Merge branch 'master' of https://github.com/materialsproject/pymatgen into fix-chargemol-path

Author: chiang-yuan

.coderabbit.yaml

@@ -83,3 +83,21 @@ jobs:
         run: |
           micromamba activate pmg
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
+
+  trigger_atomate2_ci:
+    needs: test
+    runs-on: ubuntu-latest
+    # only run if changes were pushed to master
+    if: github.ref == 'refs/heads/master'
+    steps:
+      - name: Trigger Atomate2 CI
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          curl -L \
+            -X POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            https://api.github.com/repos/materialsproject/atomate2/dispatches \
+            -d '{"event_type": "pymatgen-ci-trigger", "client_payload": {"pymatgen_ref": "${{ github.sha }}"}}'

.github/workflows/test.yml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.2
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -47,7 +47,7 @@ repos:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.39.0
+    rev: v0.40.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -64,6 +64,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.360
+    rev: v1.1.361
     hooks:
       - id: pyright

.pre-commit-config.yaml

@@ -37,17 +37,17 @@
 __date__ = "Feb 20, 2016"
 
 
-allcg = AllCoordinationGeometries()
+all_cg = AllCoordinationGeometries()
 
 
 class CoordinationEnvironmentMorphing:
-    """Class to morph a coordination environment into another one."""
+    """Morph a coordination environment into another one."""
 
     def __init__(self, initial_environment_symbol, expected_final_environment_symbol, morphing_description):
         self.initial_environment_symbol = initial_environment_symbol
         self.expected_final_environment_symbol = expected_final_environment_symbol
         self.morphing_description = morphing_description
-        self.coordination_geometry = allcg.get_geometry_from_mp_symbol(initial_environment_symbol)
+        self.coordination_geometry = all_cg.get_geometry_from_mp_symbol(initial_environment_symbol)
         self.abstract_geometry = AbstractGeometry.from_cg(self.coordination_geometry)
 
     @classmethod

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -47,7 +47,7 @@ def __init__(self, potcars: Potcar | PotcarSingle) -> None:
 
     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)))
+        bd = max(1, bloat * abs(float(input_str)))  # ensure we don't get 0
         return round(bd * np.random.rand(1)[0], n_prec)
 
     def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
@@ -172,7 +172,7 @@ def generate_fake_potcar_libraries() -> None:
 
 
 def potcar_cleanser() -> None:
-    """Function to replace copyrighted POTCARs used in io.vasp.sets testing
+    """Replace copyrighted POTCARs used in io.vasp.sets testing
     with dummy POTCARs that have scrambled PSP and kinetic energy values
     (but retain the original header information which is also found in OUTCARs
     and freely shared by VASP)

dev_scripts/potcar_scrambler.py

@@ -111,11 +111,11 @@ def main():
     del lines[start + 1 : stop]
 
     # [2] write new py module
-    with open(xc_funcpy_path, mode="w") as file:
+    with open(xc_funcpy_path, mode="w", encoding="utf-8") as file:
         file.writelines(lines)
 
     print("Files have been regenerated")
-    print("Remember to update libxc_version in libxcfuncs.py!")
+    print("Remember to update __version__ in libxcfuncs.py!")
 
     return 0
 

dev_scripts/regen_libxcfunc.py

@@ -1,7 +1,5 @@
-"""
-Developer script to convert yaml periodic table to json format.
-Created on Nov 15, 2011.
-"""
+"""Developer script to convert YAML periodic table to JSON format.
+Created on 2011-11-15."""
 
 from __future__ import annotations
 
@@ -11,12 +9,17 @@
 from itertools import product
 
 import requests
-from bs4 import BeautifulSoup
+from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
 from ruamel import yaml
 
 from pymatgen.core import Element, get_el_sp
 
+try:
+    from bs4 import BeautifulSoup
+except ImportError:
+    BeautifulSoup = None
+
 ptable_yaml_path = "periodic_table.yaml"
 
 
@@ -74,10 +77,9 @@ def parse_ionic_radii():
         el = tokens[2]
 
         ionic_radii = {}
-        for j in range(3, len(tokens)):
-            match = re.match(r"^\s*([0-9\.]+)", tokens[j])
-            if match:
-                ionic_radii[int(header[j])] = float(match.group(1))
+        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))
 
         if el in data:
             data[el]["Ionic_radii" + suffix] = ionic_radii
@@ -231,6 +233,7 @@ def gen_iupac_ordering():
         periodic_table[el]["IUPAC ordering"] = iupac_ordering_dict[get_el_sp(el)]
 
 
+@requires(BeautifulSoup, "BeautifulSoup must be installed to use this method.")
 def add_electron_affinities():
     """Update the periodic table data file with electron affinities."""
 

dev_scripts/update_pt_data.py

@@ -0,0 +1,7 @@
+All examples are housed at [matgenb]. Please consult this resource first.
+
+If there are questions that cannot be found in the examples, you may use the [pymatgen MatSci forum] or [GitHub discussion].
+
+[matgenb]: https://matgenb.materialsvirtuallab.org/
+[pymatgen MatSci forum]: https://matsci.org/pymatgen
+[github discussion]: https://github.com/materialsproject/pymatgen/discussions