Fix docs

Author: utf

docs/about/license.md

@@ -50,4 +50,3 @@ modify, prepare derivative works, incorporate into other computer
 software, distribute, and sublicense such enhancements or derivative
 works thereof, in binary and source code form.
 ```
-

docs/conf.py

@@ -72,7 +72,7 @@
 napoleon_use_ivar = True
 
 # The suffix(es) of source filenames.
-source_suffix = {'.rst': 'restructuredtext', '.md': 'restructuredtext'}
+source_suffix = {".rst": "restructuredtext", ".md": "restructuredtext"}
 
 mathjax3_config = {
     "tex": {
@@ -92,7 +92,7 @@
 """
 }
 language = "en"
-#html_extra_path = ["images/badge.svg"]
+# html_extra_path = ["images/badge.svg"]
 html_static_path = ["_static"]
 html_css_files = ["custom.css", "github.css"]
 suppress_warnings = ["etoc.toctree"]

src/atomate2/amset/schemas.py

@@ -3,7 +3,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Union
+from typing import Any, Union
 
 import numpy as np
 from emmet.core.math import Matrix3D, Vector3D
@@ -144,7 +144,7 @@ def from_directory(
         dir_name: Union[Path, str],
         additional_fields: dict[str, Any] = None,
         include_mesh: bool = False,
-    ):
+    ) -> "AmsetTaskDocument":
         """Create a task document from a directory containing VASP files.
 
         Parameters

src/atomate2/common/flows/defect.py

@@ -228,23 +228,23 @@ class FormationEnergyMaker(Maker, ABC):
 
             [
                 {
-                    'bulk_dir_name': 'computer1:/folder1',
-                    'bulk_locpot': {...},
-                    'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
-                    'defect_dir_name': 'computer1:/folder2',
-                    'defect_entry': {...},
-                    'defect_locpot': {...},
-                    'defect_uuid': 'e9af2725-d63c-49b8-a01f-391540211750'
+                    "bulk_dir_name": "computer1:/folder1",
+                    "bulk_locpot": {...},
+                    "bulk_uuid": "48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3",
+                    "defect_dir_name": "computer1:/folder2",
+                    "defect_entry": {...},
+                    "defect_locpot": {...},
+                    "defect_uuid": "e9af2725-d63c-49b8-a01f-391540211750",
                 },
                 {
-                    'bulk_dir_name': 'computer1:/folder3',
-                    'bulk_locpot': {...},
-                    'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
-                    'defect_dir_name': 'computer1:/folder4',
-                    'defect_entry': {...},
-                    'defect_locpot': {...},
-                    'defect_uuid': 'a1c31095-0494-4eed-9862-95311f80a993'
-                }
+                    "bulk_dir_name": "computer1:/folder3",
+                    "bulk_locpot": {...},
+                    "bulk_uuid": "48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3",
+                    "defect_dir_name": "computer1:/folder4",
+                    "defect_entry": {...},
+                    "defect_locpot": {...},
+                    "defect_uuid": "a1c31095-0494-4eed-9862-95311f80a993",
+                },
             ]
 
     """

src/atomate2/lobster/schemas.py

@@ -1319,7 +1319,7 @@ def _get_strong_bonds(
 def read_saved_json(
     filename: str, pymatgen_objs: bool = True, query: str = "structure"
 ) -> dict[str, Any]:
-    """
+    r"""
     Read the data from  \*.json.gz files corresponding to query.
 
     Uses ijson to parse specific keys(memory efficient)

src/atomate2/vasp/flows/defect.py

@@ -142,23 +142,23 @@ class FormationEnergyMaker(defect_flows.FormationEnergyMaker):
 
             [
                 {
-                    'bulk_dir_name': 'computer1:/folder1',
-                    'bulk_locpot': {...},
-                    'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
-                    'defect_dir_name': 'computer1:/folder2',
-                    'defect_entry': {...},
-                    'defect_locpot': {...},
-                    'defect_uuid': 'e9af2725-d63c-49b8-a01f-391540211750'
+                    "bulk_dir_name": "computer1:/folder1",
+                    "bulk_locpot": {...},
+                    "bulk_uuid": "48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3",
+                    "defect_dir_name": "computer1:/folder2",
+                    "defect_entry": {...},
+                    "defect_locpot": {...},
+                    "defect_uuid": "e9af2725-d63c-49b8-a01f-391540211750",
                 },
                 {
-                    'bulk_dir_name': 'computer1:/folder3',
-                    'bulk_locpot': {...},
-                    'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
-                    'defect_dir_name': 'computer1:/folder4',
-                    'defect_entry': {...},
-                    'defect_locpot': {...},
-                    'defect_uuid': 'a1c31095-0494-4eed-9862-95311f80a993'
-                }
+                    "bulk_dir_name": "computer1:/folder3",
+                    "bulk_locpot": {...},
+                    "bulk_uuid": "48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3",
+                    "defect_dir_name": "computer1:/folder4",
+                    "defect_entry": {...},
+                    "defect_locpot": {...},
+                    "defect_uuid": "a1c31095-0494-4eed-9862-95311f80a993",
+                },
             ]
 
     """