Merge branch 'master' into fix-pd-plot-above-hull-e

Author: DanielYang59

.github/workflows/lint.yml

@@ -14,12 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
+
       - name: Install uv with python version.
         uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.11"
+          python-version: "3.13"
           enable-cache: true
           cache-dependency-glob: "uv.lock"
+
       - name: Install dependencies
         run: |
           uv sync

.github/workflows/release.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Build source distribution
         run: |
@@ -47,7 +47,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, macos-13, windows-latest, ubuntu-24.04-arm]
-        python-version: ["310", "311", "312", "313"]
+        python-version: ["310", "311", "312", "313", "314"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
@@ -77,7 +77,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Get build artifacts
         uses: actions/download-artifact@v5

.github/workflows/test.yml

@@ -39,26 +39,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # Maximize CI coverage of different platforms and python versions while minimizing the
-        # total number of jobs. We run all pytest splits with the oldest supported python
-        # version (currently 3.10) on windows (seems most likely to surface errors) and with
-        # newest version (currently 3.13) on ubuntu (to get complete coverage on unix).
+        # Maximize CI coverage of different platforms and Python versions while minimizing the
+        # total number of jobs. We run all pytest splits with the oldest supported Python
+        # version on windows (most likely to surface errors) and with
+        # newest version on Ubuntu (to get complete coverage).
         config:
           - os: windows-latest
-            python: "3.10"
-            resolution: highest
+            python: "3.10"  # Test lowest supported Python version
+            resolution: lowest-direct
             extras: optional,prototypes
           - os: windows-latest
             python: "3.11"
             resolution: highest
             extras: prototypes,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
           - os: macos-latest
-            python: "3.12"
+            python: "3.13"
             resolution: lowest-direct
             extras: prototypes # test with only required dependencies installed
           - os: ubuntu-latest
-            python: "3.13"
-            resolution: lowest-direct
+            python: "3.14"  # Test highest supported Python version
+            resolution: highest
             extras: prototypes,optional
 
         # pytest-split automatically distributes work load so parallel jobs finish in similar time
@@ -67,7 +67,7 @@ jobs:
 
     runs-on: ${{ matrix.config.os }}
     env:
-      OPT_BIN_DIR: ${{ github.workspace }}/opt/bin # for optional Unix dependencies
+      OPT_BIN_DIR: ${{ github.workspace }}/opt/bin # for optional Ubuntu dependencies
     steps:
       - name: Check out repo
         uses: actions/checkout@v5

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.3
+    rev: v0.14.3
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -38,7 +38,7 @@ repos:
         exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.17.0
+    rev: v0.18.1
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]
@@ -67,6 +67,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.406
+    rev: v1.1.407
     hooks:
       - id: pyright

pyproject.toml

@@ -49,6 +49,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Information Analysis",
     "Topic :: Scientific/Engineering :: Physics",
@@ -79,7 +80,7 @@ dependencies = [
     "tqdm>=4.60",
     "uncertainties>=3.1.4",
 ]
-version = "2025.6.14"
+version = "2025.10.7"
 
 [project.urls]
 Homepage = "https://pymatgen.org"
@@ -100,7 +101,7 @@ matcalc = [
     "matgl>=1.2.7; python_version<'3.13'",
 ]
 mlp = ["matgl>=1.2.7 ; python_version<'3.13'"]
-numba = ["numba>=0.55"]
+numba = ["numba>=0.55; python_version<'3.14'"]
 numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 optional = [
     "pymatgen[abinit,ase,matcalc,mlp,tblite,zeopp]",
@@ -112,7 +113,7 @@ optional = [
     "f90nml>=1.1.2",
     "galore>=0.6.1",
     "h5py>=3.11.0",
-    "hiphive>=1.3.1",
+    "hiphive>=1.3.1; python_version<'3.14'",
     "jarvis-tools>=2020.7.14",
     "phonopy>=2.33.3",
     "seekpath>=2.0.1",
@@ -123,7 +124,7 @@ symmetry = ["moyopy[interface]>=0.3", "spglib>=2.5"]
 # tblite only support Python 3.12+ through conda-forge
 # https://github.com/tblite/tblite/issues/175
 tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
-vis = ["vtk>=6.0.0"]
+vis = ["vtk>=6.0.0; python_version<'3.14'"]
 zeopp = ["pyzeo; platform_system != 'Windows'"]  # Note: requires Voro++ and Zeo++ to be installed
 
 [project.scripts]
@@ -164,10 +165,6 @@ include = ["pymatgen", "pymatgen.*"]
 "pymatgen.io.lammps" = ["CoeffsDataType.yaml", "templates/*.template"]
 "pymatgen.symmetry" = ["*.json", "*.sqlite", "*.yaml"]
 
-[tool.pdm.dev-dependencies]
-lint = ["mypy>=1.10.0", "pre-commit>=3.7.1", "ruff>=0.4.9"]
-test = ["pytest-cov>=5.0.0", "pytest-split>=0.9.0", "pytest>=8.2.2","pytest-xdist>=3.0.0"]
-
 [tool.cibuildwheel.linux]
 archs = ["auto64"]
 skip = ["*musllinux*"]
@@ -261,7 +258,7 @@ docstring-code-format = true
 addopts = "-n auto --durations=30 --quiet -r xXs --color=yes --import-mode=importlib"
 filterwarnings = [
     # NOTE: the LAST matching option would be used
-    "ignore::UserWarning", # Ignore UserWarning
+    "ignore::UserWarning",
 ]
 
 [tool.coverage.run]
@@ -277,12 +274,7 @@ omit = [
 [tool.coverage.report]
 exclude_also = [
     "@deprecated",
-    "def __repr__",
     "except ImportError:",
-    "if TYPE_CHECKING:",
-    "if self.debug:",
-    "if settings.DEBUG",
-    "pragma: no cover",
     "raise NotImplementedError",
     "show_plot",
 ]

src/pymatgen/analysis/phase_diagram.py

@@ -406,12 +406,17 @@ def __repr__(self) -> str:
 
     def as_dict(self) -> dict[str, Any]:
         """Get MSONable dict representation of PhaseDiagram."""
+
+        qhull_entry_indices = [self.all_entries.index(e) for e in self.qhull_entries]
+
         return {
             "@module": type(self).__module__,
             "@class": type(self).__name__,
-            "all_entries": [e.as_dict() for e in self.all_entries],
             "elements": [e.as_dict() for e in self.elements],
-            "computed_data": self.computed_data,
+            "computed_data": self.computed_data
+            | {
+                "qhull_entries": qhull_entry_indices,
+            },
         }
 
     @classmethod
@@ -423,9 +428,19 @@ def from_dict(cls, dct: dict[str, Any]) -> Self:
         Returns:
             PhaseDiagram
         """
-        entries = [MontyDecoder().process_decoded(entry) for entry in dct["all_entries"]]
-        elements = [Element.from_dict(elem) for elem in dct["elements"]]
         computed_data = dct.get("computed_data")
+        elements = [Element.from_dict(elem) for elem in dct["elements"]]
+
+        # for backwards compatibility, check for old format
+        if "all_entries" in dct:
+            entries = [MontyDecoder().process_decoded(entry) for entry in dct["all_entries"]]
+        else:
+            entries = [MontyDecoder().process_decoded(entry) for entry in computed_data["all_entries"]]
+
+            complete_qhull_entries = [computed_data["all_entries"][i] for i in computed_data["qhull_entries"]]
+
+            computed_data = computed_data | {"qhull_entries": complete_qhull_entries}
+
         return cls(entries, elements, computed_data=computed_data)
 
     def _compute(self) -> dict[str, Any]:

src/pymatgen/analysis/structure_prediction/dopant_predictor.py

@@ -128,7 +128,7 @@ def get_dopants_from_shannon_radii(bonded_structure, num_dopants=5, match_oxi_si
 def _get_dopants(substitutions, num_dopants, match_oxi_sign) -> dict:
     """Utility method to get n- and p-type dopants from a list of substitutions."""
     dopants = {k: [] for k in ("n_type", "p_type")}
-    for k in dopants:  # noqa: PLC0206
+    for k, dop in dopants.items():
         for pred in substitutions:
             if (
                 pred["dopant_species"].oxi_state > pred["original_species"].oxi_state
@@ -138,8 +138,8 @@ def _get_dopants(substitutions, num_dopants, match_oxi_sign) -> dict:
                 not match_oxi_sign
                 or np.sign(pred["dopant_species"].oxi_state) == np.sign(pred["original_species"].oxi_state)
             ):
-                dopants[k].append(pred)
-            if len(dopants[k]) == num_dopants:
+                dop.append(pred)
+            if len(dop) == num_dopants:
                 break
     return dopants
 

src/pymatgen/cli/pmg.py

@@ -63,11 +63,11 @@ def format_lists(v):
         ["---------------", "", ""],
     ]
     output += [
-        (  # type: ignore[misc]
+        [
             k,
             format_lists(diff["Same"][k]),
             format_lists(diff["Same"][k]),
-        )
+        ]
         for k in sorted(diff["Same"])
         if k != "SYSTEM"
     ]
@@ -77,7 +77,7 @@ def format_lists(v):
         ["----------------", "", ""],
     ]
     output += [
-        [  # type: ignore[misc]
+        [
             k,
             format_lists(diff["Different"][k]["INCAR1"]),
             format_lists(diff["Different"][k]["INCAR2"]),

src/pymatgen/core/periodic_table.py

@@ -1640,9 +1640,9 @@ def get_el_sp(obj: int | SpeciesLike) -> Element | Species | DummySpecies:
     # If obj is an integer, return the Element with atomic number obj
     try:
         flt = float(obj)
-        assert flt == int(flt)  # noqa: S101
-        return Element.from_Z(int(flt))
-    except (AssertionError, ValueError, TypeError, KeyError):
+        if flt.is_integer():
+            return Element.from_Z(int(flt))
+    except (ValueError, TypeError, KeyError):
         pass
 
     # If obj is a string, attempt to parse it as a Species