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

.editorconfig

@@ -0,0 +1,16 @@
+# https://editorconfig.org/
+root = true
+
+# Default settings for all files.
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+max_line_length = 120
+
+# Set indent size for json and YAML files.
+[*.{json,yml,yaml}]
+indent_size = 2

.github/workflows/lint.yml

@@ -31,7 +31,7 @@ jobs:
           ruff format --check .
 
       - name: mypy
-        run: mypy ${{ github.event.repository.name }}
+        run: mypy src
 
       - name: pyright
         run: pyright

.github/workflows/test.yml

@@ -77,7 +77,7 @@ jobs:
           micromamba activate pmg
           # TODO remove temporary fix. added since uv install torch is flaky.
           # track https://github.com/astral-sh/uv/issues/1921 for resolution
-          pip install torch
+          pip install torch --upgrade
 
           uv pip install numpy cython
           uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}

.gitignore

@@ -40,3 +40,4 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.pdm-python

.pre-commit-config.yaml

@@ -2,16 +2,16 @@ exclude: ^(docs|tests/files|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [mypy, pyright]
+  skip: [ mypy, pyright ]
   autofix_commit_msg: pre-commit auto-fixes
   autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.5.0
     hooks:
       - id: ruff
-        args: [--fix, --unsafe-fixes]
+        args: [ --fix, --unsafe-fixes ]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -30,15 +30,15 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
-        exclude_types: [html]
-        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
+        stages: [ commit, commit-msg ]
+        exclude_types: [ html ]
+        additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
     rev: v0.16.2
     hooks:
       - id: cython-lint
-        args: [--no-pycodestyle]
+        args: [ --no-pycodestyle ]
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
@@ -55,13 +55,13 @@ repos:
         # MD033: no inline HTML
         # MD041: first line in a file should be a top-level heading
         # MD025: single title
-        args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
+        args: [ --disable, MD013, MD024, MD025, MD033, MD041, "--" ]
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1
     hooks:
       - id: nbstripout
-        args: [--drop-empty-cells, --keep-output]
+        args: [ --drop-empty-cells, --keep-output ]
 
   - repo: https://github.com/RobertCraigie/pyright-python
     rev: v1.1.366

dev_scripts/chemenv/explicit_permutations.py

@@ -10,7 +10,6 @@
 import os
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     AllCoordinationGeometries,
     ExplicitPermutationsAlgorithm,

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -9,7 +9,6 @@
 import json
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -15,7 +15,6 @@
 
 import numpy as np
 import tabulate
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,
@@ -236,7 +235,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 sym_measures = [c["symmetry_measure"] for c in csms]
                 prt1(string="Continuous symmetry measures", printing_volume=printing_volume)
                 prt1(string=sym_measures, printing_volume=printing_volume)
-                csms_with_recorded_permutation = []  # type: ignore
+                csms_with_recorded_permutation: list = []
                 explicit_permutations = []
                 for icsm, csm in enumerate(csms):
                     found = False
@@ -308,7 +307,6 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 all_planes_point_indices += algo.other_plane_points
 
             # Setup of the permutations to be used for this algorithm
-
             indices = list(range(cg.coordination_number))
             if permutations_setup_type == "all":
                 perms_iterator = itertools.permutations(indices)
@@ -400,7 +398,8 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                     else:
                         perms_used[some_perm] = 1
                 tcurrent = time.process_time()
-                time_left = (n_permutations - idx_perm) * (tcurrent - t0) / idx_perm  # type: ignore
+                assert n_permutations is not None
+                time_left = (n_permutations - idx_perm) * (tcurrent - t0) / idx_perm
                 time_left = f"{time_left:.1f}"
                 idx_perm += 1
             print(

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -8,7 +8,6 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,

dev_scripts/chemenv/test_algos.py

@@ -8,7 +8,6 @@
 from random import shuffle
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/view_environment.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import numpy as np
-
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     SEPARATION_PLANE,
     AllCoordinationGeometries,

dev_scripts/potcar_scrambler.py

@@ -9,7 +9,6 @@
 import numpy as np
 from monty.os.path import zpath
 from monty.serialization import zopen
-
 from pymatgen.core import SETTINGS
 from pymatgen.io.vasp import Potcar, PotcarSingle
 from pymatgen.io.vasp.sets import _load_yaml_config

dev_scripts/update_pt_data.py

@@ -11,9 +11,8 @@
 import requests
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
-from ruamel import yaml
-
 from pymatgen.core import Element, get_el_sp
+from ruamel import yaml
 
 try:
     from bs4 import BeautifulSoup
@@ -30,24 +29,24 @@ def parse_oxi_state():
     oxi_data = re.sub("[\n\r]", "", oxi_data)
     patt = re.compile("<tr>(.*?)</tr>", re.MULTILINE)
 
-    for m in patt.finditer(oxi_data):
-        line = m.group(1)
+    for match in patt.finditer(oxi_data):
+        line = match[1]
         line = re.sub("</td>", "", line)
         line = re.sub("(<td>)+", "<td>", line)
         line = re.sub("</*a[^>]*>", "", line)
         el = None
         oxi_states = []
         common_oxi = []
         for tok in re.split("<td>", line.strip()):
-            m2 = re.match(r"<b>([A-Z][a-z]*)</b>", tok)
-            if m2:
-                el = m2.group(1)
+            match2 = re.match(r"<b>([A-Z][a-z]*)</b>", tok)
+            if match2:
+                el = match2[1]
             else:
-                m3 = re.match(r"(<b>)*([\+\-]\d)(</b>)*", tok)
-                if m3:
-                    oxi_states += [int(m3.group(2))]
-                    if m3.group(1):
-                        common_oxi += [int(m3.group(2))]
+                match3 = re.match(r"(<b>)*([\+\-]\d)(</b>)*", tok)
+                if match3:
+                    oxi_states += [int(match3[2])]
+                    if match3[1]:
+                        common_oxi += [int(match3[2])]
         if el in data:
             del data[el]["Max oxidation state"]
             del data[el]["Min oxidation state"]
@@ -79,7 +78,7 @@ def parse_ionic_radii():
         ionic_radii = {}
         for tok_idx in range(3, len(tokens)):
             if match := re.match(r"^\s*([0-9\.]+)", tokens[tok_idx]):
-                ionic_radii[int(header[tok_idx])] = float(match.group(1))
+                ionic_radii[int(header[tok_idx])] = float(match[1])
 
         if el in data:
             data[el][f"Ionic_radii{suffix}"] = ionic_radii