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

@@ -28,18 +28,18 @@ 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"
             resolution: highest
             extras: ci,optional
           - os: windows-latest
-            python: "3.10"
+            python: "3.12"
             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
@@ -71,20 +71,15 @@ 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 bader enumlib packmol pygraphviz tblite --yes
+          # TODO: openff-toolkit doesn't support Python 3.13 yet
 
       - name: Install pymatgen and dependencies via uv
         run: |
           micromamba activate pmg
 
           pip install uv
 
-          # 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 pip install build
           python -m build --wheel

pyproject.toml

@@ -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",
@@ -64,18 +65,15 @@ dependencies = [
     "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>=1.14.1; platform_system == 'Windows'",
+    "scipy>=1.14.1",
     "spglib>=2.5.0",
     "sympy>=1.3",  # PR #4116
     "tabulate>=0.9",
     "tqdm>=4.60",
     "uncertainties>=3.1.4",
     # NumPy documentation suggests pinning the current major version as the C API is used
     # https://numpy.org/devdocs/dev/depending_on_numpy.html#runtime-dependency-version-ranges
-    "numpy>=1.25.0,<3",
+    "numpy>=1.26.2,<3",
 ]
 version = "2024.11.13"
 
@@ -90,6 +88,13 @@ Pypi = "https://pypi.org/project/pymatgen"
 # PR4128: netcdf4 1.7.[0/1] yanked, 1.7.1.post[1/2]/1.7.2 cause CI error
 abinit = ["netcdf4>=1.6.5,!=1.7.1.post1,!=1.7.1.post2,!=1.7.2"]
 ase = ["ase>=3.23.0"]
+# tblite only support Python 3.12+ through conda-forge
+# https://github.com/tblite/tblite/issues/175
+tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"]
+vis = ["vtk>=6.0.0"]
+abinit = ["netcdf4>=1.7.1; python_version<'3.13'"]
+mlp = ["chgnet>=0.4.0; python_version<'3.13'", "matgl>=1.1.3; python_version<'3.13'"]
+electronic_structure = ["fdint>=2.0.2"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
 electronic_structure = ["fdint>=2.0.2"]
@@ -100,21 +105,27 @@ optional = [
     "pymatgen[abinit,ase,mlp,tblite]",
     "beautifulsoup4",
     # BoltzTraP2 build fails on Windows GitHub runners
-    "BoltzTraP2>=24.9.4 ; platform_system != 'Windows'",
+    # TODO: BoltzTraP2 depends on netcdf4 which doesn't support Python 3.13 yet
+    "BoltzTraP2>=24.9.4 ; platform_system != 'Windows' and python_version<'3.13'",
     "chemview>=0.6",
+    "chgnet>=0.4.0; python_version<'3.13'",
     "f90nml>=1.1.2",
     "galore>=0.6.1",
-    "h5py>=3.11.0",
-    "hiphive>=1.3.1",
+    "h5py>=3.12.1",
     "jarvis-tools>=2020.7.14",
+    "matgl>=1.1.3; python_version<'3.13'",
     "matplotlib>=3.8",
+    "netcdf4>=1.6.5; python_version<'3.13'",
     "phonopy>=2.23",
     "seekpath>=2.0.1",
+    # tblite only support Python 3.12+ through conda-forge
+    # https://github.com/tblite/tblite/issues/175
+    "hiphive>=1.3.1; python_version<'3.13'",
+    "openbabel-wheel>=3.1.1.20",
+    "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
 ]
-# 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"]
+numba = ["numba>=0.55; python_version<'3.13'"]
+numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 
 [project.scripts]
 pmg = "pymatgen.cli.pmg:main"