Remove protostructure code that was upstreamed to pymatgen. (#100)

* fea: remove protostructure code that was upstreamed to pmg.

* clean: mat_bench -> matbench

* tests: fix python version for ci

Author: CompRhys

.github/workflows/test.yml

@@ -10,20 +10,26 @@ on:
 
 jobs:
   tests:
-    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14]
+        version:
+          - { python: "3.10", resolution: highest }
+          - { python: "3.12", resolution: lowest-direct }
+    runs-on: ${{ matrix.os }}
+
     steps:
       - name: Check out repo
         uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          python-version: ${{ matrix.version.python }}
 
-      - name: Install uv
-        run: pip install uv
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v2
 
       - name: Install dependencies
         run: |

aviary/wren/data.py

@@ -7,16 +7,16 @@
 
 import numpy as np
 import torch
+from pymatgen.analysis.prototypes import (
+    RE_SUBST_ONE_PREFIX,
+    RE_WYCKOFF_NO_PREFIX,
+    WYCKOFF_MULTIPLICITY_DICT,
+    WYCKOFF_POSITION_RELAB_DICT,
+)
 from torch import LongTensor, Tensor
 from torch.utils.data import Dataset
 
 from aviary import PKG_DIR
-from aviary.wren.utils import (
-    RE_SUBST_ONE_PREFIX,
-    RE_WYCKOFF_NO_PREFIX,
-    relab_dict,
-    wyckoff_multiplicity_dict,
-)
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
@@ -300,13 +300,13 @@ def parse_protostructure_label(
             elements.extend([el] * mult)
             wyckoff_set.extend([letter] * mult)
             wyckoff_site_multiplicities.extend(
-                [float(wyckoff_multiplicity_dict[spg_num][letter])] * mult
+                [float(WYCKOFF_MULTIPLICITY_DICT[spg_num][letter])] * mult
             )
 
     # Create augmented Wyckoff set
     augmented_wyckoff_set = {
         tuple(",".join(wyckoff_set).translate(str.maketrans(trans)).split(","))
-        for trans in relab_dict[spg_num]
+        for trans in WYCKOFF_POSITION_RELAB_DICT[spg_num]
     }
 
     return spg_num, wyckoff_site_multiplicities, elements, list(augmented_wyckoff_set)