Merge pull request #487 from esoteric-ephemera/main

Updating spglib attr access / improvements for MP building

robocrys/condense/component.py

@@ -183,7 +183,7 @@ def get_sym_inequiv_components(
     components = deepcopy(components)
 
     sym_inequiv_components = {}
-    equivalent_atoms = spg_analyzer.get_symmetry_dataset()["equivalent_atoms"]
+    equivalent_atoms = spg_analyzer.get_symmetry_dataset().equivalent_atoms
 
     for component in components:
         sym_indices = frozenset(equivalent_atoms[x] for x in component["site_ids"])

robocrys/condense/mineral.py

@@ -1,21 +1,28 @@
 """This module provides tools for matching structures to known mineral class."""
+
 from __future__ import annotations
 
+from importlib.resources import files as import_resource_file
 from itertools import islice
-from typing import Any
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from matminer.utils.io import load_dataframe_from_json
-from importlib.resources import files as import_resource_file
 from pymatgen.analysis.prototypes import AflowPrototypeMatcher
 from pymatgen.core.structure import IStructure
-
 from robocrys.condense.fingerprint import (
     get_fingerprint_distance,
     get_structure_fingerprint,
 )
 
 
+if TYPE_CHECKING:
+    import pandas as pd
+
+_mineral_db_file = import_resource_file("robocrys.condense") / "mineral_db.json.gz"
+
+
 class MineralMatcher:
     """Class to match a structure to a mineral name.
 
@@ -40,6 +47,8 @@ class MineralMatcher:
         fingerprint_distance_cutoff: Cutoff to determine how similar a match
             must be to be returned. The distance is measured between the
             structural fingerprints in euclidean space.
+        mineral_db : Optional path or pandas .DataFrame object containing the
+            mineral fingerprint database.
     """
 
     def __init__(
@@ -49,9 +58,12 @@ def __init__(
         initial_angle_tol: float = 5.0,
         use_fingerprint_matching: bool = True,
         fingerprint_distance_cutoff: float = 0.4,
+        mineral_db: str | Path | pd.DataFrame | None = None,
     ):
-        db_file = import_resource_file("robocrys.condense") / "mineral_db.json.gz"
-        self.mineral_db = load_dataframe_from_json(db_file)
+        self.mineral_db = mineral_db if mineral_db is not None else _mineral_db_file
+        if isinstance(self.mineral_db, (str, Path)):
+            self.mineral_db = load_dataframe_from_json(self.mineral_db)
+
         self.initial_ltol = initial_ltol
         self.initial_stol = initial_stol
         self.initial_angle_tol = initial_angle_tol
@@ -214,8 +226,7 @@ def get_fingerprint_matches(
             ]
 
         if match_n_sp:
-            n_elems = structure.n_elems
-            mineral_db = mineral_db[mineral_db["n_elems"] == n_elems]
+            mineral_db = mineral_db[mineral_db["n_elems"] == structure.n_elems]
 
         num_rows = mineral_db.shape[0]
         max_n_matches = max_n_matches or num_rows

robocrys/condense/site.py

@@ -70,7 +70,8 @@ def __init__(
         self.site_fingerprints = get_site_fingerprints(bonded_structure.structure)
 
         sga = SpacegroupAnalyzer(bonded_structure.structure, symprec=symprec)
-        equivalent_sites = sga.get_symmetry_dataset()["equivalent_atoms"]
+        equivalent_sites = sga.get_symmetry_dataset().equivalent_atoms
+
         if use_symmetry_equivalent_sites:
             self.equivalent_sites = list(equivalent_sites)
         else:

robocrys/describe/describer.py

@@ -232,7 +232,6 @@ def get_component_makeup_summary(self) -> str:
                     formula = latexify(formula)
                 elif self.fmt == "unicode":
                     formula = unicodeify(formula)
-                    print(formula)
                 elif self.fmt == "html":
                     formula = htmlify(formula)
 

setup.py

@@ -44,10 +44,10 @@
     test_suite="nose.collector",
     packages=find_packages(),
     install_requires=[
-        "spglib",
+        "spglib>=2.5.0",
         "numpy",
         "scipy",
-        "pymatgen",
+        "pymatgen>=2024.1.26",
         "inflect",
         "networkx",
         "matminer>=0.9.2",