mkdocs.yml

site_name: CGAT-core Documentation
theme:
  name: material
  logo: img/CGAT_logo.png
  favicon: img/CGAT_logo.png
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: material/toggle-switch
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to light mode
  
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.top
    - search.suggest
    - search.highlight
    - content.tabs.link
    - content.code.annotation
    - content.code.copy
  
  font:
    text: Roboto
    code: Roboto Mono
  
  icon:
    repo: fontawesome/brands/github

  custom_dir: docs/overrides

extra_css:
  - stylesheets/extra.css

plugins:
  - search
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          rendering:
            show_source: true
            show_if_no_docstring: true

markdown_extensions:
  - admonition
  - codehilite
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - attr_list
  - md_in_html
  - toc:
      permalink: true

nav:
  - Home: index.md
  - Getting Started:
    - Installation: getting_started/installation.md
    - Cluster Configuration: getting_started/run_parameters.md
    - Running a Pipeline: getting_started/examples.md
    - Running a Pipeline Tutorial: getting_started/tutorial.md
    - Run Parameters: getting_started/run_parameters.md
  - Building a Workflow:
      - Workflow Overview: defining_workflow/writing_workflows.md
      - Writing a Workflow Tutorial: defining_workflow/tutorial.md
  - Pipeline Modules:
    - Overview: pipeline_modules/overview.md
    - Control: pipeline_modules/control.md
    - Database: pipeline_modules/database.md
    - Files: pipeline_modules/files.md
    - Cluster: pipeline_modules/cluster.md
    - Execution: pipeline_modules/execution.md
    - Utils: pipeline_modules/utils.md
    - Parameters: pipeline_modules/parameters.md
    - Executors: pipeline_modules/executors.md
    - Farm: pipeline_modules/farm.md
    - Run Functions: pipeline_modules/run_function.md
  - Container support:
    - Individual tasks: container/tasks.md
    - Whole pipeline: container/whole_pipeline.md
  - S3 Cloud:
    - S3 Pipeline: s3_integration/s3_pipeline.md
    - S3 Decorators: s3_integration/s3_decorators.md
    - Configuring S3: s3_integration/configuring_s3.md
  - Working with Remote Files:
    - S3: remote/s3.md
    - Google Cloud: remote/gc.md
    - Azure: remote/azure.md
  - Core Functions:
    - Pipeline: function_doc/pipeline.md
    - Core:
      - Experiment: function_doc/experiment.md
      - csv2db: function_doc/csv2db.md
      - Database: function_doc/database.md
      - IOTools: function_doc/iotools.md
      - Logfile: function_doc/logfile.md
  - Project Info:
    - Contributing: project_info/contributing.md
    - How to Contribute: project_info/how_to_contribute.md
    - Citations: project_info/citations.md
    - FAQ: project_info/faq.md
    - License: project_info/license.md

repo_url: https://github.com/cgat-developers/cgat-core
repo_name: cgat-developers/cgat-core
edit_uri: edit/main/docs/