Eric Coissac
caf59b5658
Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
62 lines
1.6 KiB
YAML
62 lines
1.6 KiB
YAML
site_name: obikmer — User Guide
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docs_dir: UserDocMD
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site_dir: doc
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theme:
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name: material
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plugins:
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- mermaid2:
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- bibtex:
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bib_file: UserDocMD/references.bib
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csl_file: UserDocMD/ecology-letters.csl
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enable_inline_citations: false
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markdown_extensions:
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- admonition
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- footnotes
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- tables
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- pymdownx.superfences:
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custom_fences:
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- name: mermaid
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class: mermaid
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format: !!python/name:pymdownx.superfences.fence_code_format
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- pymdownx.arithmatex:
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generic: true
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extra_javascript:
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- https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
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nav:
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- Home: index.md
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- Installation: installation.md
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- Theory:
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- Kmers and super-kmers: theory/kmers_and_superkmers.md
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- DNA encoding: theory/encoding.md
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- Low-complexity kmer filter: theory/entropy_filter.md
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- Minimizer selection: theory/minimizer_selection.md
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- Partitioning and indexing architecture: theory/indexing_architecture.md
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- Usage:
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- superkmer: usage/superkmer.md
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- index: usage/index_command.md
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- merge: usage/merge.md
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- filter: usage/filter.md
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- select: usage/select.md
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- query: usage/query.md
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- dump: usage/dump.md
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- annotate: usage/annotate.md
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- phylo: usage/phylo.md
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- unitig: usage/unitig.md
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- estimate: usage/estimate.md
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- convert: usage/convert.md
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- utils: usage/utils.md
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- pack: usage/pack.md
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- Predicates and taxonomy paths: usage/predicates.md
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- Formats:
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- Index construction and on-disk layout: formats/index_layout.md
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- Architecture notes: architecture.md
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watch:
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- UserDocMD
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- mkdocs-user.yml
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