site_name: obikmer
docs_dir: docmd
site_dir: doc

theme:
  name: material

plugins:
  - mermaid2:
  - bibtex:
      bib_file: docmd/references.bib
      csl_file: docmd/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: kmers.md
      - DNA encoding: theory/encoding.md
      - Entropy filter: theory/entropy.md
      - Minimizer selection: theory/minimizer.md
      - Partitioning architecture: theory/indexing.md
  - Implementation:
      - SuperKmer: implementation/superkmer.md
      - Kmer: implementation/kmer.md
      - Chunk reader: implementation/chunkreader.md
      - Construction pipeline: implementation/pipeline.md
      - obipipeline library: implementation/obipipeline.md
      - On-disk storage: implementation/storage.md
      - MPHF selection: implementation/mphf.md
      - Unitig evidence encoding: implementation/unitig_evidence.md
      - Evidence elimination (discussion): implementation/evidence_elimination.md
      - obilayeredmap crate: implementation/obilayeredmap.md
      - PersistentCompactIntVec: implementation/persistent_compact_int_vec.md
      - PersistentBitVec: implementation/persistent_bit_vec.md
      - Merge command: implementation/merge.md
      - Merge parallelism & memory: implementation/merge_parallelism.md
      - Kmer filtering: implementation/filtering.md
      - Select command: implementation/select.md
      - obitaxonomy crate: implementation/obitaxonomy.md
  - Architecture:
      - Sequences: architecture/sequences/invariant.md
      - Kmer index: architecture/index_architecture.md
      - NUMA-aware worker pools: architecture/numa_worker_pools.md
      - NUMA-aware partition runner: architecture/numa_partition_runner.md

watch:
  - docmd
  - mkdocs.yml
