From 593f96286c7d5f97eb4f2a9dc44f6096af5be58b Mon Sep 17 00:00:00 2001 From: utf Date: Thu, 18 Jul 2024 16:06:21 +0100 Subject: [PATCH] Fix docs --- docs/about/license.md | 1 - docs/conf.py | 4 ++-- src/atomate2/amset/schemas.py | 4 ++-- src/atomate2/common/flows/defect.py | 30 ++++++++++++++--------------- src/atomate2/lobster/schemas.py | 2 +- src/atomate2/vasp/flows/defect.py | 30 ++++++++++++++--------------- 6 files changed, 35 insertions(+), 36 deletions(-) diff --git a/docs/about/license.md b/docs/about/license.md index 4efbf3c1f9..9cdf9295a8 100644 --- a/docs/about/license.md +++ b/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. ``` - diff --git a/docs/conf.py b/docs/conf.py index aa2fee5d44..3baba5e939 100644 --- a/docs/conf.py +++ b/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"] diff --git a/src/atomate2/amset/schemas.py b/src/atomate2/amset/schemas.py index 7116614f9a..ef0083916d 100644 --- a/src/atomate2/amset/schemas.py +++ b/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 diff --git a/src/atomate2/common/flows/defect.py b/src/atomate2/common/flows/defect.py index dc2fd34575..b2761d9f00 100644 --- a/src/atomate2/common/flows/defect.py +++ b/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", + }, ] """ diff --git a/src/atomate2/lobster/schemas.py b/src/atomate2/lobster/schemas.py index 293d2cfe15..23ca83c07a 100644 --- a/src/atomate2/lobster/schemas.py +++ b/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) diff --git a/src/atomate2/vasp/flows/defect.py b/src/atomate2/vasp/flows/defect.py index fbc40861be..143466a27a 100644 --- a/src/atomate2/vasp/flows/defect.py +++ b/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", + }, ] """