Eric Coissac
6acafa7f2c
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
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-user
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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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- distance: usage/distance.md
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- unitig: usage/unitig.md
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- estimate: usage/estimate.md
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- reindex: usage/reindex.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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