mkdocs.yml

# Project information
site_name: TASSEL 5
site_description: Trait Analysis by aSSociation, Evolution and Linkage
site_author: Buckler Lab
site_url: https://tassel.maizegenetics.net

# Repository configuration
repo_name: tassel
repo_url: https://github.com/maize-genetics/tassel

# Theme configuration
theme:
  icon:
    repo: fontawesome/brands/github
  name: material
  custom_dir: docs/overrides
  logo: images/tassel_logo_white.svg
  favicon: images/tassel_favicon.png
  palette:
      scheme: default
      primary: custom
      accent: custom
  features:
    - content.code.select
    - content.code.copy
    - content.code.annotate
    - navigation.tabs
    - navigation.top
    - navigation.sections
    - navigation.indexes
    - navigation.expand
    - search.highlight
    - navigation.instant: false
  language: en
  font:
    text: Inter
    code: IBM Plex Mono

# Copyright
copyright: '© 2026 <a href="https://www.maizegenetics.net"><b>Lab for Plant Genomic Diversity &amp; Design</b></a>'

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/maize-genetics
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/c/BucklerLab

# Plugins
# `search` has to be listed explicitly: naming any plugin replaces the default
# plugin list, which would otherwise drop the search index.
plugins:
  - search
  - macros:
      module_name: docs/macros
      # Opt-in rendering. Jinja2 would choke on the BibTeX blocks in the user
      # manual and rTASSEL page, which contain `{{TASSEL}`, so only pages that
      # declare `render_macros: true` in their front matter are processed.
      render_by_default: false
      # Surface a bad macro as a build failure instead of publishing the
      # rendering error into the page.
      on_error_fail: true

# Build exclusions
# docs/templates/ holds envsubst sources rendered by the release workflow, not
# publishable pages; building them would publish raw ${VERSION} placeholders.
# docs/llm_notes/ holds internal planning notes with links to repo paths outside
# docs/; they are not part of the published site.
# macros.py is the mkdocs-macros module, not site content; importing it leaves a
# __pycache__/ alongside it, which would otherwise be published too.
exclude_docs: |
  templates/
  llm_notes/
  macros.py
  __pycache__/

# Markdown extensions
markdown_extensions:
  - attr_list
  - md_in_html
  - toc:
      permalink: true
  - tables
  - admonition
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

# Extra 
extra_javascript:
  - javascript/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
  - javascript/gallery.js
  # releases.js must come before download.js and nightly.js: it defines the
  # shared, cached GitHub Releases fetch both of them use.
  - javascript/releases.js
  - javascript/download.js
  - javascript/nightly.js
  - javascript/changelog.js

extra_css:
  - assets/stylesheets/extra.css
  - https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css
  - https://fonts.googleapis.com/css2?family=Material+Symbols+Outlined:opsz,wght,FILL,GRAD@20..48,100..700,0..1,-50..200
  - https://fonts.googleapis.com/css2?family=Space+Grotesk:wght@500;600;700&display=swap

# Navigation
nav:
  - Home:
      - index.md
  - Download:
      - download/index.md
      - Nightly Builds: download/nightly.md
  - Getting Started:
      - getting_started/index.md
      - Installation:
          - Desktop Application: getting_started/install-gui.md
          - Standalone: getting_started/install-standalone.md
          - JVM Library: getting_started/install-maven.md
          - R Package (rTASSEL): getting_started/install-rtassel.md
      - User Manual:
          - Overview: user_manual/index.md
          - Introduction: user_manual/introduction/index.md
          - File Menu:
              - File Menu: user_manual/filemenu/index.md
              - Open / Open As: user_manual/load/index.md
              - Data FAQ: user_manual/load/datafaq.md
              - Save As / Export: user_manual/export/index.md
          - Data Menu:
              - Sort Genotype File: user_manual/sortgenotypefile/index.md
              - Synonymizer: user_manual/synonymizer/index.md
              - Joins: user_manual/join/index.md
              - Merge Genotype Tables: user_manual/mergegenotypetables/index.md
              - Separate: user_manual/separate/index.md
              - Homozygous Genotype: user_manual/homozygousgenotype/index.md
              - Set Low Depth Genos To Missing: user_manual/setlowdepthgenostomissing/index.md
              - Transform Phenotype: user_manual/transformphenotype/index.md
              - Numerical Genotype: user_manual/numericalgenotype/index.md
              - ABH Genotype: user_manual/genostoabh/genostoabhplugin.md
              - Thin Sites By Position: user_manual/thinsitesbyposition/thinsitesbypositionplugin.md
              - Create Hybrid Genotypes: user_manual/createhybridgenotypes/index.md
              - Geno Summary: user_manual/genosummary/index.md
          - Impute Menu:
              - FILLIN: user_manual/fillin/index.md
              - FSFHap Imputation: user_manual/fsfhapimputation/index.md
              - Numerical Impute: user_manual/numericalimpute/index.md
              - Missing Phenotype Imputation: user_manual/missingphenotypeimputation/index.md
          - Filter Menu:
              - Filter Menu: user_manual/filtermenu/index.md
              - Filter Genotype Table Sites: user_manual/filtermenu/filtersitebuilderplugin.md
              - Filter Genotype Table Taxa: user_manual/filtermenu/filtertaxabuilderplugin.md
              - Filter Traits: user_manual/filtermenu/filtertraitsplugin.md
          - Analysis Menu:
              - Diversity: user_manual/diversity/index.md
              - Linkage Disequilibrium: user_manual/linkagedisequilibrium/index.md
              - Distance Matrix: user_manual/distancematrix/index.md
              - Kinship: user_manual/kinship/index.md
              - Cladogram: user_manual/cladogram/index.md
              - Pedigree Relationship Matrix (A): user_manual/amatrix/index.md
              - Combined A and G Matrix (H): user_manual/hmatrix/index.md
              - MDS: user_manual/mds/index.md
              - PCA: user_manual/pca/index.md
              - Remove NaN from Distance Matrix: user_manual/removenan/index.md
              - GLM: user_manual/glm/index.md
              - MLM: user_manual/mlm/index.md
              - Weighted MLM: user_manual/weightedmlm/index.md
              - Genomic Selection: user_manual/genomicselection/index.md
              - Stepwise: user_manual/stepwise/index.md
              - Fast Association: user_manual/fastassociation/index.md
              - VCAP Scan: user_manual/vcapscan/index.md
              - Association Analysis using GLM: user_manual/associationanalysisusingglm/index.md
              - Association Analysis using MLM: user_manual/associationanalysisusingmlm/index.md
              - Estimation of Kinship using Genetic Markers: user_manual/estimationofkinshipusinggeneticmarkers/index.md
              - Principal Component Analysis: user_manual/principalcomponentanalysis/index.md
          - Results Menu:
              - Table: user_manual/table/index.md
              - Archaeopteryx Tree: user_manual/archaeopteryxtree/index.md
              - LD Plot: user_manual/ldplot/index.md
              - Chart: user_manual/chart/index.md
              - QQ Plot: user_manual/qqplot/index.md
              - Manhattan Plot: user_manual/manhattanplot/index.md
          - GBS Menu: user_manual/gbsmenu/index.md
          - Help Menu: user_manual/helpmenu/index.md
          - Frequently Asked Questions: user_manual/frequentlyaskedquestions/index.md
          - Executing TASSEL: user_manual/executing-tassel.md
          - User Guide (PDF): user_manual/tassel5-user-guide.md
          - Appendix:
              - Nucleotide Codes: user_manual/appendix/nucleotidecodes.md
              - Depth Encodings: user_manual/appendix/depthbytetoint.md
              - Tutorial Datasets: user_manual/appendix/tasseltutorialdatasets.md
              - References: user_manual/appendix/references.md
      - Pipelines:
          - Overview: pipelines/index.md
          - Pipeline Tutorial: pipelines/pipeline-tutorial.md
          - Pipeline Reference: pipelines/tassel5-pipeline-cli.md
          - GBSv2 Pipeline: gbsv2_pipeline/index.md
          - Archived:
              - UNEAK Pipeline: pipelines/uneak-pipeline.md
              - Pan-genome Atlas (PanA): pipelines/pangenome-atlas-pipeline.md
              - Cassava Production Pipeline: pipelines/cassava-production-pipeline.md
              - Pipeline CLI (v3 / v4): pipelines/tassel-pipeline-cli-v3-v4.md
  - Community:
      - community/index.md
      - Get Involved:
          - Contributing: CONTRIBUTING.md
          - Code of Conduct: CODE_OF_CONDUCT.md
      - Developer:
          - Overview: developer/index.md
          - Building from Source: developer/building-from-source.md
          - Project Architecture: developer/architecture.md
          - Developing Plugins: developer/plugin-development.md
          - Testing: developer/testing.md
          - Releasing: developer/releasing.md
  - Version History: changelog.md