Merge branch 'master' of https://github.com/materialsproject/pymatgen

.github/workflows/lint.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: '3.x'
 
       - name: Install dependencies
         run: |

.github/workflows/test.yml

@@ -35,11 +35,11 @@ jobs:
             resolution: highest
             extras: ci,optional
           - os: ubuntu-latest
-            python: "3.12"
+            python: '>3.9'
             resolution: lowest-direct
             extras: ci,optional
           - os: macos-latest
-            python: "3.10"
+            python: '3.10'
             resolution: lowest-direct
             extras: ci # test with only required dependencies installed
 

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.10.1
     hooks:
       - id: mypy
 
@@ -33,6 +33,7 @@ repos:
         stages: [ commit, commit-msg ]
         exclude_types: [ html ]
         additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11
+        exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
     rev: v0.16.2
@@ -42,7 +43,7 @@ repos:
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.16.0
+    rev: 1.18.0
     hooks:
       - id: blacken-docs
 
@@ -64,6 +65,6 @@ repos:
         args: [ --drop-empty-cells, --keep-output ]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.366
+    rev: v1.1.369
     hooks:
       - id: pyright

dev_scripts/update_spacegroup_data.py

@@ -0,0 +1,95 @@
+"""Script to update symm_ops.json and symm_data.yaml in symmetry module due to issues #3845 and #3862.
+symm_ops.json:
+- adds Hermann_mauguin point group key and short Hermann Mauguin space group symbol
+- converts screw axis notation to symm_data standard
+symm_data.json
+- removes mapping of rhombohedral space group types onto symbol + appended H
+- replaces I/P2_12_121 key with I/P2_12_12_1
+"""
+
+from __future__ import annotations
+
+import sys
+
+from monty.serialization import dumpfn, loadfn
+from pymatgen.symmetry.groups import PointGroup
+
+__author__ = "Katharina Ueltzen @kaueltzen"
+__date__ = "2024-06-06"
+
+SYMM_OPS = loadfn("../src/pymatgen/symmetry/symm_ops.json")
+SYMM_DATA = loadfn("../src/pymatgen/symmetry/symm_data.json")
+
+
+def convert_symmops_to_sg_encoding(symbol: str) -> str:
+    """
+    Utility function to convert SYMMOPS space group type symbol notation
+    into SYMM_DATA["space_group_encoding"] key notation with underscores before
+    translational part of screw axes.
+    Args:
+        symbol (str): "hermann_mauguin" or "universal_h_m" key of symmops.json
+    Returns:
+        symbol in the format of SYMM_DATA["space_group_encoding"] keys
+    """
+    symbol_representation = symbol.split(":")
+    representation = ":" + "".join(symbol_representation[1].split(" ")) if len(symbol_representation) > 1 else ""
+
+    blickrichtungen = symbol_representation[0].split(" ")
+    blickrichtungen_new = []
+    for br in blickrichtungen:
+        if len(br) > 1 and br[0].isdigit() and br[1].isdigit():
+            blickrichtungen_new.append(br[0] + "_" + br[1:])
+        else:
+            blickrichtungen_new.append(br)
+    return "".join(blickrichtungen_new) + representation
+
+
+def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
+    """
+    Utility function to remove identity along blickrichtung (except in P1).
+    Args:
+        symbol (str): "hermann_mauguin" key of symmops.json
+    Returns:
+        short "hermann_mauguin" key
+    """
+    if symbol in ("P 1", "C 1", "P 1 "):
+        return symbol
+    blickrichtungen = symbol.split(" ")
+    blickrichtungen_new = []
+    for br in blickrichtungen:
+        if br != "1":
+            blickrichtungen_new.append(br + " ")
+    return "".join(blickrichtungen_new)
+
+
+new_symm_data = {}
+for k, v in SYMM_DATA["space_group_encoding"].items():
+    if k.endswith("H"):
+        new_symm_data[k.removesuffix("H")] = v
+    elif k == "I2_12_121":
+        new_symm_data["I2_12_12_1"] = v
+    elif k == "P2_12_121":
+        new_symm_data["P2_12_12_1"] = v
+    else:
+        new_symm_data[k] = v
+
+SYMM_DATA["space_group_encoding"] = new_symm_data
+
+for spg_idx, spg in enumerate(SYMM_OPS):
+    if "(" in spg["hermann_mauguin"]:
+        SYMM_OPS[spg_idx]["hermann_mauguin"] = spg["hermann_mauguin"].split("(")[0]
+
+    short_h_m = remove_identity_from_full_hermann_mauguin(SYMM_OPS[spg_idx]["hermann_mauguin"])
+    SYMM_OPS[spg_idx]["short_h_m"] = convert_symmops_to_sg_encoding(short_h_m)
+    SYMM_OPS[spg_idx]["hermann_mauguin_u"] = convert_symmops_to_sg_encoding(spg["hermann_mauguin"])
+
+for spg_idx, spg in enumerate(SYMM_OPS):
+    try:
+        pg = PointGroup.from_space_group(spg["short_h_m"])
+    except AssertionError as e:
+        print(spg, str(e))
+        sys.exit(1)
+    SYMM_OPS[spg_idx]["point_group"] = pg.symbol
+
+dumpfn(SYMM_DATA, "../src/pymatgen/symmetry/symm_data.json")
+dumpfn(SYMM_OPS, "../src/pymatgen/symmetry/symm_ops.json")