chore: improve type annotations (#659)

I give up fix type annotations in all files, but it's meaningful to fix
the top-module files `dpdata/*.py`.

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

## Summary by CodeRabbit

- **New Features**
  - Added `name` property to `DPDataCalculator` class.
  - Introduced assertion for `rdkit_mol` in bond order system.

- **Improvements**
  - Enhanced type hinting across various functions and methods.
- Added decorators and type assertion checks for better code validation.

- **Maintenance**
- Introduced a GitHub Actions workflow for running Pyright type checker.
  - Updated dependencies and configurations in `pyproject.toml`.

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

---------

Signed-off-by: Jinzhe Zeng <[email protected]>

Author: njzjz

.github/workflows/pyright.yml

@@ -0,0 +1,19 @@
+on:
+  - push
+  - pull_request
+
+name: Type checker
+jobs:
+  pyright:
+    name: pyright
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - run: pip install uv
+    - run: uv pip install --system -e .[amber,ase,pymatgen] rdkit openbabel-wheel
+    - uses: jakebailey/pyright-action@v2
+      with:
+        version: 1.1.363

benchmark/test_import.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import subprocess
 import sys
 

docs/conf.py

@@ -11,6 +11,8 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+from __future__ import annotations
+
 import os
 import subprocess as sp
 import sys

docs/make_format.py

@@ -1,8 +1,15 @@
+from __future__ import annotations
+
 import csv
 import os
+import sys
 from collections import defaultdict
 from inspect import Parameter, Signature, cleandoc, signature
-from typing import Literal
+
+if sys.version_info >= (3, 8):
+    from typing import Literal
+else:
+    from typing_extensions import Literal
 
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
 from numpydoc.docscrape_sphinx import SphinxDocString

docs/nb/try_dpdata.ipynb

@@ -13,6 +13,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "import dpdata"
    ]
   },

dpdata/__about__.py

@@ -1 +1,3 @@
+from __future__ import annotations
+
 __version__ = "unknown"

dpdata/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from . import lammps, md, vasp
 from .bond_order_system import BondOrderSystem
 from .system import LabeledSystem, MultiSystems, System

dpdata/__main__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from dpdata.cli import dpdata_cli
 
 if __name__ == "__main__":

dpdata/abacus/md.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 import warnings
 

dpdata/abacus/relax.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 
 import numpy as np