site_name: obikmer — User Guide
docs_dir: UserDocMD
site_dir: doc-user

theme:
  name: material

plugins:
  - mermaid2:
  - bibtex:
      bib_file: UserDocMD/references.bib
      csl_file: UserDocMD/ecology-letters.csl
      enable_inline_citations: false

markdown_extensions:
  - admonition
  - footnotes
  - tables
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.arithmatex:
      generic: true

extra_javascript:
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

nav:
  - Home: index.md
  - Installation: installation.md
  - Theory:
      - Kmers and super-kmers: theory/kmers_and_superkmers.md
      - DNA encoding: theory/encoding.md
      - Low-complexity kmer filter: theory/entropy_filter.md
      - Minimizer selection: theory/minimizer_selection.md
      - Partitioning and indexing architecture: theory/indexing_architecture.md
  - Usage:
      - superkmer: usage/superkmer.md
      - index: usage/index_command.md
      - merge: usage/merge.md
      - filter: usage/filter.md
      - select: usage/select.md
      - query: usage/query.md
      - dump: usage/dump.md
      - annotate: usage/annotate.md
      - distance: usage/distance.md
      - unitig: usage/unitig.md
      - estimate: usage/estimate.md
      - reindex: usage/reindex.md
      - utils: usage/utils.md
      - pack: usage/pack.md
      - Predicates and taxonomy paths: usage/predicates.md
  - Formats:
      - Index construction and on-disk layout: formats/index_layout.md
  - Architecture notes: architecture.md

watch:
  - UserDocMD
  - mkdocs-user.yml