[arg-type]
         return cls(battery_id=battery_id, thermo_type=thermo_type, **d)
 
     @staticmethod

From 3b54fed362f1f00329ba630a72481903e12a26ee Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 09:03:53 -0700
Subject: [PATCH 15/27] mypy fixes for electronic_structure

---
 emmet-core/emmet/core/electronic_structure.py | 25 ++++++++++---------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/emmet-core/emmet/core/electronic_structure.py b/emmet-core/emmet/core/electronic_structure.py
index 54b38c2144..50e5873f38 100644
--- a/emmet-core/emmet/core/electronic_structure.py
+++ b/emmet-core/emmet/core/electronic_structure.py
@@ -1,10 +1,12 @@
 """ Core definition of an Electronic Structure """
+
 from __future__ import annotations
 
 from collections import defaultdict
 from datetime import datetime
+from enum import Enum
 from math import isnan
-from typing import Dict, Optional, Type, TypeVar, Union, List
+from typing import Dict, List, Optional, Type, TypeVar, Union
 
 import numpy as np
 from pydantic import BaseModel, Field
@@ -20,11 +22,10 @@
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.bandstructure import HighSymmKpath
 from typing_extensions import Literal
-from enum import Enum
 
-from emmet.core.settings import EmmetSettings
 from emmet.core.material_property import PropertyDoc
 from emmet.core.mpid import MPID
+from emmet.core.settings import EmmetSettings
 
 SETTINGS = EmmetSettings()
 
@@ -279,7 +280,7 @@ def from_bsdos(  # type: ignore[override]
             except KeyError:
                 spin_polarization = None
 
-            dos_data["total"][spin] = DosSummaryData(
+            dos_data["total"][spin] = DosSummaryData(  # type: ignore[index]
                 task_id=dos_task,
                 band_gap=band_gap,
                 cbm=cbm,
@@ -296,7 +297,7 @@ def from_bsdos(  # type: ignore[override]
 
                 spin_polarization = None
 
-                dos_data["orbital"][orbital][spin] = DosSummaryData(
+                dos_data["orbital"][orbital][spin] = DosSummaryData(  # type: ignore[index]
                     task_id=dos_task,
                     band_gap=band_gap,
                     cbm=cbm,
@@ -309,7 +310,7 @@ def from_bsdos(  # type: ignore[override]
         for ele in ele_dos:
             orb_dos = dos_obj.get_element_spd_dos(ele)
 
-            for orbital in ["total"] + list(orb_dos.keys()):
+            for orbital in ["total"] + list(orb_dos.keys()):  # type: ignore[assignment]
                 if orbital == "total":
                     proj_dos = ele_dos
                     label = ele
@@ -323,7 +324,7 @@ def from_bsdos(  # type: ignore[override]
 
                     spin_polarization = None
 
-                    dos_data["elemental"][ele][orbital][spin] = DosSummaryData(
+                    dos_data["elemental"][ele][orbital][spin] = DosSummaryData(  # type: ignore[index]
                         task_id=dos_task,
                         band_gap=band_gap,
                         cbm=cbm,
@@ -349,7 +350,7 @@ def from_bsdos(  # type: ignore[override]
                     ).ordering
                 else:
                     bs_mag_ordering = CollinearMagneticStructureAnalyzer(
-                        bs.structure
+                        bs.structure  # type: ignore[arg-type]
                     ).ordering
 
                 gap_dict = bs.get_band_gap()
@@ -358,8 +359,8 @@ def from_bsdos(  # type: ignore[override]
 
                 if is_metal:
                     band_gap = 0.0
-                    cbm = None
-                    vbm = None
+                    cbm = None  # type: ignore[assignment]
+                    vbm = None  # type: ignore[assignment]
                     is_gap_direct = False
                 else:
                     band_gap = gap_dict["energy"]
@@ -399,7 +400,7 @@ def from_bsdos(  # type: ignore[override]
 
                     if not gen_labels.issubset(kpath_labels):
                         new_structure = SpacegroupAnalyzer(
-                            bs.structure
+                            bs.structure  # type: ignore[arg-type]
                         ).get_primitive_standard_structure(
                             international_monoclinic=False
                         )
@@ -428,7 +429,7 @@ def from_bsdos(  # type: ignore[override]
                 )
 
         bs_entry = BandstructureData(**bs_data)  # type: ignore
-        dos_entry = DosData(**dos_data)
+        dos_entry = DosData(**dos_data)  # type: ignore[arg-type]
 
         # Obtain summary data
 

From a6ec3f55042a5a3f20787564573e2e1890e04db9 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 09:47:53 -0700
Subject: [PATCH 16/27] pre-commit formatting

---
 emmet-core/emmet/core/thermo.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/emmet-core/emmet/core/thermo.py b/emmet-core/emmet/core/thermo.py
index f3cef9fbd3..c687d00366 100644
--- a/emmet-core/emmet/core/thermo.py
+++ b/emmet-core/emmet/core/thermo.py
@@ -201,9 +201,11 @@ def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
 
             # Store different info if stable vs decomposes
             if d["is_stable"]:
-                d["equilibrium_reaction_energy_per_atom"] = (
-                    pd.get_equilibrium_reaction_energy(blessed_entry)  # type: ignore[arg-type]
-                )
+                d[
+                    "equilibrium_reaction_energy_per_atom"
+                ] = pd.get_equilibrium_reaction_energy(
+                    blessed_entry
+                )  # type: ignore[arg-type]
             else:
                 d["decomposes_to"] = [
                     {

From 22cfe4ea4b7caf9b306acdc71b4d46f17e68a5a7 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 10:18:09 -0700
Subject: [PATCH 17/27] future annotations for type hint compatibility w/ py3.9

---
 emmet-core/emmet/core/feff/task.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/emmet-core/emmet/core/feff/task.py b/emmet-core/emmet/core/feff/task.py
index ab94ae5b6d..74c50d8d1a 100644
--- a/emmet-core/emmet/core/feff/task.py
+++ b/emmet-core/emmet/core/feff/task.py
@@ -1,4 +1,7 @@
 """ Core definition of a VASP Task Document """
+
+from __future__ import annotations
+
 from typing import Any, Dict, List
 
 from pydantic import Field
@@ -7,8 +10,8 @@
 from pymatgen.core.periodic_table import Element, Species
 
 from emmet.core.structure import StructureMetadata
-from emmet.core.vasp.task_valid import TaskDocument as BaseTaskDocument
 from emmet.core.utils import ValueEnum
+from emmet.core.vasp.task_valid import TaskDocument as BaseTaskDocument
 
 
 class CalcType(ValueEnum):

From ad2213079453a1850bc9e2301bae586b9a57d5b2 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 10:32:06 -0700
Subject: [PATCH 18/27] more py3.9 typing compat fixes

---
 emmet-core/emmet/core/elasticity.py |  2 ++
 emmet-core/emmet/core/electrode.py  | 17 +++++++++--------
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/emmet-core/emmet/core/elasticity.py b/emmet-core/emmet/core/elasticity.py
index 646f78f84a..4ac8ed1857 100644
--- a/emmet-core/emmet/core/elasticity.py
+++ b/emmet-core/emmet/core/elasticity.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import numpy as np
diff --git a/emmet-core/emmet/core/electrode.py b/emmet-core/emmet/core/electrode.py
index 46982256a4..8e98a9b98c 100644
--- a/emmet-core/emmet/core/electrode.py
+++ b/emmet-core/emmet/core/electrode.py
@@ -1,21 +1,22 @@
+from __future__ import annotations
+
 import re
-from datetime import datetime
-from typing import List, Union, Dict, Optional
 from collections import defaultdict
+from datetime import datetime
+from typing import Dict, List, Optional, Union
 
-from emmet.core.utils import ValueEnum
-from emmet.core.common import convert_datetime
-
-from pydantic import field_validator, BaseModel, Field
+from pydantic import BaseModel, Field, field_validator
+from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.apps.battery.battery_abc import AbstractElectrode
 from pymatgen.apps.battery.conversion_battery import ConversionElectrode
 from pymatgen.apps.battery.insertion_battery import InsertionElectrode
-from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.core import Composition, Structure
 from pymatgen.core.periodic_table import DummySpecies, Element, Species
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
+from emmet.core.common import convert_datetime
 from emmet.core.mpid import MPID
+from emmet.core.utils import ValueEnum
 
 
 class BatteryType(str, ValueEnum):
@@ -138,7 +139,7 @@ class EntriesCompositionSummary(BaseModel):
         description="Anonymous formulas for material entries across all voltage pairs.",
     )
 
-    all_elements: Optional[List[Element | Species | DummySpecies]] = Field(
+    all_elements: Optional[List[Union[Element, Species, DummySpecies]]] = Field(
         None,
         description="Elements in material entries across all voltage pairs.",
     )

From b1b5f42333ffef465869fabb2970de9effa1bf58 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 10:50:57 -0700
Subject: [PATCH 19/27] mypy directive on wrong line

---
 emmet-core/emmet/core/thermo.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/emmet-core/emmet/core/thermo.py b/emmet-core/emmet/core/thermo.py
index c687d00366..2a47a5678d 100644
--- a/emmet-core/emmet/core/thermo.py
+++ b/emmet-core/emmet/core/thermo.py
@@ -1,17 +1,18 @@
 """ Core definition of a Thermo Document """
+
 from collections import defaultdict
-from typing import Dict, List, Optional, Union
 from datetime import datetime
-from emmet.core.base import EmmetMeta
-from emmet.core.utils import ValueEnum
+from typing import Dict, List, Optional, Union
 
 from pydantic import BaseModel, Field
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
-from emmet.core.material_property import PropertyDoc
+from emmet.core.base import EmmetMeta
 from emmet.core.material import PropertyOrigin
+from emmet.core.material_property import PropertyDoc
 from emmet.core.mpid import MPID
+from emmet.core.utils import ValueEnum
 from emmet.core.vasp.calc_types.enums import RunType
 
 
@@ -204,8 +205,8 @@ def _energy_eval(entry: Union[ComputedStructureEntry, ComputedEntry]):
                 d[
                     "equilibrium_reaction_energy_per_atom"
                 ] = pd.get_equilibrium_reaction_energy(
-                    blessed_entry
-                )  # type: ignore[arg-type]
+                    blessed_entry  # type: ignore[arg-type]
+                )
             else:
                 d["decomposes_to"] = [
                     {

From 8fe8e9087a4580da4b5b3a6df9f536702d664b30 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:14:04 -0700
Subject: [PATCH 20/27] builers - provenance mypy fix

---
 emmet-builders/emmet/builders/materials/provenance.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/emmet-builders/emmet/builders/materials/provenance.py b/emmet-builders/emmet/builders/materials/provenance.py
index d2525b64aa..6a88e1e019 100644
--- a/emmet-builders/emmet/builders/materials/provenance.py
+++ b/emmet-builders/emmet/builders/materials/provenance.py
@@ -1,7 +1,7 @@
 from collections import defaultdict
-from typing import Dict, Iterable, List, Optional, Tuple
-from math import ceil
 from datetime import datetime
+from math import ceil
+from typing import Dict, Iterable, List, Optional, Tuple
 
 from maggma.core import Builder, Store
 from maggma.utils import grouper
@@ -168,7 +168,7 @@ def get_items(self) -> Tuple[List[Dict], List[Dict]]:  # type: ignore
             for snl in snls:
                 struc = Structure.from_dict(snl)
                 snl_sg = get_sg(struc)
-                struc.snl = SNLDict(**snl)
+                struc.snl = SNLDict(**snl)  # type: ignore[attr-defined]
                 snl_groups[snl_sg].append(struc)
 
             mat_sg = get_sg(Structure.from_dict(mat["structure"]))

From b0b4c8b23063ab7e2b264406546136dfbb99d7cd Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:17:04 -0700
Subject: [PATCH 21/27] builders - mypy for ce builder

---
 .../builders/materials/corrected_entries.py   | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/emmet-builders/emmet/builders/materials/corrected_entries.py b/emmet-builders/emmet/builders/materials/corrected_entries.py
index 0c819217fe..cf4632281c 100644
--- a/emmet-builders/emmet/builders/materials/corrected_entries.py
+++ b/emmet-builders/emmet/builders/materials/corrected_entries.py
@@ -1,20 +1,20 @@
+import copy
 import warnings
 from collections import defaultdict
+from datetime import datetime
 from itertools import chain
-from typing import Dict, Iterable, Iterator, List, Optional
 from math import ceil
-import copy
-from datetime import datetime
+from typing import Dict, Iterable, Iterator, List, Optional, Union
 
 from maggma.core import Builder, Store
 from maggma.utils import grouper
-from pymatgen.entries.computed_entries import ComputedStructureEntry
 from pymatgen.entries.compatibility import Compatibility
+from pymatgen.entries.computed_entries import ComputedStructureEntry
 
-from emmet.core.utils import jsanitize
-from emmet.builders.utils import chemsys_permutations, HiddenPrints
-from emmet.core.thermo import ThermoType
+from emmet.builders.utils import HiddenPrints, chemsys_permutations
 from emmet.core.corrected_entries import CorrectedEntriesDoc
+from emmet.core.thermo import ThermoType
+from emmet.core.utils import jsanitize
 
 
 class CorrectedEntriesBuilder(Builder):
@@ -24,7 +24,7 @@ def __init__(
         corrected_entries: Store,
         oxidation_states: Optional[Store] = None,
         query: Optional[Dict] = None,
-        compatibility: Optional[List[Compatibility]] = None,
+        compatibility: Optional[Union[List[Compatibility], List[None]]] = [None],
         chunk_size: int = 1000,
         **kwargs,
     ):
@@ -45,10 +45,10 @@ def __init__(
         self.materials = materials
         self.query = query if query else {}
         self.corrected_entries = corrected_entries
-        self.compatibility = compatibility or [None]
+        self.compatibility = compatibility
         self.oxidation_states = oxidation_states
         self.chunk_size = chunk_size
-        self._entries_cache: Dict[str, List[ComputedStructureEntry]] = defaultdict(list)
+        self._entries_cache: Dict[str, List[Dict]] = defaultdict(list)
 
         if self.corrected_entries.key != "chemsys":
             warnings.warn(

From 093ed667958d9090eb0e16b31c027ef8525bdf2d Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:17:22 -0700
Subject: [PATCH 22/27] builders - mypy for utils

---
 emmet-builders/emmet/builders/utils.py | 28 ++++++++++++++------------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/emmet-builders/emmet/builders/utils.py b/emmet-builders/emmet/builders/utils.py
index 75633637ef..42948a9037 100644
--- a/emmet-builders/emmet/builders/utils.py
+++ b/emmet-builders/emmet/builders/utils.py
@@ -1,17 +1,19 @@
 from __future__ import annotations
-from typing import Set, Union, Any, Literal, Optional
-import sys
+
+import json
 import os
-from pathlib import Path
+import sys
 from gzip import GzipFile
-import orjson
-import json
 from io import BytesIO
-from monty.serialization import MontyDecoder
-from botocore.exceptions import ClientError
 from itertools import chain, combinations
-from pymatgen.core import Structure
+from pathlib import Path
+from typing import Any, Literal, Optional, Set, Union
+
+import orjson
+from botocore.exceptions import ClientError
+from monty.serialization import MontyDecoder
 from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph
+from pymatgen.core import Structure
 from pymatgen.io.vasp.inputs import PotcarSingle
 
 from emmet.builders.settings import EmmetBuildSettings
@@ -275,16 +277,16 @@ def get_potcar_stats(
                 # fallback method for validation - use header hash and symbol
                 # note that the potcar_spec assigns PotcarSingle.symbol to "titel"
                 # whereas the ***correct*** field is `header`
-                summary_stats["titel"] = potcar.header
-                summary_stats["hash"] = potcar.md5_header_hash
-                summary_stats = [summary_stats]
+                summary_stats["titel"] = potcar.header  # type: ignore[assignment]
+                summary_stats["hash"] = potcar.md5_header_hash  # type: ignore[assignment]
+                summary_stats = [summary_stats]  # type: ignore[assignment]
 
             elif method == "pymatgen":
-                summary_stats = []
+                summary_stats = []  # type: ignore[assignment]
                 for _, entries in PotcarSingle._potcar_summary_stats[
                     functional
                 ].items():
-                    summary_stats += [
+                    summary_stats += [  # type: ignore[operator]
                         {**entry, "titel": None, "hash": None}
                         for entry in entries
                         if entry["symbol"] == potcar_symbol

From 3677afd7eb34e762e3a46d9f8f54d78df91991c6 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:27:42 -0700
Subject: [PATCH 23/27] builders - mypy for phonon

---
 .../emmet/builders/abinit/phonon.py           | 46 +++++++++----------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/emmet-builders/emmet/builders/abinit/phonon.py b/emmet-builders/emmet/builders/abinit/phonon.py
index 9be05d7b91..8974b5bd29 100644
--- a/emmet-builders/emmet/builders/abinit/phonon.py
+++ b/emmet-builders/emmet/builders/abinit/phonon.py
@@ -1,41 +1,39 @@
-import tempfile
 import os
+import tempfile
 from math import ceil
-from emmet.builders.settings import EmmetBuildSettings
+from typing import Dict, Iterator, List, Optional, Tuple
+
 import numpy as np
-from typing import Optional, Dict, List, Iterator, Tuple
+from abipy.abio.inputs import AnaddbInput
+from abipy.core.abinit_units import eV_to_THz
+from abipy.dfpt.anaddbnc import AnaddbNcFile
+from abipy.dfpt.ddb import AnaddbError, DdbFile, DielectricTensorGenerator
+from abipy.dfpt.phonons import PhononBands
+from abipy.flowtk.tasks import AnaddbTask, TaskManager
+from maggma.builders import Builder
+from maggma.core import Store
 from maggma.utils import grouper
-
+from pymatgen.core.structure import Structure
+from pymatgen.io.abinit.abiobjects import KSampling
 from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
 from pymatgen.phonon.dos import CompletePhononDos
 from pymatgen.phonon.ir_spectra import IRDielectricTensor
-from pymatgen.core.structure import Structure
-from pymatgen.io.abinit.abiobjects import KSampling
-from pymatgen.symmetry.bandstructure import HighSymmKpath
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from abipy.dfpt.anaddbnc import AnaddbNcFile
-from abipy.abio.inputs import AnaddbInput
-from abipy.flowtk.tasks import AnaddbTask, TaskManager
-from abipy.dfpt.ddb import AnaddbError, DielectricTensorGenerator, DdbFile
-from abipy.dfpt.phonons import PhononBands
-from abipy.core.abinit_units import eV_to_THz
-from maggma.builders import Builder
-from maggma.core import Store
+from pymatgen.symmetry.bandstructure import HighSymmKpath
 
+from emmet.builders.settings import EmmetBuildSettings
 from emmet.core.phonon import (
-    PhononWarnings,
-    ThermodynamicProperties,
     AbinitPhonon,
-    VibrationalEnergy,
-)
-from emmet.core.phonon import (
-    PhononDos,
+    Ddb,
     PhononBandStructure,
+    PhononDos,
+    PhononWarnings,
     PhononWebsiteBS,
-    Ddb,
     ThermalDisplacement,
+    ThermodynamicProperties,
+    VibrationalEnergy,
 )
-from emmet.core.polar import DielectricDoc, BornEffectiveCharges, IRDielectric
+from emmet.core.polar import BornEffectiveCharges, DielectricDoc, IRDielectric
 from emmet.core.utils import jsanitize
 
 SETTINGS = EmmetBuildSettings()
@@ -679,7 +677,7 @@ def get_pmg_bs(
         )
 
         ph_bs_sl = PhononBandStructureSymmLine(
-            qpoints=qpts,
+            qpoints=qpts,  # type: ignore[arg-type]
             frequencies=ph_freqs,
             lattice=structure.reciprocal_lattice,
             has_nac=phbands.non_anal_ph is not None,

From c87b93111ad3e5dd683766e007c07f11c7059198 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:28:00 -0700
Subject: [PATCH 24/27] builders - mypy for alloys

---
 .../emmet/builders/materials/alloys.py         | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/emmet-builders/emmet/builders/materials/alloys.py b/emmet-builders/emmet/builders/materials/alloys.py
index 35831db5b1..04276c9b92 100644
--- a/emmet-builders/emmet/builders/materials/alloys.py
+++ b/emmet-builders/emmet/builders/materials/alloys.py
@@ -1,19 +1,19 @@
-from itertools import combinations, chain
-from typing import Tuple, List, Dict, Union
+from itertools import chain, combinations
+from typing import Dict, List, Tuple, Union
 
-from tqdm import tqdm
 from maggma.builders import Builder
-from pymatgen.core.structure import Structure
 from matminer.datasets import load_dataset
-from emmet.core.thermo import ThermoType
-
 from pymatgen.analysis.alloys.core import (
-    AlloyPair,
-    InvalidAlloy,
     KNOWN_ANON_FORMULAS,
     AlloyMember,
+    AlloyPair,
     AlloySystem,
+    InvalidAlloy,
 )
+from pymatgen.core.structure import Structure
+from tqdm import tqdm
+
+from emmet.core.thermo import ThermoType
 
 # rough sort of ANON_FORMULAS by "complexity"
 ANON_FORMULAS = sorted(KNOWN_ANON_FORMULAS, key=lambda af: len(af))
@@ -291,7 +291,7 @@ def process_item(self, item: Tuple[List[AlloyPair], Dict[str, Structure]]):
                             is_ordered=structure.is_ordered,
                             x=pair.get_x(structure.composition),
                         )
-                        pair_members["members"].append(member.as_dict())
+                        pair_members["members"].append(member.as_dict())  # type: ignore[attr-defined]
                 except Exception as exc:
                     print(f"Exception for {db_id}: {exc}")
             if pair_members["members"]:

From 117989f277e949692de4e659daf9bdc6f364a44b Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:29:01 -0700
Subject: [PATCH 25/27] builders - mypy for electrodes

---
 .../emmet/builders/materials/electrodes.py    | 34 ++++++++++---------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/emmet-builders/emmet/builders/materials/electrodes.py b/emmet-builders/emmet/builders/materials/electrodes.py
index b00114ec63..a93e840426 100644
--- a/emmet-builders/emmet/builders/materials/electrodes.py
+++ b/emmet-builders/emmet/builders/materials/electrodes.py
@@ -1,22 +1,22 @@
 import operator
+from collections import defaultdict
 from datetime import datetime
 from functools import lru_cache
 from itertools import chain
 from math import ceil
-from typing import Any, Iterator, Dict, List, Optional
-from collections import defaultdict
+from typing import Any, Dict, Iterator, List, Optional
 
 from maggma.builders import Builder
 from maggma.stores import MongoStore
 from maggma.utils import grouper
-from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+from pymatgen.analysis.phase_diagram import Composition, PhaseDiagram
 from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
-from pymatgen.analysis.phase_diagram import PhaseDiagram, Composition
+from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
-from emmet.core.electrode import InsertionElectrodeDoc, ConversionElectrodeDoc
+from emmet.builders.settings import EmmetBuildSettings
+from emmet.core.electrode import ConversionElectrodeDoc, InsertionElectrodeDoc
 from emmet.core.structure_group import StructureGroupDoc, _get_id_lexi
 from emmet.core.utils import jsanitize
-from emmet.builders.settings import EmmetBuildSettings
 
 
 def s_hash(el):
@@ -115,9 +115,9 @@ def __init__(
         self.check_newer = check_newer
         self.chunk_size = chunk_size
 
-        self.query[
-            "deprecated"
-        ] = False  # Ensure only non-deprecated materials are chosen
+        self.query["deprecated"] = (
+            False  # Ensure only non-deprecated materials are chosen
+        )
 
         super().__init__(
             sources=[materials], targets=[sgroups], chunk_size=chunk_size, **kwargs
@@ -465,9 +465,9 @@ def update_targets(self, items: List):
         if len(items) > 0:
             self.logger.info("Updating {} battery documents".format(len(items)))
             for struct_group_dict in items:
-                struct_group_dict[
-                    self.grouped_materials.last_updated_field
-                ] = datetime.utcnow()
+                struct_group_dict[self.grouped_materials.last_updated_field] = (
+                    datetime.utcnow()
+                )
             self.insertion_electrode.update(docs=items, key=["battery_id"])
         else:
             self.logger.info("No items to update")
@@ -564,9 +564,11 @@ def process_item(self, item) -> Dict:
                 # Get lowest material_id with matching composition
                 material_ids = [
                     (
-                        lambda x: x.data["material_id"]
-                        if x.composition.reduced_formula == v[1].reduced_formula
-                        else None
+                        lambda x: (
+                            x.data["material_id"]  # type: ignore[attr-defined]
+                            if x.composition.reduced_formula == v[1].reduced_formula
+                            else None
+                        )
                     )(e)
                     for e in pd.entries
                 ]
@@ -597,7 +599,7 @@ def process_item(self, item) -> Dict:
             relevant_entry_data = []
             for e in pd.entries:
                 if e.composition == Composition(c):
-                    relevant_entry_data.append((e.energy_per_atom, e.entry_id))
+                    relevant_entry_data.append((e.energy_per_atom, e.entry_id))  # type: ignore[attr-defined]
             relevant_entry_data.sort(key=lambda x: x[0])
             entry_id_mapping[c] = relevant_entry_data[0][1]
 

From b77e622de85a4bde8101869824e24e9389a7b4e6 Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:57:03 -0700
Subject: [PATCH 26/27] API - mypy fix for FindStructureQuery operator

also remove skip for FindStructureQuery test
---
 .../materials/materials/query_operators.py      | 17 +++++++++--------
 .../materials/materials/test_query_operators.py |  9 ++++-----
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/emmet-api/emmet/api/routes/materials/materials/query_operators.py b/emmet-api/emmet/api/routes/materials/materials/query_operators.py
index 7dff0439a0..122b6570a2 100644
--- a/emmet-api/emmet/api/routes/materials/materials/query_operators.py
+++ b/emmet-api/emmet/api/routes/materials/materials/query_operators.py
@@ -1,18 +1,19 @@
 from itertools import permutations
-from typing import Literal, Optional
+from typing import Dict, Literal, Optional
 
-from emmet.core.symmetry import CrystalSystem
 from fastapi import Body, HTTPException, Query
 from maggma.api.query_operator import QueryOperator
 from maggma.api.utils import STORE_PARAMS
-from emmet.api.routes.materials.materials.utils import (
-    formula_to_criteria,
-    chemsys_to_criteria,
-)
 from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
 from pymatgen.core.composition import Composition, CompositionError
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.structure import Structure
+
+from emmet.api.routes.materials.materials.utils import (
+    chemsys_to_criteria,
+    formula_to_criteria,
+)
+from emmet.core.symmetry import CrystalSystem
 from emmet.core.vasp.calc_types import RunType
 
 
@@ -281,9 +282,9 @@ class FindStructureQuery(QueryOperator):
 
     def query(
         self,
-        structure: Structure = Body(
+        structure: Dict = Body(
             ...,
-            description="Pymatgen structure object to query with",
+            description="Dictionary representaion of Pymatgen structure object to query with",
         ),
         ltol: float = Query(
             0.2,
diff --git a/emmet-api/tests/materials/materials/test_query_operators.py b/emmet-api/tests/materials/materials/test_query_operators.py
index e4266ee3ea..8033bdebb5 100644
--- a/emmet-api/tests/materials/materials/test_query_operators.py
+++ b/emmet-api/tests/materials/materials/test_query_operators.py
@@ -1,6 +1,9 @@
 import os
 
-import pytest
+from monty.serialization import dumpfn, loadfn
+from monty.tempfile import ScratchDir
+from pymatgen.core.structure import Structure
+
 from emmet.api.core.settings import MAPISettings
 from emmet.api.routes.materials.materials.query_operators import (
     ChemsysQuery,
@@ -14,9 +17,6 @@
     SymmetryQuery,
 )
 from emmet.core.symmetry import CrystalSystem
-from monty.serialization import dumpfn, loadfn
-from monty.tempfile import ScratchDir
-from pymatgen.core.structure import Structure
 
 
 def test_formula_query():
@@ -158,7 +158,6 @@ def test_multi_material_id_query():
         }
 
 
-@pytest.mark.skip(reason="Pmg cif reader issue")
 def test_find_structure_query():
     op = FindStructureQuery()
 

From 6f985f66b40d91f444fbb2ba46b44eb51ddb4efc Mon Sep 17 00:00:00 2001
From: Tyler Mathis <35553152+tsmathis@users.noreply.github.com>
Date: Mon, 22 Jul 2024 11:59:49 -0700
Subject: [PATCH 27/27] pre-commit linting

---
 .../emmet/builders/materials/electrodes.py           | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/emmet-builders/emmet/builders/materials/electrodes.py b/emmet-builders/emmet/builders/materials/electrodes.py
index a93e840426..a7b2c23f2c 100644
--- a/emmet-builders/emmet/builders/materials/electrodes.py
+++ b/emmet-builders/emmet/builders/materials/electrodes.py
@@ -115,9 +115,9 @@ def __init__(
         self.check_newer = check_newer
         self.chunk_size = chunk_size
 
-        self.query["deprecated"] = (
-            False  # Ensure only non-deprecated materials are chosen
-        )
+        self.query[
+            "deprecated"
+        ] = False  # Ensure only non-deprecated materials are chosen
 
         super().__init__(
             sources=[materials], targets=[sgroups], chunk_size=chunk_size, **kwargs
@@ -465,9 +465,9 @@ def update_targets(self, items: List):
         if len(items) > 0:
             self.logger.info("Updating {} battery documents".format(len(items)))
             for struct_group_dict in items:
-                struct_group_dict[self.grouped_materials.last_updated_field] = (
-                    datetime.utcnow()
-                )
+                struct_group_dict[
+                    self.grouped_materials.last_updated_field
+                ] = datetime.utcnow()
             self.insertion_electrode.update(docs=items, key=["battery_id"])
         else:
             self.logger.info("No items to update")