docs: add obikmer user guide and MkDocs build configuration

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.
2026-08-13 17:19:01 +02:00
parent 0c86ea0385
commit 6acafa7f2c
28 changed files with 1497 additions and 1 deletions
@@ -0,0 +1,61 @@
+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