Merge remote-tracking branch 'upstream/master' into 4158-fix-eq-check

Author: DanielYang59

.github/workflows/test.yml

@@ -52,11 +52,10 @@ jobs:
         split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
 
     runs-on: ${{ matrix.config.os }}
-
     env:
-      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
       MPLBACKEND: Agg  # non-interactive backend for matplotlib
-
+      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+      PYTHONWARNDEFAULTENCODING: "true"  # PEP 597: Enable optional EncodingWarning
     steps:
       - name: Check out repo
         uses: actions/checkout@v4
@@ -106,6 +105,8 @@ jobs:
 
       - name: pytest split ${{ matrix.split }}
         env:
+          MPLBACKEND: Agg  # non-interactive backend for matplotlib
+          PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
           PMG_TEST_FILES_DIR: "${{ github.workspace }}/tests/files"
         run: |
           micromamba activate pmg

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.9.0
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
 
@@ -65,6 +65,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.389
+    rev: v1.1.391
     hooks:
       - id: pyright

dev_scripts/chemenv/explicit_permutations.py

@@ -93,5 +93,5 @@ class Algo:
         cg._algorithms = [ExplicitPermutationsAlgorithm(permutations=explicit_permutations)]
         new_geom_dir = "new_geometry_files"
         os.makedirs(new_geom_dir, exist_ok=True)
-        with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w") as file:
+        with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w", encoding="utf-8") as file:
             json.dump(cg.as_dict(), file)

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -159,5 +159,5 @@
     if test == "y":
         cg._algorithms = new_algos
         cg_dict = cg.as_dict()
-        with open(f"../coordination_geometries_files_new/{cg_symbol}.json", mode="w") as file:
+        with open(f"../coordination_geometries_files_new/{cg_symbol}.json", mode="w", encoding="utf-8") as file:
             json.dump(cg_dict, file)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -444,5 +444,5 @@ def random_permutations_iterator(initial_permutation, n_permutations):
         if test == "y":
             new_geom_dir = "new_geometry_files"
             os.makedirs(new_geom_dir, exist_ok=True)
-            with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w") as file:
+            with open(f"{new_geom_dir}/{cg_symbol}.json", mode="w", encoding="utf-8") as file:
                 json.dump(cg.as_dict(), file)

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -171,7 +171,7 @@ def get_structure(self, morphing_factor):
 
         for morphing in self.morphing_description:
             if morphing["site_type"] != "neighbor":
-                raise ValueError(f"Key \"site_type\" is {morphing['site_type']} while it can only be neighbor")
+                raise ValueError(f'Key "site_type" is {morphing["site_type"]} while it can only be neighbor')
 
             site_idx = morphing["ineighbor"] + 1
             if morphing["expansion_origin"] == "central_site":

dev_scripts/chemenv/view_environment.py

@@ -29,8 +29,7 @@
     vis = None
     while True:
         cg_symbol = input(
-            'Enter symbol of the geometry you want to see, "l" to see the list '
-            'of existing geometries or "q" to quit : '
+            'Enter symbol of the geometry you want to see, "l" to see the list of existing geometries or "q" to quit : '
         )
         if cg_symbol == "q":
             break

dev_scripts/potcar_scrambler.py

@@ -124,7 +124,7 @@ def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         return scrambled_potcar_str
 
     def to_file(self, filename: str) -> None:
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod

dev_scripts/regen_libxcfunc.py

@@ -10,10 +10,11 @@
 from __future__ import annotations
 
 import json
-import os
 import sys
 from copy import deepcopy
 
+from pymatgen.core import PKG_DIR
+
 
 def parse_libxc_docs(path):
     """Parse libxc_docs.txt file, return dictionary {libxc_id: info_dict}."""
@@ -27,7 +28,7 @@ def parse_section(section):
         return int(dct["Number"]), dct
 
     dct = {}
-    with open(path) as file:
+    with open(path, encoding="utf-8") as file:
         section = []
         for line in file:
             if not line.startswith("-"):
@@ -62,7 +63,7 @@ def write_libxc_docs_json(xc_funcs, json_path):
             if desc is not None:
                 xc_funcs[num][opt] = desc
 
-    with open(json_path, "w") as fh:
+    with open(json_path, "w", encoding="utf-8") as fh:
         json.dump(xc_funcs, fh)
 
     return xc_funcs
@@ -85,8 +86,7 @@ def main():
     xc_funcs = parse_libxc_docs(path)
 
     # Generate new JSON file in pycore
-    pmg_core = os.path.abspath("../pymatgen/core/")
-    json_path = f"{pmg_core}/libxc_docs.json"
+    json_path = f"{PKG_DIR}/core/libxc_docs.json"
     write_libxc_docs_json(xc_funcs, json_path)
 
     # Build new enum list.
@@ -99,8 +99,8 @@ def main():
 
     # Re-generate enumerations.
     # [0] read py module.
-    xc_funcpy_path = f"{pmg_core}/libxcfunc.py"
-    with open(xc_funcpy_path) as file:
+    xc_funcpy_path = f"{PKG_DIR}/core/libxcfunc.py"
+    with open(xc_funcpy_path, encoding="utf-8") as file:
         lines = file.readlines()
 
     # [1] insert new enum values in list

dev_scripts/update_pt_data.py

@@ -13,7 +13,7 @@
 from monty.serialization import dumpfn, loadfn
 from ruamel import yaml
 
-from pymatgen.core import Element, get_el_sp
+from pymatgen.core import PKG_DIR, Element, get_el_sp
 
 try:
     from bs4 import BeautifulSoup
@@ -25,7 +25,7 @@
 
 def parse_oxi_state():
     data = loadfn(PTABLE_YAML_PATH)
-    with open("oxidation_states.txt") as file:
+    with open("oxidation_states.txt", encoding="utf-8") as file:
         oxi_data = file.read()
     oxi_data = re.sub("[\n\r]", "", oxi_data)
     patt = re.compile("<tr>(.*?)</tr>", re.MULTILINE)
@@ -57,13 +57,13 @@ def parse_oxi_state():
             data[el]["Common oxidation states"] = common_oxi
         else:
             print(el)
-    with open("periodic_table2.yaml", mode="w") as file:
+    with open("periodic_table2.yaml", mode="w", encoding="utf-8") as file:
         yaml.dump(data, file)
 
 
 def parse_ionic_radii():
     data = loadfn(PTABLE_YAML_PATH)
-    with open("ionic_radii.csv") as file:
+    with open("ionic_radii.csv", encoding="utf-8") as file:
         radii_data = file.read()
     radii_data = radii_data.split("\r")
     header = radii_data[0].split(",")
@@ -87,13 +87,13 @@ def parse_ionic_radii():
                 data[el]["Ionic_radii"] = ionic_radii
         else:
             print(el)
-    with open("periodic_table2.yaml", mode="w") as file:
+    with open("periodic_table2.yaml", mode="w", encoding="utf-8") as file:
         yaml.dump(data, file)
 
 
 def parse_radii():
     data = loadfn(PTABLE_YAML_PATH)
-    with open("radii.csv") as file:
+    with open("radii.csv", encoding="utf-8") as file:
         radii_data = file.read()
     radii_data = radii_data.split("\r")
 
@@ -121,9 +121,9 @@ def parse_radii():
             data[el]["Van der waals radius"] = vdw_radii
         else:
             print(el)
-    with open("periodic_table2.yaml", mode="w") as file:
+    with open("periodic_table2.yaml", mode="w", encoding="utf-8") as file:
         yaml.dump(data, file)
-    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
+    with open(f"{PKG_DIR}/core/periodic_table.json", mode="w", encoding="utf-8") as file:
         json.dump(data, file)
 
 
@@ -140,9 +140,9 @@ def update_ionic_radii():
         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:
+    with open("periodic_table2.yaml", mode="w", encoding="utf-8") as file:
         yaml.dump(data, file)
-    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
+    with open(f"{PKG_DIR}/core/periodic_table.json", mode="w", encoding="utf-8") as file:
         json.dump(data, file)
 
 
@@ -180,19 +180,19 @@ def parse_shannon_radii():
             data[el]["Shannon radii"] = dict(radii[el])
 
     dumpfn(data, PTABLE_YAML_PATH)
-    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
+    with open(f"{PKG_DIR}/core/periodic_table.json", mode="w", encoding="utf-8") as file:
         json.dump(data, file)
 
 
 def gen_periodic_table():
     data = loadfn(PTABLE_YAML_PATH)
 
-    with open("../pymatgen/core/periodic_table.json", mode="w") as file:
+    with open(f"{PKG_DIR}/core/periodic_table.json", mode="w", encoding="utf-8") as file:
         json.dump(data, file)
 
 
 def gen_iupac_ordering():
-    periodic_table = loadfn("../pymatgen/core/periodic_table.json")
+    periodic_table = loadfn(f"{PKG_DIR}/core/periodic_table.json")
     order = [
         ([18], range(6, 0, -1)),  # noble gasses
         ([1], range(7, 1, -1)),  # alkali metals
@@ -274,16 +274,16 @@ def add_electron_affinities():
         missing_electron_affinities = set(range(1, 93)) - Z_set
         raise ValueError(f"{missing_electron_affinities=}")
     print(element_electron_affinities)
-    pt = loadfn("../pymatgen/core/periodic_table.json")
+    pt = loadfn(f"{PKG_DIR}/core/periodic_table.json")
     for key, val in pt.items():
         val["Electron affinity"] = element_electron_affinities.get(Element(key).long_name)
-    dumpfn(pt, "../pymatgen/core/periodic_table.json")
+    dumpfn(pt, f"{PKG_DIR}/core/periodic_table.json")
 
 
 def add_ionization_energies():
     """Update the periodic table data file with ground level and ionization energies from NIST."""
 
-    with open("NIST Atomic Ionization Energies Output.html") as file:
+    with open("NIST Atomic Ionization Energies Output.html", encoding="utf-8") as file:
         soup = BeautifulSoup(file.read(), "html.parser")
     table = None
     for table in soup.find_all("table"):
@@ -302,11 +302,11 @@ def add_ionization_energies():
     if not set(data).issuperset(range(1, 93)):
         raise RuntimeError("Failed to get data up to Uranium")
 
-    pt = loadfn("../pymatgen/core/periodic_table.json")
+    pt = loadfn(f"{PKG_DIR}/core/periodic_table.json")
     for key, val in pt.items():
         del val["Ionization energy"]
         val["Ionization energies"] = data.get(Element(key).long_name, [])
-    dumpfn(pt, "../pymatgen/core/periodic_table.json")
+    dumpfn(pt, f"{PKG_DIR}/core/periodic_table.json")
 
 
 if __name__ == "__main__":