molforge/mkdocs.yml at master · DoctorDean/molforge · GitHub

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site_name: molforge
site_description: A unified Python library for structural bioinformatics, MD, protein engineering, and ML.
site_url: https://doctordean.github.io/molforge/
repo_url: https://github.com/DoctorDean/molforge
repo_name: DoctorDean/molforge
edit_uri: edit/master/docs/

docs_dir: docs

extra_css:
  - stylesheets/extra.css

theme:
  name: material
  custom_dir: docs/overrides
  logo: assets/emblem.png
  favicon: assets/favicon.png
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.top
    - navigation.indexes
    - navigation.footer
    - content.code.copy
    - content.code.annotate
    - content.action.edit
    - search.suggest
    - search.highlight
    - toc.follow
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode

nav:
  - Home: index.md
  - Getting started:
      - Installation: getting-started/installation.md
      - Quickstart: getting-started/quickstart.md
      - Coming from another library: getting-started/migrating.md
  - User guide:
      - Data model: guide/data-model.md
      - File I/O: guide/io.md
      - Engine wrappers: guide/wrappers.md
      - Plugins: guide/plugins.md
      - Validation: guide/validation.md
      - Ensembles: guide/ensembles.md
      - Design loop: guide/design.md
      - Scoring: guide/scoring.md
      - Reproducibility: guide/reproducibility.md
  - Cookbook:
      - Overview: cookbook/index.md
      - "End to end: design → reproduce": cookbook/end-to-end.md
      - Fold a sequence: cookbook/folding.md
      - Multi-component cofolding: cookbook/multi-component-folding.md
      - Fold then dock: cookbook/folding-then-docking.md
      - Prepare for MD: cookbook/prep-for-md.md
      - MD and RMSD: cookbook/md-and-rmsd.md
      - Design then refold: cookbook/design-then-refold.md
      - Inspect provenance: cookbook/inspect-provenance.md
      - Validate structures: cookbook/validating-structures.md
      - Caching results: cookbook/caching-results.md
      - Rank binders (MM/GBSA): cookbook/ranking-binders.md
      - Rank binders (FEP): cookbook/rank-binders-fep.md
      - Absolute binding FEP: cookbook/absolute-binding-fep.md
      - Work with small molecules: cookbook/small-molecules.md
      - Fetch and search databases: cookbook/fetch-and-search.md
      - "Choosing: folding engines": cookbook/choosing-folding.md
      - "Choosing: docking engines": cookbook/choosing-docking.md
      - "Choosing: generative engines": cookbook/choosing-generative.md
  - Walkthroughs:
      - Sequences: walkthroughs/01_sequences.ipynb
      - Structures: walkthroughs/02_structures.ipynb
      - MD simulations: walkthroughs/03_md_simulations.ipynb
      - Docking: walkthroughs/04_docking.ipynb
      - ML featurization: walkthroughs/05_ml_featurization.ipynb
      - Plugin authoring: walkthroughs/06_plugin_authoring.ipynb
  - Examples:
      - Overview: examples/index.md
      - Cross-engine validation: examples/cross_engine_validation.ipynb
      - De novo design: examples/de_novo_design.ipynb
      - End-to-end design: examples/end_to_end_design.ipynb
  - Architecture:
      - Overview: architecture/overview.md
      - Binding free energy: architecture/free-energy.md
      - Performance benchmarks: architecture/benchmarks.md
      - API stability: architecture/api-stability.md
      - Roadmap: architecture/roadmap.md
  - API reference:
      - molforge.core: reference/core.md
      - molforge.io: reference/io.md
      - molforge.sequence: reference/sequence.md
      - molforge.structure: reference/structure.md
      - molforge.ml: reference/ml.md
      - molforge.metrics: reference/metrics.md
      - molforge.validation: reference/validation.md
      - molforge.ensembles: reference/ensembles.md
      - molforge.design: reference/design.md
      - molforge.scoring: reference/scoring.md
      - molforge.reproducibility: reference/reproducibility.md
      - molforge.md: reference/md.md
      - molforge.prep: reference/prep.md
      - molforge.docking: reference/docking.md
      - molforge.chem: reference/chem.md
      - molforge.freeenergy: reference/freeenergy.md
      - molforge.plugins: reference/plugins.md
      - molforge.parallel: reference/parallel.md
      - molforge.cache: reference/cache.md
      - molforge.wrappers:
          - Overview: reference/wrappers.md
          - molforge.wrappers.folding: reference/wrappers/folding.md
          - molforge.wrappers.docking: reference/wrappers/docking.md
          - molforge.wrappers.md: reference/wrappers/md.md
          - molforge.wrappers.freeenergy: reference/wrappers/freeenergy.md
          - molforge.wrappers.generative: reference/wrappers/generative.md
          - molforge.wrappers.pockets: reference/wrappers/pockets.md
  - Project:
      - Releasing: RELEASING.md

plugins:
  - search
  - social:
      # Card generation needs cairosvg + system cairo (installed in the docs
      # CI job). Gate on the CI env var so local `mkdocs serve` / build works
      # without those system libraries; cards are still generated on deploy.
      cards: !ENV [CI, false]
      cards_layout_options:
        background_color: "#30419b"
        color: "#ffffff"
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [src]
          options:
            docstring_style: google
            show_root_heading: true
            show_root_full_path: false
            show_source: false
            show_signature_annotations: true
            separate_signature: true
            merge_init_into_class: true
            members_order: source
            filters: ["!^_"]
            heading_level: 2
  - mkdocs-jupyter:
      # Notebooks are authored in the top-level notebooks/ directory and
      # copied into docs/walkthroughs/ and docs/examples/ at build time
      # by the docs/_hooks/copy_notebooks.py hook (see `hooks:` below).
      # The copies are git-ignored. CI runs the notebooks separately;
      # here we just render the already-baked outputs.
      execute: false
      include_source: true
      ignore_h1_titles: true
      include: ["walkthroughs/*.ipynb", "examples/*.ipynb"]

# Build hooks. copy_notebooks.py stages the canonical notebooks/ files
# into docs/ at build time so mkdocs-jupyter can render them without
# symlinks (which break on Windows tarball extraction and on CI).
hooks:
  - docs/_hooks/copy_notebooks.py

markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - toc:
      permalink: true
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/DoctorDean/molforge
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/molforge/