Merge branch 'master' into aims_control_in_None_value_fix

.github/workflows/jekyll-gh-pages.yml

@@ -1,15 +1,11 @@
-# Sample workflow for building and deploying a Jekyll site to GitHub Pages
 name: Deploy Jekyll with GitHub Pages dependencies preinstalled
 
 on:
-  # Runs on pushes targeting the default branch
   push:
     branches: ["master"]
+  workflow_dispatch: # enable manual workflow execution
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+# Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: read
   pages: write
@@ -22,25 +18,26 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  # Build job
   build:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/pymatgen'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+
       - name: Setup Pages
         uses: actions/configure-pages@v3
+
       - name: Build with Jekyll
         uses: actions/jekyll-build-pages@v1
         with:
           source: ./docs
           destination: ./_site
+
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2
 
-  # Deployment job
   deploy:
     environment:
       name: github-pages

.github/workflows/lint.yml

@@ -27,7 +27,7 @@ jobs:
       - name: ruff
         run: |
           ruff --version
-          ruff .
+          ruff check .
           ruff format --check .
 
       - name: mypy

.github/workflows/test.yml

@@ -109,7 +109,7 @@ jobs:
           uv pip install -e '.[dev,optional]' --system
 
           # TODO remove next line installing ase from main branch when FrechetCellFilter is released
-          uv pip install --upgrade 'ase@git+https://gitlab.com/ase/ase' --system
+          uv pip install --upgrade 'git+https://gitlab.com/ase/ase' --system
 
       - name: pytest split ${{ matrix.split }}
         run: |

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.3.4
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -279,7 +279,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 f"Get the explicit optimized permutations for geometry {cg.name!r} (symbol : "
                 f'{cg_symbol!r}) ? ("y" to confirm, "q" to quit)\n'
             )
-            if test not in ["y", "q"]:
+            if test not in ("y", "q"):
                 print("Wrong key, try again")
                 continue
             if test == "y":

dev_scripts/potcar_scrambler.py

@@ -4,6 +4,7 @@
 import shutil
 import warnings
 from glob import glob
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.os.path import zpath
@@ -14,6 +15,9 @@
 from pymatgen.io.vasp.sets import _load_yaml_config
 from pymatgen.util.testing import VASP_IN_DIR
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 
 class PotcarScrambler:
     """
@@ -34,26 +38,22 @@ class PotcarScrambler:
     from existing POTCAR `input_filename`
     """
 
-    def __init__(self, potcars: Potcar | PotcarSingle):
-        if isinstance(potcars, PotcarSingle):
-            self.PSP_list = [potcars]
-        else:
-            self.PSP_list = potcars
+    def __init__(self, potcars: Potcar | PotcarSingle) -> None:
+        self.PSP_list = [potcars] if isinstance(potcars, PotcarSingle) else potcars
         self.scrambled_potcars_str = ""
         for psp in self.PSP_list:
             scrambled_potcar_str = self.scramble_single_potcar(psp)
             self.scrambled_potcars_str += scrambled_potcar_str
-        return
 
-    def _rand_float_from_str_with_prec(self, input_str: str, bloat: float = 1.5):
+    def _rand_float_from_str_with_prec(self, input_str: str, bloat: float = 1.5) -> float:
         n_prec = len(input_str.split(".")[1])
         bd = max(1, bloat * abs(float(input_str)))
         return round(bd * np.random.rand(1)[0], n_prec)
 
     def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
         input_str = input_str.strip()
 
-        if input_str.lower() in ("t", "f", "true", "false"):
+        if input_str.lower() in {"t", "f", "true", "false"}:
             return bool(np.random.randint(2))
 
         if input_str.upper() == input_str.lower() and input_str[0].isnumeric():
@@ -68,7 +68,7 @@ def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
         except ValueError:
             return input_str
 
-    def scramble_single_potcar(self, potcar: PotcarSingle):
+    def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         """
         Scramble the body of a POTCAR, retain the PSCTR header information.
 
@@ -124,20 +124,20 @@ def scramble_single_potcar(self, potcar: PotcarSingle):
             )
         return scrambled_potcar_str
 
-    def to_file(self, filename: str):
+    def to_file(self, filename: str) -> None:
         with zopen(filename, mode="wt") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod
-    def from_file(cls, input_filename: str, output_filename: str | None = None):
+    def from_file(cls, input_filename: str, output_filename: str | None = None) -> Self:
         psp = Potcar.from_file(input_filename)
         psp_scrambled = cls(psp)
         if output_filename:
             psp_scrambled.to_file(output_filename)
         return psp_scrambled
 
 
-def generate_fake_potcar_libraries():
+def generate_fake_potcar_libraries() -> None:
     """
     To test the `_gen_potcar_summary_stats` function in `pymatgen.io.vasp.inputs`,
     need a library of fake POTCARs which do not violate copyright
@@ -173,7 +173,7 @@ def generate_fake_potcar_libraries():
                     break
 
 
-def potcar_cleanser():
+def potcar_cleanser() -> None:
     """
     Function to replace copyrighted POTCARs used in io.vasp.sets testing
     with dummy POTCARs that have scrambled PSP and kinetic energy values

dev_scripts/regen_libxcfunc.py

@@ -50,16 +50,16 @@ def write_libxc_docs_json(xc_funcs, json_path):
     xc_funcs = deepcopy(xc_funcs)
 
     # Remove XC_FAMILY from Family and XC_ from Kind to make strings more human-readable.
-    for d in xc_funcs.values():
-        d["Family"] = d["Family"].replace("XC_FAMILY_", "", 1)
-        d["Kind"] = d["Kind"].replace("XC_", "", 1)
+    for dct in xc_funcs.values():
+        dct["Family"] = dct["Family"].replace("XC_FAMILY_", "", 1)
+        dct["Kind"] = dct["Kind"].replace("XC_", "", 1)
 
     # Build lightweight version with a subset of keys.
-    for num, d in xc_funcs.items():
-        xc_funcs[num] = {key: d[key] for key in ("Family", "Kind", "References")}
+    for num, dct in xc_funcs.items():
+        xc_funcs[num] = {key: dct[key] for key in ("Family", "Kind", "References")}
         # Descriptions are optional
         for opt in ("Description 1", "Description 2"):
-            desc = d.get(opt)
+            desc = dct.get(opt)
             if desc is not None:
                 xc_funcs[num][opt] = desc
 

dev_scripts/update_pt_data.py

@@ -128,16 +128,16 @@ def parse_radii():
 def update_ionic_radii():
     data = loadfn(ptable_yaml_path)
 
-    for d in data.values():
-        if "Ionic_radii" in d:
-            d["Ionic radii"] = {k: v / 100 for k, v in d["Ionic_radii"].items()}
-            del d["Ionic_radii"]
-        if "Ionic_radii_hs" in d:
-            d["Ionic radii hs"] = {k: v / 100 for k, v in d["Ionic_radii_hs"].items()}
-            del d["Ionic_radii_hs"]
-        if "Ionic_radii_ls" in d:
-            d["Ionic radii ls"] = {k: v / 100 for k, v in d["Ionic_radii_ls"].items()}
-            del d["Ionic_radii_ls"]
+    for dct in data.values():
+        if "Ionic_radii" in dct:
+            dct["Ionic radii"] = {k: v / 100 for k, v in dct["Ionic_radii"].items()}
+            del dct["Ionic_radii"]
+        if "Ionic_radii_hs" in dct:
+            dct["Ionic radii hs"] = {k: v / 100 for k, v in dct["Ionic_radii_hs"].items()}
+            del dct["Ionic_radii_hs"]
+        if "Ionic_radii_ls" in dct:
+            dct["Ionic radii ls"] = {k: v / 100 for k, v in dct["Ionic_radii_ls"].items()}
+            del dct["Ionic_radii_ls"]
     with open("periodic_table2.yaml", mode="w") as file:
         yaml.dump(data, file)
     with open("../pymatgen/core/periodic_table.json", mode="w") as file:
@@ -162,8 +162,7 @@ def parse_shannon_radii():
             radii[el][charge] = {}
         if sheet[f"C{i}"].value:
             cn = sheet[f"C{i}"].value
-            if cn not in radii[el][charge]:
-                radii[el][charge][cn] = {}
+            radii[el][charge].setdefault(cn, {})
 
         spin = sheet[f"D{i}"].value if sheet[f"D{i}"].value is not None else ""