precommit

Author: esoteric-ephemera

mp_api/client/core/utils.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import re
 from typing import TYPE_CHECKING, Literal
 
 import orjson
@@ -12,7 +11,7 @@
 from mp_api.client.core.settings import MAPIClientSettings
 
 if TYPE_CHECKING:
-    from monty.json import MSONable
+    pass
 
 
 def _compare_emmet_ver(
@@ -40,6 +39,7 @@ def _compare_emmet_ver(
         f"__{op_to_op.get(op,op)}__",
     )(parse_version(ref_version))
 
+
 def load_json(json_like: str | bytes, deser: bool = False, encoding: str = "utf-8"):
     """Utility to load json in consistent manner."""
     data = orjson.loads(

mp_api/client/routes/materials/phonon.py

@@ -11,6 +11,7 @@
 
 if TYPE_CHECKING:
     from typing import Any
+
     from emmet.core.math import Matrix3D
 
 
@@ -68,7 +69,9 @@ def search(
             **query_params,
         )
 
-    def get_bandstructure_from_material_id(self, material_id: str, phonon_method: str) -> PhononBS | dict[str,Any]:
+    def get_bandstructure_from_material_id(
+        self, material_id: str, phonon_method: str
+    ) -> PhononBS | dict[str, Any]:
         """Get the phonon band structure pymatgen object associated with a given material ID and phonon method.
 
         Arguments:
@@ -94,7 +97,9 @@ def get_bandstructure_from_material_id(self, material_id: str, phonon_method: st
 
         return result[0]
 
-    def get_dos_from_material_id(self, material_id: str, phonon_method: str) -> PhononDOS | dict[str,Any]:
+    def get_dos_from_material_id(
+        self, material_id: str, phonon_method: str
+    ) -> PhononDOS | dict[str, Any]:
         """Get the phonon dos pymatgen object associated with a given material ID and phonon method.
 
         Arguments:
@@ -120,7 +125,9 @@ def get_dos_from_material_id(self, material_id: str, phonon_method: str) -> Phon
 
         return result[0]
 
-    def get_forceconstants_from_material_id(self, material_id: str) -> list[list[Matrix3D]]:
+    def get_forceconstants_from_material_id(
+        self, material_id: str
+    ) -> list[list[Matrix3D]]:
         """Get the force constants associated with a given material ID.
 
         Arguments:

mp_api/client/routes/materials/xas.py

@@ -9,7 +9,7 @@
 from mp_api.client.core.utils import validate_ids
 
 if TYPE_CHECKING:
-   from emmet.core.types.enums import XasEdge, XasType
+    from emmet.core.types.enums import XasEdge, XasType
 
 
 class XASRester(BaseRester):

tests/core/test_oxygen_evolution.py

@@ -9,7 +9,11 @@
 from pymatgen.core import Composition
 from pymatgen.entries.computed_entries import ComputedEntry
 
-from mp_api.client.core._oxygen_evolution import DEFAULT_CACHE_FILE, NIST_JANAF_O2_MU_T, OxygenEvolution
+from mp_api.client.core._oxygen_evolution import (
+    DEFAULT_CACHE_FILE,
+    NIST_JANAF_O2_MU_T,
+    OxygenEvolution,
+)
 
 
 def test_interp():
@@ -38,19 +42,16 @@ def test_interp():
         with pytest.warns(UserWarning, match="outside the fitting range"):
             oxyevo.mu_to_temp_spline(badval)
 
+
 def test_get():
     """Test data retrieval from NIST."""
 
     data = {}
     data["temperature"], data["mu-mu_0K"] = OxygenEvolution().get_chempot_temp_data()
     assert DEFAULT_CACHE_FILE.exists()
-    assert all(
-        np.allclose(data[k],v) for k, v in NIST_JANAF_O2_MU_T.items()
-    )
+    assert all(np.allclose(data[k], v) for k, v in NIST_JANAF_O2_MU_T.items())
     json_data = json.loads(DEFAULT_CACHE_FILE.read_text())
-    assert all(
-        np.allclose(json_data[k],v) for k, v in NIST_JANAF_O2_MU_T.items()
-    )
+    assert all(np.allclose(json_data[k], v) for k, v in NIST_JANAF_O2_MU_T.items())
 
 
 def test_oxy_evo():

tests/core/test_utils.py

@@ -6,49 +6,43 @@
 from emmet.core.mpid import MPID, AlphaID
 
 
-def test_emmet_core_version_checks(monkeypatch : pytest.MonkeyPatch):
-
-    ref_ver = (1,2,"3rc5")
+def test_emmet_core_version_checks(monkeypatch: pytest.MonkeyPatch):
+    ref_ver = (1, 2, "3rc5")
     ref_ver_str = ".".join(str(x) for x in ref_ver)
 
     import emmet.core
-    monkeypatch.setattr(emmet.core,"__version__",ref_ver_str)
+
+    monkeypatch.setattr(emmet.core, "__version__", ref_ver_str)
     from mp_api.client.core.utils import _compare_emmet_ver
 
-    assert _compare_emmet_ver(ref_ver_str,"==")
+    assert _compare_emmet_ver(ref_ver_str, "==")
 
-    next_ver = ".".join(str(x) for x in [ref_ver[0] + 1,*ref_ver[1:]])
-    assert _compare_emmet_ver(next_ver,"<")
-    assert _compare_emmet_ver(next_ver,"<=")
+    next_ver = ".".join(str(x) for x in [ref_ver[0] + 1, *ref_ver[1:]])
+    assert _compare_emmet_ver(next_ver, "<")
+    assert _compare_emmet_ver(next_ver, "<=")
 
-    prior_ver = ".".join(str(x) for x in [ref_ver[0],ref_ver[1]-1,*ref_ver[2:]])
-    assert _compare_emmet_ver(prior_ver,">")
-    assert _compare_emmet_ver(prior_ver,">=")
+    prior_ver = ".".join(str(x) for x in [ref_ver[0], ref_ver[1] - 1, *ref_ver[2:]])
+    assert _compare_emmet_ver(prior_ver, ">")
+    assert _compare_emmet_ver(prior_ver, ">=")
 
-def test_id_validation():
 
+def test_id_validation():
     from mp_api.client.core.utils import validate_ids
     from mp_api.client.core.settings import MAPIClientSettings
 
     max_num_idxs = MAPIClientSettings().MAX_LIST_LENGTH
 
-    with pytest.raises(ValueError,match="too long"):
-        _ = validate_ids(
-            [f"mp-{x}" for x in range(max_num_idxs + 1)]
-        )
+    with pytest.raises(ValueError, match="too long"):
+        _ = validate_ids([f"mp-{x}" for x in range(max_num_idxs + 1)])
 
     # For all legacy MPIDs, ensure these validate correctly
     assert all(
-        isinstance(x,str) and MPID(x).string == x
-        for x in validate_ids(
-            [f"mp-{y}" for y in range(max_num_idxs)]
-        )
+        isinstance(x, str) and MPID(x).string == x
+        for x in validate_ids([f"mp-{y}" for y in range(max_num_idxs)])
     )
 
     # For all new AlphaIDs, ensure these validate correctly
     assert all(
-        isinstance(x,str) and AlphaID(x).string == x
-        for x in validate_ids(
-            [y + AlphaID._cut_point for y in range(max_num_idxs)]
-        )
-    )
+        isinstance(x, str) and AlphaID(x).string == x
+        for x in validate_ids([y + AlphaID._cut_point for y in range(max_num_idxs)])
+    )

tests/materials/test_phonon.py

@@ -1,4 +1,3 @@
-
 import os
 
 import numpy as np
@@ -11,6 +10,7 @@
 
 from core_function import client_search_testing
 
+
 @pytest.mark.skipif(os.getenv("MP_API_KEY") is None, reason="No API key found.")
 def test_phonon_search():
     client_search_testing(
@@ -24,23 +24,23 @@ def test_phonon_search():
         alt_name_dict={
             "material_ids": "material_id",
         },
-        custom_field_tests = {
-            "material_ids": ["mp-149","mp-13"],
+        custom_field_tests={
+            "material_ids": ["mp-149", "mp-13"],
             "material_ids": "mp-149",
             "phonon_method": "dfpt",
         },
         sub_doc_fields=[],
     )
 
+
 @pytest.mark.skipif(os.getenv("MP_API_KEY") is None, reason="No API key found.")
-@pytest.mark.parametrize("use_document_model",[True,False])
+@pytest.mark.parametrize("use_document_model", [True, False])
 def test_phonon_get_methods(use_document_model):
-    
     rester = PhononRester(use_document_model=use_document_model)
 
     # TODO: update when there is force constant data
     for func_name, schema in {
-        "bandstructure" : PhononBS,
+        "bandstructure": PhononBS,
         "dos": PhononDOS,
         # "forceconstants": list
     }.items():
@@ -49,31 +49,29 @@ def test_phonon_get_methods(use_document_model):
             f"get_{func_name}_from_material_id",
         )
         assert isinstance(
-            search_method("mp-149","dfpt"),
-            schema if use_document_model else dict
+            search_method("mp-149", "dfpt"), schema if use_document_model else dict
         )
 
-        with pytest.raises(MPRestError,match="No object found"):
-            _ = search_method("mp-0","dfpt")
+        with pytest.raises(MPRestError, match="No object found"):
+            _ = search_method("mp-0", "dfpt")
+
 
 @pytest.mark.skipif(os.getenv("MP_API_KEY") is None, reason="No API key found.")
-@pytest.mark.parametrize("use_document_model",[True,False])
+@pytest.mark.parametrize("use_document_model", [True, False])
 def test_phonon_thermo(use_document_model):
-
-    with pytest.raises(MPRestError,match="No phonon document found"):
+    with pytest.raises(MPRestError, match="No phonon document found"):
         _ = PhononRester(
             use_document_model=use_document_model
-        ).compute_thermo_quantities("mp-0","dfpt")
+        ).compute_thermo_quantities("mp-0", "dfpt")
 
     thermo_props = PhononRester(
         use_document_model=use_document_model
-    ).compute_thermo_quantities("mp-149","dfpt")
-    
+    ).compute_thermo_quantities("mp-149", "dfpt")
+
     # Default set in the method
     num_vals = 100
-    
+
     assert all(
-        isinstance(v, np.ndarray if k == "temperature" else list)
-        and len(v) == num_vals
+        isinstance(v, np.ndarray if k == "temperature" else list) and len(v) == num_vals
         for k, v in thermo_props.items()
-    )
+    )

tests/materials/test_similarity.py

@@ -1,4 +1,3 @@
-
 import os
 
 import numpy as np
@@ -12,6 +11,7 @@
 
 from core_function import client_search_testing
 
+
 @pytest.fixture(scope="module")
 def test_struct():
     poscar = """Al2
@@ -25,7 +25,8 @@ def test_struct():
    0.875    0.875    0.875 Al
    0.125    0.125    0.125 Al
 """
-    return Structure.from_str(poscar,fmt="poscar")
+    return Structure.from_str(poscar, fmt="poscar")
+
 
 @pytest.mark.skipif(os.getenv("MP_API_KEY") is None, reason="No API key found.")
 def test_similarity_search():
@@ -40,45 +41,48 @@ def test_similarity_search():
         alt_name_dict={
             "material_ids": "material_id",
         },
-        custom_field_tests = {
-            "material_ids": ["mp-149","mp-13"],
-            "material_ids": "mp-149"
+        custom_field_tests={
+            "material_ids": ["mp-149", "mp-13"],
+            "material_ids": "mp-149",
         },
         sub_doc_fields=[],
     )
 
+
 @pytest.mark.skipif(os.getenv("MP_API_KEY") is None, reason="No API key found.")
 def test_similarity_vector_search(test_struct):
-
     rester = SimilarityRester()
     fv = rester.fingerprint_structure(test_struct)
-    assert isinstance(fv,np.ndarray)
+    assert isinstance(fv, np.ndarray)
     assert len(fv) == 122
-    assert isinstance(rester._fingerprinter,SimilarityScorer)
-
+    assert isinstance(rester._fingerprinter, SimilarityScorer)
 
     get_top = 5
-    sim_entries = rester.find_similar("mp-149",top=get_top)
-    assert all(
-        isinstance(entry,SimilarityEntry) for entry in sim_entries
-    )
+    sim_entries = rester.find_similar("mp-149", top=get_top)
+    assert all(isinstance(entry, SimilarityEntry) for entry in sim_entries)
     assert len(sim_entries) == get_top
 
-    sim_dict_entries = SimilarityRester(use_document_model=False).find_similar("mp-149",top=get_top)
+    sim_dict_entries = SimilarityRester(use_document_model=False).find_similar(
+        "mp-149", top=get_top
+    )
     assert all(
-        isinstance(entry,dict) and all(
-            k in entry for k in SimilarityEntry.model_fields
-        )
+        isinstance(entry, dict)
+        and all(k in entry for k in SimilarityEntry.model_fields)
         for entry in sim_dict_entries
     )
 
-    with pytest.raises(MPRestError,match="No similarity data available for"):
+    with pytest.raises(MPRestError, match="No similarity data available for"):
         _ = rester.find_similar("mp-0")
 
     assert all(
-        isinstance(entry,SimilarityEntry) and isinstance(entry.dissimilarity,float)
-        for entry in rester.find_similar(test_struct, top = 2,)
+        isinstance(entry, SimilarityEntry) and isinstance(entry.dissimilarity, float)
+        for entry in rester.find_similar(
+            test_struct,
+            top=2,
+        )
     )
 
-    with pytest.raises(MPRestError,match="Please submit a pymatgen Structure or MP ID"):
-        _ = rester.find_similar(fv)
+    with pytest.raises(
+        MPRestError, match="Please submit a pymatgen Structure or MP ID"
+    ):
+        _ = rester.find_similar(fv)