ruff automatic type annotations (#3498)

* rm pymatgen/cli/pmg_query.py which used the recently removed legacy MPRester

ruff pre-commit enable --unsafe-fixes

* ruff pymatgen/core --select ANN --fix --unsafe-fixes

* ruff pymatgen/electronic_structure --select ANN --fix --unsafe-fixes

* remove np.array call

* del broken do_query import from pymatgen.cli.pmg_query

* split test_entrypoint into pmg_analyze, pmg_structure, pmg_diff

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     rev: v0.1.8
     hooks:
       - id: ruff
-        args: [--fix]
+        args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks

pymatgen/cli/__init__.py

@@ -1,6 +1,3 @@
-# Copyright (c) Materials Virtual Lab.
-# Distributed under the terms of the BSD License.
-
 """This package contains various command line interfaces for common
 pymatgen functionality such as file conversion, etc. Entry points to these
 interfaces are defined in setup.py.

pymatgen/cli/get_environment.py

@@ -11,7 +11,7 @@
 __author__ = "David Waroquiers"
 
 
-def main():
+def main() -> int:
     """Main function for get_environment CLI."""
     parser = ArgumentParser(description="Welcome to the Chemical Environment Package.")
     setup_help = "Used to setup the configuration of the package "
@@ -43,6 +43,8 @@ def main():
 
     print("Thank you for using the ChemEnv package")
 
+    return 0
+
 
 if __name__ == "__main__":
     raise SystemExit(main())

pymatgen/cli/pmg.py

@@ -13,7 +13,6 @@
 from pymatgen.cli.pmg_config import configure_pmg
 from pymatgen.cli.pmg_plot import plot
 from pymatgen.cli.pmg_potcar import generate_potcar
-from pymatgen.cli.pmg_query import do_query
 from pymatgen.cli.pmg_structure import analyze_structures
 from pymatgen.core import SETTINGS
 from pymatgen.core.structure import Structure
@@ -244,7 +243,6 @@ def main():
         "By default, the Materials Project id, formula, spacegroup, "
         "energy per atom, energy above hull are shown.",
     )
-    parser_query.set_defaults(func=do_query)
 
     parser_plot = subparsers.add_parser("plot", help="Plotting tool for DOS, CHGCAR, XRD, etc.")
     group = parser_plot.add_mutually_exclusive_group(required=True)

pymatgen/core/bonds.py

@@ -33,7 +33,7 @@ def _load_bond_length_data():
 class CovalentBond:
     """Defines a covalent bond between two sites."""
 
-    def __init__(self, site1: Site, site2: Site):
+    def __init__(self, site1: Site, site2: Site) -> None:
         """Initializes a covalent bond between two sites.
 
         Args:
@@ -103,7 +103,7 @@ def is_bonded(site1, site2, tol: float = 0.2, bond_order: float | None = None, d
             return dist < (1 + tol) * default_bl
         raise ValueError(f"No bond data for elements {syms[0]} - {syms[1]}")
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return f"Covalent bond between {self.site1} and {self.site2}"