mkdocs.yml

site_name: "medchem"
site_description: "Medchem: Molecular filtering for drug discovery."
site_url: "https://github.com/datamol-io/medchem"
repo_url: "https://github.com/datamol-io/medchem"
repo_name: "datamol-io/medchem"
copyright: Copyright 2020 - 2023 datamol.io

remote_branch: "gh-pages"
use_directory_urls: false
docs_dir: "docs"

# Fail on warnings to detect issues with types and docstring
strict: true

nav:
  - Overview: index.md
  - Tutorials:
      - Basic Concepts: tutorials/Basic_Concepts.ipynb
      - Functional API: tutorials/Functional_API.ipynb
      - Medchem Rules: tutorials/Medchem_Rules.ipynb
      - Structural Filters: tutorials/Structural_Filters.ipynb
      - Catalogs: tutorials/Catalogs.ipynb
      - Chemical Groups: tutorials/Chemical_Groups.ipynb
      - Medchem Query Language: tutorials/Medchem_Query_Language.ipynb
      - Molecular Complexity: tutorials/Molecular_Complexity.ipynb
      - Constraints Filtering: tutorials/Constraints_Filtering.ipynb
  - CLI: cli.md
  - API:
      - medchem.rules: api/medchem.rules.md
      - medchem.structural: api/medchem.structural.md
      - medchem.catalogs: api/medchem.catalogs.md
      - medchem.complexity: api/medchem.complexity.md
      - medchem.groups: api/medchem.groups.md
      - medchem.constraints: api/medchem.constraints.md
      - medchem.functional: api/medchem.functional.md
      - medchem.query: api/medchem.query.md
      - medchem.utils: api/medchem.utils.md

theme:
  name: material
  # NOTE(hadim): to customize the material primary and secondary
  # color check `docs/assets/css/custom.css`.
  features:
    - navigation.tabs
    - navigation.tracking
    - navigation.top

  favicon: images/logo.png
  logo: images/logo.svg

extra_css:
  - _assets/css/custom.css
  - _assets/css/tweak-width.css


extra_javascript:
  - _assets/js/mathjax.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

markdown_extensions:
  - admonition
  - markdown_include.include
  - pymdownx.emoji
  - pymdownx.magiclink
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.tasklist
  - pymdownx.details
  - mkdocs-click
  - pymdownx.arithmatex:
      generic: true
  - toc:
      permalink: true

watch:
  - medchem/

plugins:
  - search

  - mkdocstrings:
      handlers:
        python:
          setup_commands:
            - import sys
            - sys.path.append("docs")
            - sys.path.append("medchem")
          options:
            new_path_syntax: yes
            show_root_heading: yes
            heading_level: 3
            show_source: false

  - mkdocs-jupyter:
      execute: False
      remove_tag_config:
        remove_cell_tags: [remove_cell]
        remove_all_outputs_tags: [remove_output]
        remove_input_tags: [remove_input]

  - mike:
      version_selector: true

extra:
  version:
    # Multi versioning provider for mkdocs-material (used for the JS selector)
    provider: mike