breaking: drop Python 3.8 support (#4185)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

## Release Notes

- **New Features**
- Introduced new functionality for handling input data conversion
between different versions.
- Added `EnvMatStatSe` class for enhanced environmental matrix
statistics calculations.
- Implemented a mechanism to track the status of atoms (real vs.
virtual) in `BaseAtomicModel`.

- **Bug Fixes**
- Updated Python version requirements across documentation and
configuration files to Python 3.9 or above.

- **Documentation**
- Updated installation guides to reflect the new Python version
requirement and clarified virtual environment setup instructions.

- **Chores**
- Refined dependency management in `pyproject.toml` to support newer
Python versions and improve version control.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/test_python.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         group: [1, 2, 3, 4, 5, 6]
-        python: ["3.8", "3.12"]
+        python: ["3.9", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -34,7 +34,7 @@ jobs:
         # existing TensorFlow package. Currently, it uses
         # TensorFlow in the build dependency, but if it
         # changes, setting `TENSORFLOW_ROOT`.
-        TENSORFLOW_VERSION: ${{ matrix.python == '3.8' && '2.13.1' || '2.16.1' }}
+        TENSORFLOW_VERSION: 2.16.1
         DP_ENABLE_PYTORCH: 1
         DP_BUILD_TESTING: 1
         UV_EXTRA_INDEX_URL: "https://pypi.anaconda.org/njzjz/simple https://pypi.anaconda.org/mpi4py/simple"
@@ -69,7 +69,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.8", "3.12"]
+        python: ["3.9", "3.12"]
     needs: testpython
     steps:
     - name: Get durations from cache

backend/dp_backend.py

@@ -1,10 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """A PEP-517 backend to find TensorFlow."""
 
-from typing import (
-    List,
-)
-
 from scikit_build_core import build as _orig
 
 from .find_pytorch import (
@@ -26,7 +22,7 @@
 ]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> list[str]:
     return __all__
 
 
@@ -42,7 +38,7 @@ def __dir__() -> List[str]:
 
 def get_requires_for_build_wheel(
     config_settings: dict,
-) -> List[str]:
+) -> list[str]:
     return (
         _orig.get_requires_for_build_wheel(config_settings)
         + find_tensorflow()[1]
@@ -52,7 +48,7 @@ def get_requires_for_build_wheel(
 
 def get_requires_for_build_editable(
     config_settings: dict,
-) -> List[str]:
+) -> list[str]:
     return (
         _orig.get_requires_for_build_editable(config_settings)
         + find_tensorflow()[1]

backend/dynamic_metadata.py

@@ -4,8 +4,6 @@
     Path,
 )
 from typing import (
-    Dict,
-    List,
     Optional,
 )
 
@@ -27,13 +25,13 @@
 __all__ = ["dynamic_metadata"]
 
 
-def __dir__() -> List[str]:
+def __dir__() -> list[str]:
     return __all__
 
 
 def dynamic_metadata(
     field: str,
-    settings: Optional[Dict[str, object]] = None,
+    settings: Optional[dict[str, object]] = None,
 ):
     assert field in ["optional-dependencies", "entry-points", "scripts"]
     _, _, find_libpython_requires, extra_scripts, tf_version, pt_version = (

backend/find_pytorch.py

@@ -18,9 +18,7 @@
     get_path,
 )
 from typing import (
-    List,
     Optional,
-    Tuple,
     Union,
 )
 
@@ -30,7 +28,7 @@
 
 
 @lru_cache
-def find_pytorch() -> Tuple[Optional[str], List[str]]:
+def find_pytorch() -> tuple[Optional[str], list[str]]:
     """Find PyTorch library.
 
     Tries to find PyTorch in the order of:

backend/find_tensorflow.py

@@ -17,9 +17,7 @@
     get_path,
 )
 from typing import (
-    List,
     Optional,
-    Tuple,
     Union,
 )
 
@@ -29,7 +27,7 @@
 
 
 @lru_cache
-def find_tensorflow() -> Tuple[Optional[str], List[str]]:
+def find_tensorflow() -> tuple[Optional[str], list[str]]:
     """Find TensorFlow library.
 
     Tries to find TensorFlow in the order of:

backend/read_env.py

@@ -5,9 +5,6 @@
 from functools import (
     lru_cache,
 )
-from typing import (
-    Tuple,
-)
 
 from packaging.version import (
     Version,
@@ -24,7 +21,7 @@
 
 
 @lru_cache
-def get_argument_from_env() -> Tuple[str, list, list, dict, str, str]:
+def get_argument_from_env() -> tuple[str, list, list, dict, str, str]:
     """Get the arguments from environment variables.
 
     The environment variables are assumed to be not changed during the build.

deepmd/backend/backend.py

@@ -10,9 +10,6 @@
     TYPE_CHECKING,
     Callable,
     ClassVar,
-    Dict,
-    List,
-    Type,
 )
 
 from deepmd.utils.plugin import (
@@ -45,7 +42,7 @@ class Backend(PluginVariant, make_plugin_registry("backend")):
     """
 
     @staticmethod
-    def get_backend(key: str) -> Type["Backend"]:
+    def get_backend(key: str) -> type["Backend"]:
         """Get the backend by key.
 
         Parameters
@@ -61,7 +58,7 @@ def get_backend(key: str) -> Type["Backend"]:
         return Backend.get_class_by_type(key)
 
     @staticmethod
-    def get_backends() -> Dict[str, Type["Backend"]]:
+    def get_backends() -> dict[str, type["Backend"]]:
         """Get all the registered backend names.
 
         Returns
@@ -74,7 +71,7 @@ def get_backends() -> Dict[str, Type["Backend"]]:
     @staticmethod
     def get_backends_by_feature(
         feature: "Backend.Feature",
-    ) -> Dict[str, Type["Backend"]]:
+    ) -> dict[str, type["Backend"]]:
         """Get all the registered backend names with a specific feature.
 
         Parameters
@@ -94,7 +91,7 @@ def get_backends_by_feature(
         }
 
     @staticmethod
-    def detect_backend_by_model(filename: str) -> Type["Backend"]:
+    def detect_backend_by_model(filename: str) -> type["Backend"]:
         """Detect the backend of the given model file.
 
         Parameters
@@ -128,7 +125,7 @@ class Feature(Flag):
 
     features: ClassVar[Feature] = Feature(0)
     """The features of the backend."""
-    suffixes: ClassVar[List[str]] = []
+    suffixes: ClassVar[list[str]] = []
     """The supported suffixes of the saved model.
 
     The first element is considered as the default suffix."""
@@ -157,7 +154,7 @@ def entry_point_hook(self) -> Callable[["Namespace"], None]:
 
     @property
     @abstractmethod
-    def deep_eval(self) -> Type["DeepEvalBackend"]:
+    def deep_eval(self) -> type["DeepEvalBackend"]:
         """The Deep Eval backend of the backend.
 
         Returns
@@ -169,7 +166,7 @@ def deep_eval(self) -> Type["DeepEvalBackend"]:
 
     @property
     @abstractmethod
-    def neighbor_stat(self) -> Type["NeighborStat"]:
+    def neighbor_stat(self) -> type["NeighborStat"]:
         """The neighbor statistics of the backend.
 
         Returns

deepmd/backend/dpmodel.py

@@ -3,8 +3,6 @@
     TYPE_CHECKING,
     Callable,
     ClassVar,
-    List,
-    Type,
 )
 
 from deepmd.backend.backend import (
@@ -37,7 +35,7 @@ class DPModelBackend(Backend):
         Backend.Feature.DEEP_EVAL | Backend.Feature.NEIGHBOR_STAT | Backend.Feature.IO
     )
     """The features of the backend."""
-    suffixes: ClassVar[List[str]] = [".dp", ".yaml", ".yml"]
+    suffixes: ClassVar[list[str]] = [".dp", ".yaml", ".yml"]
     """The suffixes of the backend."""
 
     def is_available(self) -> bool:
@@ -62,7 +60,7 @@ def entry_point_hook(self) -> Callable[["Namespace"], None]:
         raise NotImplementedError(f"Unsupported backend: {self.name}")
 
     @property
-    def deep_eval(self) -> Type["DeepEvalBackend"]:
+    def deep_eval(self) -> type["DeepEvalBackend"]:
         """The Deep Eval backend of the backend.
 
         Returns
@@ -77,7 +75,7 @@ def deep_eval(self) -> Type["DeepEvalBackend"]:
         return DeepEval
 
     @property
-    def neighbor_stat(self) -> Type["NeighborStat"]:
+    def neighbor_stat(self) -> type["NeighborStat"]:
         """The neighbor statistics of the backend.
 
         Returns

deepmd/backend/jax.py

@@ -6,8 +6,6 @@
     TYPE_CHECKING,
     Callable,
     ClassVar,
-    List,
-    Type,
 )
 
 from deepmd.backend.backend import (
@@ -41,7 +39,7 @@ class JAXBackend(Backend):
         # | Backend.Feature.IO
     )
     """The features of the backend."""
-    suffixes: ClassVar[List[str]] = []
+    suffixes: ClassVar[list[str]] = []
     """The suffixes of the backend."""
 
     def is_available(self) -> bool:
@@ -66,7 +64,7 @@ def entry_point_hook(self) -> Callable[["Namespace"], None]:
         raise NotImplementedError
 
     @property
-    def deep_eval(self) -> Type["DeepEvalBackend"]:
+    def deep_eval(self) -> type["DeepEvalBackend"]:
         """The Deep Eval backend of the backend.
 
         Returns
@@ -77,7 +75,7 @@ def deep_eval(self) -> Type["DeepEvalBackend"]:
         raise NotImplementedError
 
     @property
-    def neighbor_stat(self) -> Type["NeighborStat"]:
+    def neighbor_stat(self) -> type["NeighborStat"]:
         """The neighbor statistics of the backend.
 
         Returns

deepmd/backend/pytorch.py

@@ -6,8 +6,6 @@
     TYPE_CHECKING,
     Callable,
     ClassVar,
-    List,
-    Type,
 )
 
 from deepmd.backend.backend import (
@@ -41,7 +39,7 @@ class PyTorchBackend(Backend):
         | Backend.Feature.IO
     )
     """The features of the backend."""
-    suffixes: ClassVar[List[str]] = [".pth", ".pt"]
+    suffixes: ClassVar[list[str]] = [".pth", ".pt"]
     """The suffixes of the backend."""
 
     def is_available(self) -> bool:
@@ -68,7 +66,7 @@ def entry_point_hook(self) -> Callable[["Namespace"], None]:
         return deepmd_main
 
     @property
-    def deep_eval(self) -> Type["DeepEvalBackend"]:
+    def deep_eval(self) -> type["DeepEvalBackend"]:
         """The Deep Eval backend of the backend.
 
         Returns
@@ -81,7 +79,7 @@ def deep_eval(self) -> Type["DeepEvalBackend"]:
         return DeepEvalPT
 
     @property
-    def neighbor_stat(self) -> Type["NeighborStat"]:
+    def neighbor_stat(self) -> type["NeighborStat"]:
         """The neighbor statistics of the backend.
 
         Returns

deepmd/backend/suffix.py

@@ -6,7 +6,6 @@
 )
 from typing import (
     Optional,
-    Type,
     Union,
 )
 
@@ -18,7 +17,7 @@
 def format_model_suffix(
     filename: str,
     feature: Optional[Backend.Feature] = None,
-    preferred_backend: Optional[Union[str, Type["Backend"]]] = None,
+    preferred_backend: Optional[Union[str, type["Backend"]]] = None,
     strict_prefer: Optional[bool] = None,
 ) -> str:
     """Check and format the suffixes of a filename.

deepmd/backend/tensorflow.py

@@ -6,8 +6,6 @@
     TYPE_CHECKING,
     Callable,
     ClassVar,
-    List,
-    Type,
 )
 
 from deepmd.backend.backend import (
@@ -41,7 +39,7 @@ class TensorFlowBackend(Backend):
         | Backend.Feature.IO
     )
     """The features of the backend."""
-    suffixes: ClassVar[List[str]] = [".pb"]
+    suffixes: ClassVar[list[str]] = [".pb"]
     """The suffixes of the backend."""
 
     def is_available(self) -> bool:
@@ -77,7 +75,7 @@ def entry_point_hook(self) -> Callable[["Namespace"], None]:
         return deepmd_main
 
     @property
-    def deep_eval(self) -> Type["DeepEvalBackend"]:
+    def deep_eval(self) -> type["DeepEvalBackend"]:
         """The Deep Eval backend of the backend.
 
         Returns
@@ -90,7 +88,7 @@ def deep_eval(self) -> Type["DeepEvalBackend"]:
         return DeepEvalTF
 
     @property
-    def neighbor_stat(self) -> Type["NeighborStat"]:
+    def neighbor_stat(self) -> type["NeighborStat"]:
         """The neighbor statistics of the backend.
 
         Returns