mkdocs.yml

site_name: HPC@UCD Documentation
site_url: http://docs.hpc.ucdavis.edu
repo_url: https://github.com/ucdavis/hpccf-docs
copyright: Copyright © 2023-25 The Regents of the University of California, Davis

nav:
  - General:
      - Accessing Clusters: general/access.md
      - Account Requests: general/account-requests.md
      - Backups: backups/index.md
      - Contact Support: support.md
      - Data Transfer: data-transfer.md
      - Job Scheduling:
          - About: scheduler/index.md
          - Commands: scheduler/commands.md
          - Free Access: scheduler/free-access.md
          - Job Scripts: scheduler/jobscripts.md
          - Resources: scheduler/resources.md
      - Software:
          - About: software/index.md
          - Apptainer: software/apptainer.md
          - Conda and Python: software/conda.md
          - Development: software/developing.md
          - Module System: software/modules.md
          - Open OnDemand: software/ondemand.md
          - R and RStudio: software/rstudio.md
      - Storage:
          - Quobyte: storage/quobyte.md
      - Troubleshooting: general/troubleshooting.md
  - Farm:
      - About: farm/index.md
      - Job Scheduling: farm/scheduling.md
      - Resources: farm/resources.md
      - Software:
          - Modules: farm/software/modules.md
      #- Storage: # TODO: write this.
      # - Farm: farm/storage.md
  - Franklin:
      - About: franklin/index.md
      - Job Scheduling: franklin/scheduling.md
      - Resources: franklin/resources.md
      - Software:
          - alphafold: franklin/software/alphafold.md
          - cryo-EM: franklin/software/cryoem.md
          - Modules: franklin/software/modules.md
      - Databases: franklin/databases.md
      - Storage: franklin/storage.md
  - Hive:
      - About: hive/index.md
      - Job Scheduling: hive/scheduling.md
      - Migrating from LSSC0: hive/lssc0-data-migration.md
      - Waltz temporary access: hive/waltz.md
  - Maintenance:
      - December 2025: maintenance/december-2025.md
  - Meta:
      - Style Guide: meta/style.md

#
# Here be dragons! Don't edit these settings unless you Know What You're Doing (tm).
#

validation:
  nav:
    omitted_files: info
    not_found: warn
    absolute_links: warn
  links:
    not_found: warn
    anchors: warn
    absolute_links: warn
    unrecognized_links: warn

strict: true

markdown_extensions:
  - toc:
      permalink: true

  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables

  - pymdownx.arithmatex:
      generic: true
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format

plugins:
  - search
  - git-revision-date-localized:
      enable_creation_date: true
  - macros:
      module_name: macros
  - spellcheck:
      backends: # the backends you want to use
        - symspellpy # as strings
        - codespell: # or nested configs
            dictionaries: [clear, rare, names, code, usage]
            C: 2
      # known_words can also be a list of words
      known_words: extra-dictionary.txt
      # ignore words in <code> tags
      ignore_code: true
      skip_files:
        - franklin/software/modules.md

extra:
  spack_modulefiles_path: spack-ucdavis/modulefiles/hpccf/franklin/
  social:
    - icon: material/email-edit
      link: "mailto:hpc-help@ucdavis.edu"
      name: Email HPC@UCD Support
    - icon: fontawesome/brands/slack
      link: https://ucdavis.slack.com/archives/C053NKA88
      name: "#hpc Channel on ucdavis.slack.com"
extra_css:
  - stylesheets/extra.css
extra_javascript:
  - javascript/mathjax.js
  - https://cdnjs.cloudflare.com/polyfill/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

theme:
  name: material
  custom_dir: overrides
  features:
    - content.code.annotate
    #- navigation.tabs
    - navigation.sections
    - navigation.expand
    #- navigation.indexes
    - navigation.instant
    - navigation.top
    #- navigation.footer
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
  logo: assets/HPCCF-logo-dark.png
  favicon: assets/HPCCF-logo.png
  icon:
    repo: fontawesome/brands/github
  palette:
    # Palette toggle for light mode
    - scheme: ucdavis
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode

    # Palette toggle for dark mode
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode