move files to src layout

.pre-commit-config.yaml

@@ -25,6 +25,7 @@ repos:
     rev: v1.11.1
     hooks:
       - id: mypy
+        entry: env MYPYPATH=src mypy
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0

pyproject.toml

@@ -172,6 +172,7 @@ repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest
 [tool.ruff]
 target-version = "py39"
 line-length = 120
+output-format = "concise"
 
 [tool.ruff.lint]
 select = ["ALL"]

pymatgen/io/vasp/sets/__init__.py → src/pymatgen/io/vasp/sets/__init__.py

@@ -1,3 +1,7 @@
+"""Re-export all VASP input sets, for more convenient imports and to maintain backwards compatible imports
+following the split up of sets.py into submodules in #3865.
+"""
+
 from __future__ import annotations
 
 from pymatgen.io.vasp.sets.base import (

pymatgen/io/vasp/sets/base.py → src/pymatgen/io/vasp/sets/base.py

@@ -1,3 +1,4 @@
+# ruff: noqa: PGH003
 """
 This module defines the VaspInputSet abstract base class and a concrete implementation for the parameters developed
 and tested by the core team of pymatgen, including the Materials Virtual Lab, Materials Project and the MIT high
@@ -369,7 +370,7 @@ def as_dict(self, verbosity=2):
         return dct
 
     @property  # type: ignore
-    def structure(self) -> Structure:
+    def structure(self) -> Structure:  # noqa: F811
         """Structure."""
         return self._structure
 
@@ -840,7 +841,7 @@ def kpoints(self) -> Kpoints | None:
                 self.structure, kconfig["zero_weighted_reciprocal_density"], self.force_gamma
             )
             sga = SpacegroupAnalyzer(self.structure, symprec=self.sym_prec)
-            mesh = sga.get_ir_reciprocal_mesh(zero_weighted_kpoints.kpts[0])
+            mesh = sga.get_ir_reciprocal_mesh(zero_weighted_kpoints.kpts[0])  # type: ignore[arg-type]
             zero_weighted_kpoints = Kpoints(
                 comment="Uniform grid",
                 style=Kpoints.supported_modes.Reciprocal,

pymatgen/io/vasp/sets/lobster.py → src/pymatgen/io/vasp/sets/lobster.py

@@ -1,3 +1,5 @@
+# ruff: noqa: PGH003
+
 from __future__ import annotations
 
 import warnings

pymatgen/io/vasp/sets/matpes.py → src/pymatgen/io/vasp/sets/matpes.py

@@ -37,7 +37,7 @@ class MatPESStaticSet(VaspInputSet):
     # These are parameters that we will inherit from any previous INCAR supplied. They are mostly parameters related
     # to symmetry and convergence set by Custodian when errors are encountered in a previous run. Given that our goal
     # is to have a strictly homogeneous PES data, all other parameters (e.g., ISMEAR, ALGO, etc.) are not inherited.
-    inherit_incar: list[str] | bool = (  # type: ignore
+    inherit_incar: list[str] | bool = (  # type: ignore  # noqa: PGH003
         "LPEAD",
         "NGX",
         "NGY",

pymatgen/io/vasp/sets/mp.py → src/pymatgen/io/vasp/sets/mp.py

@@ -1,3 +1,5 @@
+# ruff: noqa: PGH003
+
 from __future__ import annotations
 
 import warnings

pymatgen/io/vasp/sets/mvl.py → src/pymatgen/io/vasp/sets/mvl.py

@@ -1,3 +1,5 @@
+# ruff: noqa: PGH003
+
 from __future__ import annotations
 
 from dataclasses import dataclass
@@ -381,7 +383,7 @@ def incar_updates(self) -> dict:
             "LDAU": False,
         }
         # Set NPT-AIMD ENCUT = 1.5 * VASP_default
-        enmax = [self.potcar[i].keywords["ENMAX"] for i in range(self.structure.ntypesp)]  # type: ignore
+        enmax = [self.potcar[i].keywords["ENMAX"] for i in range(self.structure.ntypesp)]  # type: ignore[union-attr]
         updates["ENCUT"] = max(enmax) * 1.5
         return updates