mkdocs.yml

# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json

site_name: Automated Research Assistant
repo_url: 'https://github.com/autoresearch/autora/'
site_url: 'https://autoresearch.github.io/autora/'
edit_uri: 'blob/main/docs/'

extra:
  colab_base_url: 'https://colab.research.google.com/github/AutoResearch/autora/blob/gh-pages/'

theme:
  name: material
  logo: img/logo.png
  palette:
    # Palette toggle for light mode
    - scheme: default
      primary: black
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode

    # Palette toggle for dark mode
    - scheme: slate
      primary: black
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  custom_dir: mkdocs/overrides
  features:
    - navigation.indexes
    - content.code.copy
    - announce.dismiss

plugins:
  multirepo:
    nav_repos:
      - name: core
        import_url: "https://github.com/autoresearch/autora-core/?branch=main"
        imports: [
          "docs/",
          "src/",
        ]
      - name: synthetic
        import_url: "https://github.com/AutoResearch/autora-synthetic/?branch=main"
        imports: [
          "src/"
        ]
      - name: user-cookiecutter
        import_url: "https://github.com/autoresearch/autora-user-cookiecutter/?branch=main"
        imports: [
          "docs/",
        ]
      - name: darts
        import_url: "https://github.com/autoresearch/autora-theorist-darts/?branch=main"
        imports: [ "src/" ]
      - name: bsr
        import_url: "https://github.com/autoresearch/autora-theorist-bsr/?branch=main"
        imports: [ "src/" ]
      - name: bms
        import_url: "https://github.com/autoresearch/autora-theorist-bms/?branch=main"
        imports: [ "src/" ]
      - name: novelty
        import_url: "https://github.com/autoresearch/autora-experimentalist-novelty?branch=main"
        imports: [ "src/" ]
      - name: inequality
        import_url: "https://github.com/autoresearch/autora-experimentalist-inequality/?branch=main"
        imports: [ "src/" ]
      - name: nearest-value
        import_url: "https://github.com/autoresearch/autora-experimentalist-nearest-value/?branch=main"
        imports: [ "src/" ]
      - name: disagreement
        import_url: "https://github.com/autoresearch/autora-experimentalist-model-disagreement/?branch=main"
        imports: [ "src/" ]
      - name: uncertainty
        import_url: "https://github.com/autoresearch/autora-experimentalist-uncertainty/?branch=main"
        imports: [ "src/" ]
      - name: leverage
        import_url: "https://github.com/autoresearch/autora-experimentalist-leverage/?branch=main"
        imports: [ "src/" ]
      - name: falsification
        import_url: "https://github.com/autoresearch/autora-experimentalist-falsification/?branch=main"
        imports: [ "src/" ]
      - name: mixture
        import_url: "https://github.com/blinodelka/mixture_experimental_strategies/?branch=main"
        imports: [ "src/" ]
      - name: prediction-filter
        import_url: "https://github.com/AutoResearch/autora-experimentalist-prediction-filter/?branch=main"
        imports: ["src/"]

  gen-files:
    scripts: [ "mkdocs/generate_code_reference.py" ]
  literate-nav: {}
  mkdocstrings:
    handlers:
      python:
        paths: [
          # from nav_repos above
          "./temp_dir/core/src/",
          "./temp_dir/darts/src/",
          "./temp_dir/bms/src/",
          "./temp_dir/bsr/src/",
          "./temp_dir/novelty/src/",
          "./temp_dir/inequality/src/",
          "./temp_dir/nearest-value/src/",
          "./temp_dir/disagreement/src/",
          "./temp_dir/uncertainty/src/",
          "./temp_dir/leverage/src/",
          "./temp_dir/falsification/src/",
          "./temp_dir/mixture/src/",
          "./temp_dir/synthetic/src/",
          "./temp_dir/prediction-filter/src/",
        ]
        import:
          - https://scikit-learn.org/stable/objects.inv


  mkdocs-jupyter: # required to convert Jupyter notebooks
    include_source: true
    execute: false
    ignore_h1_titles: true
    ignore: [
      # ignore all files in the src/ directories – these don't need to be converted
      # this is needed because the pathlib PurePath.match doesn't allow for "**" patterns
      # (see https://github.com/python/cpython/pull/11171)
      # We don't want to just ignore all python files, because someone may at some point want to
      # use a .py notebook.
      # Alternatively, we could just have ignore: [ "*.py" ], but then we wouldn't be able to use
      #
      "src/autora/*.py",
      "src/autora/*/*.py",
      "src/autora/*/*/*.py",
      "src/autora/*/*/*/*.py",
      "src/autora/*/*/*/*/*.py",
    ]

  search: {}

hooks:
  - mkdocs/hooks.py

markdown_extensions:
  admonition: {}
  pymdownx.details: {}
  pymdownx.superfences: {}
  pymdownx.arithmatex: # required for equation display
    generic: true
  pymdownx.snippets: { url_download: True }
  pymdownx.tabbed:
    alternate_style: true

extra_javascript: [
  # requirements for pymdownx.arithmetex:
  "javascripts/mathjax.js",
  "https://polyfill.io/v3/polyfill.min.js?features=es6",
  "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js"
]

nav:
- Introduction: 'index.md'
- Tutorials:
  - Home: 'tutorials/index.md'
  - I - Components: 'tutorials/basic/Tutorial I Components.ipynb'
  - II - Loop Constructs: 'tutorials/basic/Tutorial II Loop Constructs.ipynb'
  - III - Functional Workflow: 'tutorials/basic/Tutorial III Functional Workflow.ipynb'
  - IV - Customization: 'tutorials/basic/Tutorial IV Customization.ipynb'
- Examples:
  - Equation Discovery: 'theorist/Equation Discovery.ipynb'
  - Experimentalists: 'tutorials/Experimentalist.ipynb'
  - Online Closed-Loop Discovery:
    - 'user-cookiecutter/docs/index.md'
- User Guide:
  - Installation: 'installation.md'
  - Terminology: 'terminology.md'
  - Core:
    - Home: 'core/docs/index.md'
    - State: 'core/docs/The State Mechanism.ipynb'
    - Variable: 'core/docs/Variable.ipynb'
    - Examples:
      - 'core/docs/cycle/Basic Introduction to Functions and States.ipynb'
      - 'core/docs/cycle/Combining Experimentalists with State.ipynb'
      - 'core/docs/cycle/Linear and Cyclical Workflows using Functions and States.ipynb'
  - Theorists:
    - Home: 'theorist/index.md'
    - DARTS: '!import https://github.com/autoresearch/autora-theorist-darts/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - BMS: '!import https://github.com/autoresearch/autora-theorist-bms/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - BSR: '!import https://github.com/autoresearch/autora-theorist-bsr/?branch=main&extra_imports=["mkdocs/base.yml"]'
  - Experimentalists:
    - Home: 'experimentalist/index.md'
    - Pipeline: 'core/docs/pipeline/Experimentalist Pipeline Examples.ipynb'
    - Random:
      - Home: 'core/docs/experimentalists/random/index.md'
      - Quickstart: 'core/docs/experimentalists/random/quickstart.md'
    - Grid:
      - Home: 'core/docs/experimentalists/grid/index.md'
      - Quickstart: 'core/docs/experimentalists/grid/quickstart.md'
    - Novelty: '!import https://github.com/autoresearch/autora-experimentalist-novelty/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Inequality: '!import https://github.com/autoresearch/autora-experimentalist-inequality/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Nearest Value: '!import https://github.com/autoresearch/autora-experimentalist-nearest-value/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Model Disagreement: '!import https://github.com/autoresearch/autora-experimentalist-model-disagreement/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Uncertainty: '!import https://github.com/autoresearch/autora-experimentalist-uncertainty/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Leverage: '!import https://github.com/autoresearch/autora-experimentalist-leverage/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Falsification: '!import https://github.com/autoresearch/autora-experimentalist-falsification/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Mixture: '!import https://github.com/blinodelka/mixture_experimental_strategies/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Prediction Filter: '!import https://github.com/AutoResearch/autora-experimentalist-prediction-filter/?branch=main&extra_imports=["mkdocs/base.yml"]'
  - Experiment Runners:
    - Home: 'experiment-runner/index.md'
    - Synthetic: '!import https://github.com/autoresearch/autora-synthetic/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Firebase-Prolific: '!import https://github.com/autoresearch/autora-experiment-runner-firebase-prolific/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Experimentation Managers:
      - Firebase: '!import https://github.com/autoresearch/autora-experiment-runner-experimentation-manager-firebase/?branch=main&extra_imports=["mkdocs/base.yml"]'
    - Recruitment Managers:
      - Prolific: '!import https://github.com/autoresearch/autora-experiment-runner-recruitment-manager-prolific/?branch=main&extra_imports=["mkdocs/base.yml"]'
  - "Command Line Interface":
    - "Home": "core/docs/cli/index.md"
    - "Basic Usage": "core/docs/cli/basic-usage/README.md"
    - "Using Cylc": "core/docs/cli/cylc-pip/README.md"
    - "Using Cylc and Slurm": "core/docs/cli/cylc-slurm-pip/README.md"
  - Online Experiments:
    - Home: 'online-experiments/index.md'
    - Firebase: 'online-experiments/firebase.md'
- Contributor Guide:
  - Home: 'contribute/index.md'
  - Modules:
    - Home: 'contribute/modules/index.md'
    - Theorist: 'contribute/modules/theorist.md'
    - Experimentalist: 'contribute/modules/experimentalist.md'
    - Experiment Runner: 'contribute/modules/experiment-runner.md'
  - Core: 'contribute/core.md'
  - Notebooks: 'contribute/Notebook.ipynb'
  - Development Setup: 'contribute/setup.md'
  - Pre-Commit Hooks: 'contribute/pre-commit-hooks.md'
- Code Reference: reference/