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mkdocs.yml
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mkdocs.yml
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site_name: "absolv"
site_description: "Absolute solvation free energy calculations using OpenMM"
site_url: "https://github.com/SimonBoothroyd/absolv"
repo_url: "https://github.com/SimonBoothroyd/absolv"
repo_name: "SimonBoothroyd/absolv"
site_dir: "site"
watch: [mkdocs.yml, README.md, absolv/, docs]
copyright: Copyright © 2023 Simon Boothroyd
edit_uri: edit/main/docs/
validation:
omitted_files: warn
absolute_links: warn
unrecognized_links: warn
extra:
version:
provider: mike
nav:
- Home:
- Overview: index.md
- Guide:
- user-guide/overview.md
- user-guide/theory.md
- user-guide/transformations.md
- reproducibility.md
- API reference: reference/
- Development: development.md
theme:
name: material
features:
- announce.dismiss
- content.code.annotate
- content.code.copy
- content.tooltips
- navigation.footer
- navigation.indexes
- navigation.sections
- navigation.tabs
- navigation.tabs.sticky
- navigation.top
- search.highlight
- search.suggest
- toc.follow
palette:
- media: "(prefers-color-scheme: light)"
scheme: default
primary: teal
accent: purple
toggle:
icon: material/weather-sunny
name: Switch to dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: black
accent: lime
toggle:
icon: material/weather-night
name: Switch to light mode
markdown_extensions:
- attr_list
- md_in_html
- def_list
- admonition
- footnotes
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.superfences
- pymdownx.magiclink
- pymdownx.snippets:
check_paths: true
- pymdownx.details
- pymdownx.arithmatex:
generic: true
- pymdownx.tabbed:
alternate_style: true
- toc:
permalink: "#"
plugins:
- autorefs
- search
- gen-files:
scripts:
- docs/scripts/gen_ref_pages.py
- literate-nav:
nav_file: SUMMARY.md
- bibtex:
bib_file: "docs/references.bib"
- mkdocstrings:
handlers:
python:
paths: [absolv/]
import:
- https://parmed.github.io/ParmEd/html/objects.inv
- http://docs.openmm.org/latest/api-python/objects.inv
- https://www.mdtraj.org/1.9.6/objects.inv
options:
extensions: [ griffe_pydantic ]
docstring_options:
ignore_init_summary: true
returns_multiple_items: false
returns_named_value: false
docstring_section_style: list
heading_level: 1
inherited_members: true
merge_init_into_class: true
separate_signature: true
show_root_heading: true
show_root_full_path: false
show_signature_annotations: true
show_symbol_type_heading: true
show_symbol_type_toc: true
signature_crossrefs: true
summary: true
members_order: source
extra_javascript:
- javascripts/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js