mkdocs.yml

site_name: The safedata_validator package
repo_url: https://github.com/ImperialCollegeLondon/safedata_validator/
theme:
  name: material
markdown_extensions:
  - admonition
  - def_list
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true

plugins:
  - search
  - mkdocstrings
  - include-markdown
  - table-reader
hooks:
  - docs/scripts/hooks.py
extra_css:
  - custom.css
use_directory_urls: false
nav:
  - 'Overview': 'index.md'
  - 'Data providers':
    - 'Overview': 'data_providers/overview.md'
    - 'Data availability': 'data_providers/availability.md'
    - 'Excel format details':
      - 'Overview': 'data_providers/data_format/overview.md'
      - 'Summary worksheet': 'data_providers/data_format/summary.md'
      - 'Taxa worksheets': 'data_providers/data_format/taxa.md'
      - 'GBIFTaxa worksheet': 'data_providers/data_format/gbif_taxa.md'
      - 'NCBITaxa worksheet': 'data_providers/data_format/ncbi_taxa.md'
      - 'Locations worksheet': 'data_providers/data_format/locations.md'
      - 'Data worksheets': 'data_providers/data_format/data.md'
      - 'Other file formats': 'data_providers/data_format/other_formats.md'
      - 'Data format FAQs': 'data_providers/data_format/faqs.md'
  - 'Data managers':
    - 'Overview': 'data_managers/overview.md'
    - 'Installation and configuration':
      - 'Installation': 'data_managers/install/install.md'
      - 'Configuration': 'data_managers/install/configuration.md'
      - 'Building the GBIF database': 'data_managers/install/build_local_gbif.md'
      - 'Building the NCBI database': 'data_managers/install/build_local_ncbi.md'
      - 'The gazetteer': 'data_managers/install/gazetteer_files.md'
      - 'Creating a gazetteer': 'data_managers/install/gazetteer_creation.md'
      - 'Taxonomic validation details': 'data_managers/install/taxonomic_validation.md'
    - 'Using the safedata system':
      - 'Overview': 'data_managers/using_safedata/overview.md'
      - 'Validating datasets': 'data_managers/using_safedata/validating_datasets.md'
      - 'Publishing datasets': 'data_managers/using_safedata/publishing_datasets.md'
      - 'Updating the metadata server': 'data_managers/using_safedata/posting_metadata.md'
    - 'Command line tools': 
      - 'Overview': 'data_managers/command_line_tools/overview.md'
      - 'safedata_validate': 'data_managers/command_line_tools/safedata_validate.md'
      - 'safedata_zenodo': 'data_managers/command_line_tools/safedata_zenodo.md'
      - 'safedata_metadata': 'data_managers/command_line_tools/safedata_metadata.md'
  - 'Developers':
    - 'API Reference':
      - 'Overview': 'developers/api//overview.md'
      - 'Resources': 'developers/api/resources.md'
      - 'Taxon database': 'developers/api/taxondb.md'
      - 'Logger': 'developers/api/logger.md'
      - 'Extents': 'developers/api/extent.md'
      - 'Summary': 'developers/api/summary.md'
      - 'Locations': 'developers/api/locations.md'
      - 'Fields and dataworksheets': 'developers/api/field.md'
      - 'Taxa': 'developers/api/taxa.md'
      - 'Zenodo': 'developers/api/zenodo.md'
      - 'Server': 'developers/api/server.md'
      - 'Utilities': 'developers/api/utilities.md'
    - 'Package development': developers/package_development.md
    - 'Strange problems': developers/strange_problems.md
  - 'safedata at the SAFE project': 'safedata_at_SAFE.md'