Support python3.13

.github/workflows/release.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Build source distribution
         run: |
@@ -76,7 +76,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Get build artifacts
         uses: actions/download-artifact@v4

.github/workflows/test.yml

@@ -28,22 +28,22 @@ jobs:
         # 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 3.12) on ubuntu (to get complete coverage on unix).
+        # newest version (currently 3.13) on ubuntu (to get complete coverage on unix).
         config:
           - os: windows-latest
-            python: "3.10"
+            python: "3.13"
             resolution: highest
             extras: ci,optional
           - os: windows-latest
-            python: "3.10"
+            python: "3.13"
             resolution: highest
             extras: ci,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
           - os: ubuntu-latest
-            python: "3.12"
+            python: "3.13"
             resolution: lowest-direct
             extras: ci,optional
           - os: macos-latest
-            python: "3.11"
+            python: "3.13"
             resolution: lowest-direct
             extras: ci # test with only required dependencies installed
 
@@ -70,19 +70,17 @@ jobs:
       - name: Install ubuntu-only conda dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |
-          micromamba install -n pmg -c conda-forge bader enumlib \
-            openff-toolkit packmol pygraphviz tblite --yes
+          micromamba install -n pmg -c conda-forge --yes \
+            bader enumlib packmol pygraphviz tblite
+          # openff-toolkit
+          # TODO: openff-toolkit doesn't support Python 3.13 yet
 
       - name: Install uv
         uses: astral-sh/setup-uv@v4
 
       - name: Install pymatgen and dependencies via uv
         run: |
           micromamba activate pmg
-          # TODO1 (use uv over pip) uv install torch is flaky, track #3826
-          # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1,
-          # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
-          pip install torch==2.2.1
 
           # Install from wheels to test the content
           uv build --wheel --no-build-logs

pyproject.toml

@@ -21,7 +21,7 @@ Python Materials Genomics is a robust materials analysis code that defines core
 and molecules with support for many electronic structure codes. It is currently the core analysis code powering the
 Materials Project (https://materialsproject.org)."""
 readme = "README.md"
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.10,<3.14"
 keywords = [
     "ABINIT",
     "VASP",
@@ -48,6 +48,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Information Analysis",
     "Topic :: Scientific/Engineering :: Physics",
@@ -61,12 +62,11 @@ dependencies = [
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=5.0.0",
-    "pybtex>=0.24.0",
     "requests>=2.32",
     "ruamel.yaml>=0.17.0",
-    "scipy>=1.13.0",
     # scipy<1.14.1 is incompatible with NumPy 2.0 on Windows
     # https://github.com/scipy/scipy/issues/21052
+    "scipy>=1.13.0",
     "scipy>=1.14.1; platform_system == 'Windows'",
     "spglib>=2.5",
     "sympy>=1.3",  # PR #4116
@@ -92,9 +92,9 @@ ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8", "pymatgen[symmetry]"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
 electronic_structure = ["fdint>=2.0.2"]
-mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
+mlp = ["chgnet>=0.4.0; python_version<'3.13'", "matgl>=1.1.3; python_version<'3.13'"]
 numba = ["numba>=0.55"]
-numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
+numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (buggy at this moment)
 optional = [
     "pymatgen[abinit,ase,mlp,tblite]",
     "beautifulsoup4",
@@ -107,14 +107,16 @@ optional = [
     "hiphive>=1.3.1",
     "jarvis-tools>=2020.7.14",
     "matplotlib>=3.8",
+    "openbabel-wheel>=3.1.1.20",
     "phonopy>=2.33.3",
+    "pybtex>=0.24.0",  # TODO: don't work on MacOS Python 3.13
     "seekpath>=2.0.1",
 ]
 # moyopy[interface] includes ase
 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'"]
+tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
 vis = ["vtk>=6.0.0"]
 
 [project.scripts]

src/pymatgen/analysis/prototypes.py

@@ -25,7 +25,10 @@
     from pymatgen.core.structure import Structure
 
 MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
-AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{MODULE_DIR}/aflow_prototypes.json")
+try:
+    AFLOW_PROTOTYPE_LIBRARY = loadfn(f"{MODULE_DIR}/aflow_prototypes.json")
+except RuntimeError as exc:
+    raise ImportError("pybtex is needed to load AFLOW library") from exc
 
 
 @due.dcite(

src/pymatgen/io/cif.py

@@ -1357,8 +1357,8 @@ def get_bibtex_string(self) -> str:
         """
         try:
             from pybtex.database import BibliographyData, Entry
-        except ImportError:
-            raise RuntimeError("Bibliographic data extraction requires pybtex.")
+        except ImportError as exc:
+            raise RuntimeError("Bibliographic data extraction requires pybtex.") from exc
 
         bibtex_keys: dict[str, tuple[str, ...]] = {
             "author": ("_publ_author_name", "_citation_author_name"),

src/pymatgen/io/vasp/outputs.py

@@ -4732,9 +4732,8 @@ def concatenate(
                 raise ValueError("preamble is None")
             poscar = Poscar.from_str("\n".join([*preamble, "Direct", *coords_str]))
 
-            if (
-                (ionicstep_end is None and ionicstep_cnt >= ionicstep_start)
-                or ionicstep_start <= ionicstep_cnt < ionicstep_end  # type: ignore[operator]
+            if (ionicstep_end is None and ionicstep_cnt >= ionicstep_start) or (
+                ionicstep_end is not None and ionicstep_start <= ionicstep_cnt < ionicstep_end
             ):
                 structures.append(poscar.structure)
         self.structures = structures

src/pymatgen/util/provenance.py

@@ -9,6 +9,7 @@
 from io import StringIO
 from typing import TYPE_CHECKING, NamedTuple
 
+from monty.dev import requires
 from monty.json import MontyDecoder, MontyEncoder
 
 from pymatgen.core.structure import Molecule, Structure
@@ -36,6 +37,7 @@
 MAX_BIBTEX_CHARS: int = 20_000  # maximum number of characters for BibTeX reference
 
 
+@requires(bibtex is not None, "pybtex is not available")
 def is_valid_bibtex(reference: str) -> bool:
     """Use pybtex to validate that a reference is in proper BibTeX format.
 

tests/analysis/test_cost.py

@@ -2,11 +2,19 @@
 
 from unittest import TestCase
 
+import pytest
 from pytest import approx
 
 from pymatgen.analysis.cost import CostAnalyzer, CostDBCSV, CostDBElements
 from pymatgen.util.testing import TEST_FILES_DIR
 
+try:
+    # Not using find_spec because it would error out during import
+    import pybtex.database  # noqa: F401
+
+except ImportError:
+    pytest.skip("pybtex is not available", allow_module_level=True)
+
 TEST_DIR = f"{TEST_FILES_DIR}/analysis/cost"
 
 

tests/analysis/test_eos.py

@@ -426,7 +426,7 @@ def test_numerical_eos_values(self):
         assert_allclose(self.num_eos_fit.e0, -10.84749, atol=1e-3)
         assert_allclose(self.num_eos_fit.v0, 40.857201, atol=1e-1)
         assert_allclose(self.num_eos_fit.b0, 0.55, atol=1e-2)
-        assert_allclose(self.num_eos_fit.b0_GPa, 89.0370727, atol=1e-1)
+        assert_allclose(self.num_eos_fit.b0_GPa, 89.0370727, atol=0.3)  # PR 4100
         assert_allclose(self.num_eos_fit.b1, 4.344039, atol=1e-2)
 
     def test_eos_func(self):

tests/analysis/test_prototypes.py

@@ -1,6 +1,12 @@
 from __future__ import annotations
 
-from pymatgen.analysis.prototypes import AflowPrototypeMatcher
+import pytest
+
+try:
+    from pymatgen.analysis.prototypes import AflowPrototypeMatcher
+except ImportError:
+    pytest.skip("pybtex is not available", allow_module_level=True)
+
 from pymatgen.util.testing import PymatgenTest
 
 

tests/io/test_cif.py

@@ -14,6 +14,7 @@
 
 try:
     import pybtex
+    import pybtex.database
 except ImportError:
     pybtex = None
 
@@ -166,6 +167,7 @@ def test_long_loop(self):
 
 
 class TestCifIO(PymatgenTest):
+    @pytest.mark.skipif(pybtex is None, reason="pybtex not present")
     def test_cif_parser(self):
         parser = CifParser(f"{TEST_FILES_DIR}/cif/LiFePO4.cif")
         for struct in parser.parse_structures():

tests/util/test_provenance.py

@@ -11,6 +11,13 @@
 from pymatgen.core.structure import Molecule, Structure
 from pymatgen.util.provenance import Author, HistoryNode, StructureNL
 
+try:
+    # Not using find_spec because it would error out during import
+    import pybtex.database  # noqa: F401
+
+except ImportError:
+    pytest.skip("pybtex is not available", allow_module_level=True)
+
 __author__ = "Anubhav Jain"
 __credits__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"