breaking: drop Python 3.9

.github/workflows/test_python.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         group: [1, 2, 3, 4, 5, 6]
-        python: ["3.9", "3.12"]
+        python: ["3.10", "3.12"]
 
     steps:
     - uses: actions/checkout@v6
@@ -85,7 +85,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.9", "3.12"]
+        python: ["3.10", "3.12"]
     needs: testpython
     steps:
     - name: Get durations from cache

AGENTS.md

@@ -94,7 +94,7 @@ source/               # C++ source code and tests
 
 ### Build Dependencies and Setup
 
-- **Python 3.9+** required
+- **Python 3.10+** required
 - **Virtual environment** strongly recommended: `uv venv venv && source venv/bin/activate`
 - **Backend dependencies**: TensorFlow, PyTorch, JAX, or Paddle (install before building)
 - **Build tools**: CMake, C++ compiler, scikit-build-core

backend/dynamic_metadata.py

@@ -3,9 +3,6 @@
 from pathlib import (
     Path,
 )
-from typing import (
-    Optional,
-)
 
 from .find_pytorch import (
     get_pt_requirement,
@@ -31,7 +28,7 @@ def __dir__() -> list[str]:
 
 def dynamic_metadata(
     field: str,
-    settings: Optional[dict[str, object]] = None,
+    settings: dict[str, object] | None = None,
 ):
     assert field in ["optional-dependencies", "entry-points", "scripts"]
     _, _, find_libpython_requires, extra_scripts, tf_version, pt_version = (

backend/find_paddle.py

@@ -17,14 +17,10 @@
 from sysconfig import (
     get_path,
 )
-from typing import (
-    Optional,
-    Union,
-)
 
 
 @lru_cache
-def find_paddle() -> tuple[Optional[str], list[str]]:
+def find_paddle() -> tuple[str | None, list[str]]:
     """Find PaddlePadle library.
 
     Tries to find PaddlePadle in the order of:
@@ -111,7 +107,7 @@ def get_pd_requirement(pd_version: str = "") -> dict:
 
 
 @lru_cache
-def get_pd_version(pd_path: Optional[Union[str, Path]]) -> str:
+def get_pd_version(pd_path: str | Path | None) -> str:
     """Get Paddle version from a Paddle Python library path.
 
     Parameters

backend/find_pytorch.py

@@ -17,10 +17,6 @@
 from sysconfig import (
     get_path,
 )
-from typing import (
-    Optional,
-    Union,
-)
 
 from packaging.specifiers import (
     SpecifierSet,
@@ -35,7 +31,7 @@
 
 
 @lru_cache
-def find_pytorch() -> tuple[Optional[str], list[str]]:
+def find_pytorch() -> tuple[str | None, list[str]]:
     """Find PyTorch library.
 
     Tries to find PyTorch in the order of:
@@ -150,7 +146,7 @@ def get_pt_requirement(pt_version: str = "") -> dict:
 
 
 @lru_cache
-def get_pt_version(pt_path: Optional[Union[str, Path]]) -> str:
+def get_pt_version(pt_path: str | Path | None) -> str:
     """Get TF version from a TF Python library path.
 
     Parameters

backend/find_tensorflow.py

@@ -17,10 +17,6 @@
 from sysconfig import (
     get_path,
 )
-from typing import (
-    Optional,
-    Union,
-)
 
 from packaging.specifiers import (
     SpecifierSet,
@@ -32,7 +28,7 @@
 
 
 @lru_cache
-def find_tensorflow() -> tuple[Optional[str], list[str]]:
+def find_tensorflow() -> tuple[str | None, list[str]]:
     """Find TensorFlow library.
 
     Tries to find TensorFlow in the order of:
@@ -208,7 +204,7 @@ def get_tf_requirement(tf_version: str = "") -> dict:
 
 
 @lru_cache
-def get_tf_version(tf_path: Optional[Union[str, Path]]) -> str:
+def get_tf_version(tf_path: str | Path | None) -> str:
     """Get TF version from a TF Python library path.
 
     Parameters

deepmd/backend/backend.py

@@ -2,13 +2,15 @@
 from abc import (
     abstractmethod,
 )
+from collections.abc import (
+    Callable,
+)
 from enum import (
     Flag,
     auto,
 )
 from typing import (
     TYPE_CHECKING,
-    Callable,
     ClassVar,
 )
 

deepmd/backend/dpmodel.py

@@ -1,7 +1,9 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
+from collections.abc import (
+    Callable,
+)
 from typing import (
     TYPE_CHECKING,
-    Callable,
     ClassVar,
 )
 

deepmd/backend/jax.py

@@ -1,10 +1,12 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
+from collections.abc import (
+    Callable,
+)
 from importlib.util import (
     find_spec,
 )
 from typing import (
     TYPE_CHECKING,
-    Callable,
     ClassVar,
 )
 

deepmd/backend/paddle.py

@@ -1,10 +1,12 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
+from collections.abc import (
+    Callable,
+)
 from importlib.util import (
     find_spec,
 )
 from typing import (
     TYPE_CHECKING,
-    Callable,
     ClassVar,
 )
 

deepmd/backend/pytorch.py

@@ -1,10 +1,12 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
+from collections.abc import (
+    Callable,
+)
 from importlib.util import (
     find_spec,
 )
 from typing import (
     TYPE_CHECKING,
-    Callable,
     ClassVar,
 )
 

deepmd/backend/suffix.py

@@ -4,10 +4,6 @@
 from pathlib import (
     Path,
 )
-from typing import (
-    Optional,
-    Union,
-)
 
 from deepmd.backend.backend import (
     Backend,
@@ -16,9 +12,9 @@
 
 def format_model_suffix(
     filename: str,
-    feature: Optional[Backend.Feature] = None,
-    preferred_backend: Optional[Union[str, type["Backend"]]] = None,
-    strict_prefer: Optional[bool] = None,
+    feature: Backend.Feature | None = None,
+    preferred_backend: str | type["Backend"] | None = None,
+    strict_prefer: bool | None = None,
 ) -> str:
     """Check and format the suffixes of a filename.
 

deepmd/backend/tensorflow.py

@@ -1,10 +1,12 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
+from collections.abc import (
+    Callable,
+)
 from importlib.util import (
     find_spec,
 )
 from typing import (
     TYPE_CHECKING,
-    Callable,
     ClassVar,
 )
 

deepmd/calculator.py

@@ -88,9 +88,9 @@ def __init__(
         self,
         model: Union[str, "Path"],
         label: str = "DP",
-        type_dict: Optional[dict[str, int]] = None,
+        type_dict: dict[str, int] | None = None,
         neighbor_list: Optional["NeighborList"] = None,
-        head: Optional[str] = None,
+        head: str | None = None,
         **kwargs: Any,
     ) -> None:
         Calculator.__init__(self, label=label, **kwargs)

deepmd/common.py

@@ -15,14 +15,13 @@
     TYPE_CHECKING,
     Any,
     TypeVar,
-    Union,
     get_args,
 )
 
 try:
     from typing import Literal  # python >=3.8
 except ImportError:
-    from typing_extensions import Literal  # type: ignore
+    from typing import Literal  # type: ignore
 
 import numpy as np
 import yaml
@@ -159,7 +158,7 @@ def j_deprecated(
         return jdata[key]
 
 
-def j_loader(filename: Union[str, Path]) -> dict[str, Any]:
+def j_loader(filename: str | Path) -> dict[str, Any]:
     """Load yaml or json settings file.
 
     Parameters
@@ -188,7 +187,7 @@ def j_loader(filename: Union[str, Path]) -> dict[str, Any]:
         raise TypeError("config file must be json, or yaml/yml")
 
 
-def expand_sys_str(root_dir: Union[str, Path]) -> list[str]:
+def expand_sys_str(root_dir: str | Path) -> list[str]:
     """Recursively iterate over directories taking those that contain `type.raw` file.
 
     Parameters

deepmd/dpmodel/array_api.py

@@ -1,11 +1,11 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Utilities for the array API."""
 
+from collections.abc import (
+    Callable,
+)
 from typing import (
     Any,
-    Callable,
-    Optional,
-    Union,
 )
 
 import array_api_compat
@@ -15,7 +15,7 @@
 )
 
 # Type alias for array_api compatible arrays
-Array = Union[np.ndarray, Any]  # Any to support JAX, PyTorch, etc. arrays
+Array = np.ndarray | Any  # Any to support JAX, PyTorch, etc. arrays
 
 
 def support_array_api(version: str) -> Callable:
@@ -125,7 +125,7 @@ def xp_add_at(x: Array, indices: Array, values: Array) -> Array:
         return x
 
 
-def xp_bincount(x: Array, weights: Optional[Array] = None, minlength: int = 0) -> Array:
+def xp_bincount(x: Array, weights: Array | None = None, minlength: int = 0) -> Array:
     """Counts the number of occurrences of each value in x."""
     xp = array_api_compat.array_namespace(x)
     if array_api_compat.is_numpy_array(x) or array_api_compat.is_jax_array(x):

deepmd/dpmodel/atomic_model/base_atomic_model.py

@@ -2,7 +2,6 @@
 import math
 from typing import (
     Any,
-    Optional,
 )
 
 import array_api_compat
@@ -45,8 +44,8 @@ def __init__(
         type_map: list[str],
         atom_exclude_types: list[int] = [],
         pair_exclude_types: list[tuple[int, int]] = [],
-        rcond: Optional[float] = None,
-        preset_out_bias: Optional[dict[str, Array]] = None,
+        rcond: float | None = None,
+        preset_out_bias: dict[str, Array] | None = None,
     ) -> None:
         super().__init__()
         self.type_map = type_map
@@ -133,7 +132,7 @@ def atomic_output_def(self) -> FittingOutputDef:
         )
 
     def change_type_map(
-        self, type_map: list[str], model_with_new_type_stat: Optional[Any] = None
+        self, type_map: list[str], model_with_new_type_stat: Any | None = None
     ) -> None:
         """Change the type related params to new ones, according to `type_map` and the original one in the model.
         If there are new types in `type_map`, statistics will be updated accordingly to `model_with_new_type_stat` for these new types.
@@ -154,9 +153,9 @@ def forward_common_atomic(
         extended_coord: Array,
         extended_atype: Array,
         nlist: Array,
-        mapping: Optional[Array] = None,
-        fparam: Optional[Array] = None,
-        aparam: Optional[Array] = None,
+        mapping: Array | None = None,
+        fparam: Array | None = None,
+        aparam: Array | None = None,
     ) -> dict[str, Array]:
         """Common interface for atomic inference.
 
@@ -230,9 +229,9 @@ def call(
         extended_coord: Array,
         extended_atype: Array,
         nlist: Array,
-        mapping: Optional[Array] = None,
-        fparam: Optional[Array] = None,
-        aparam: Optional[Array] = None,
+        mapping: Array | None = None,
+        fparam: Array | None = None,
+        aparam: Array | None = None,
     ) -> dict[str, Array]:
         return self.forward_common_atomic(
             extended_coord,

deepmd/dpmodel/atomic_model/dp_atomic_model.py

@@ -1,7 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 from typing import (
     Any,
-    Optional,
 )
 
 from deepmd.dpmodel.array_api import (
@@ -130,9 +129,9 @@ def forward_atomic(
         extended_coord: Array,
         extended_atype: Array,
         nlist: Array,
-        mapping: Optional[Array] = None,
-        fparam: Optional[Array] = None,
-        aparam: Optional[Array] = None,
+        mapping: Array | None = None,
+        fparam: Array | None = None,
+        aparam: Array | None = None,
     ) -> dict[str, Array]:
         """Models' atomic predictions.
 
@@ -177,7 +176,7 @@ def forward_atomic(
         return ret
 
     def change_type_map(
-        self, type_map: list[str], model_with_new_type_stat: Optional[Any] = None
+        self, type_map: list[str], model_with_new_type_stat: Any | None = None
     ) -> None:
         """Change the type related params to new ones, according to `type_map` and the original one in the model.
         If there are new types in `type_map`, statistics will be updated accordingly to `model_with_new_type_stat` for these new types.