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Remove protostructure code that was upstreamed to pymatgen. #100

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Merged
CompRhys merged 4 commits into from
Apr 12, 2025
Merged

Remove protostructure code that was upstreamed to pymatgen. #100

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c566e07
fea: remove protostructure code that was upstreamed to pmg.
CompRhys Mar 26, 2025
8ce99d6
clean: mat_bench -> matbench
CompRhys Mar 26, 2025
32eb98e
Merge remote-tracking branch 'origin/main' into remove-wren-utils-for…
CompRhys Apr 11, 2025
4b858ac
tests: fix python version for ci
CompRhys Apr 11, 2025
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18 changes: 12 additions & 6 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: |
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16 changes: 8 additions & 8 deletions aviary/wren/data.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
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