zensical.toml

[project]
site_name = "CyVerse Core Software Documentation"
site_url = "https://cyverse.github.io/docs"
site_description = "CyVerse USA Documentation"
site_author = "CyVerse USA"
docs_dir = "docs/"
site_dir = "site"

# Repository information
repo_url = "https://github.com/cyverse/docs"
edit_uri = "edit/main/docs"

# Copyright notice
copyright = "Copyright © 2016-2026 CyVerse"

# Theme configuration
[project.theme]
name = "classic"  # Use classic theme for Material for MkDocs appearance
logo = "assets/de/cyverse_ball_2022.png"
favicon = "images/favicon.ico"

# Theme features
[project.theme.features]
navigation_instant = true
navigation_tracking = true
navigation_tabs = true
navigation_tabs_sticky = true
navigation_indexes = true
navigation_top = true
toc_integrate = true
toc_follow = true

# Theme palette configuration
[[project.theme.palette]]
media = "(prefers-color-scheme: white)"
primary = "white"

[[project.theme.palette]]
media = "(prefers-color-scheme: dark)"
scheme = "slate"

# Font configuration
[project.theme.font]
text = "Open Sans"
code = "Roboto Mono"

# Navigation structure
[[project.nav]]
About = "index.md"

[[project.nav]]
"Getting Started" = [
  { "Overview & Prerequisites" = "services/getting_started.md" },
  { "System Overview" = "services/system_overview.md" },
  { "Subscriptions" = "services/subscriptions.md" }
]

[[project.nav]]
"Deployment Guide" = [
  { "Overview" = "deployments/deployment_overview.md" },
  { "Prerequisites & Setup" = [
    { "Ansible Setup" = "guides/setup/ansible.md" },
    { "Docker Setup" = "guides/setup/docker.md" },
    { "Database Setup" = "guides/setup/database.md" }
  ]},
  { "Core Infrastructure" = [
    { "Kubernetes Cluster" = "deployments/kubernetes-deploy.md" },
    { "Kubernetes Resources" = "deployments/k8s-resources.md" },
    { "Kubernetes Namespaces" = "deployments/k8s-namespace.md" },
    { "Storage (OpenEBS)" = "deployments/openebs.md" },
    { "iRODS CSI Driver" = "deployments/irods-csi-driver.md" },
    { "Networking (Ingress NGINX)" = "deployments/ingress-nginx.md" }
  ]},
  { "Core Services" = [
    { "Authentication (KeyCloak)" = "deployments/keycloak.md" },
    { "Message Queue (RabbitMQ)" = "deployments/RabbitMQ.md" },
    { "Cache (Redis HA)" = "deployments/redis-ha.md" },
    { "Search (ElasticSearch)" = "deployments/elasticsearch.md" },
    { "Monitoring (Jaeger)" = "deployments/jaeger.md" }
  ]},
  { "Application Services" = [
    { "Discovery Environment" = "deployments/DiscoveryEnvironment.md" },
    { "User Portal" = "deployments/userportal.md" },
    { "VICE" = "deployments/vice.md" },
    { "Mail (Exim4)" = "deployments/exim4.md" },
    { "Local Exim" = "deployments/local-exim.md" }
  ]},
  { "Supporting Services" = [
    { "Grouper" = "deployments/grouper.md" },
    { "Unleash" = "deployments/unleash.md" }
  ]}
]

[[project.nav]]
"Administration Guide" = [
  { "DevOps Tools" = "guides/devops.md" },
  { "Discovery Environment" = "guides/de.md" },
  { "Data Store" = "guides/ds.md" },
  { "User Portal" = "guides/user_portal.md" },
  { "FAQ" = "guides/faq.md" }
]

[[project.nav]]
"API Reference" = [
  { "Overview" = "services/api_overview.md" },
  { "Endpoints" = [
    { "Overview" = "services/api/endpoints/endpoints.md" },
    { "App Metadata" = "services/api/endpoints/app-metadata.md" },
    { "App Ontologies" = "services/api/endpoints/app-ontologies.md" },
    { "Callbacks" = "services/api/endpoints/callbacks.md" },
    { "Comments" = "services/api/endpoints/comments.md" },
    { "Favorites" = "services/api/endpoints/favorites.md" },
    { "File I/O" = "services/api/endpoints/fileio.md" },
    { "Filesystem" = [
      { "Search" = "services/api/endpoints/filesystem/search.md" },
      { "Directory Listing" = "services/api/endpoints/filesystem/directory-listing.md" },
      { "Directory Create" = "services/api/endpoints/filesystem/directory-create.md" },
      { "Root Listing" = "services/api/endpoints/filesystem/root-listing.md" },
      { "File Operations" = "services/api/endpoints/filesystem/read-chunk.md" },
      { "CSV/TSV Parsing" = "services/api/endpoints/filesystem/csv-tsv-parsing.md" },
      { "Move" = "services/api/endpoints/filesystem/move.md" },
      { "Rename" = "services/api/endpoints/filesystem/rename.md" },
      { "Delete" = "services/api/endpoints/filesystem/delete.md" },
      { "Restore" = "services/api/endpoints/filesystem/restore.md" },
      { "Empty Trash" = "services/api/endpoints/filesystem/empty-trash.md" },
      { "Metadata" = "services/api/endpoints/filesystem/metadata.md" },
      { "Permissions" = "services/api/endpoints/filesystem/permissions.md" },
      { "Sharing" = "services/api/endpoints/filesystem/sharing.md" },
      { "Tickets" = "services/api/endpoints/filesystem/tickets.md" },
      { "CoGe" = "services/api/endpoints/filesystem/coge.md" },
      { "ORE" = "services/api/endpoints/filesystem/ore.md" },
      { "Manifest" = "services/api/endpoints/filesystem/manifest.md" },
      { "Path Lists" = "services/api/endpoints/filesystem/path-lists.md" },
      { "Stat" = "services/api/endpoints/filesystem/stat.md" },
      { "Existence" = "services/api/endpoints/filesystem/existence.md" },
      { "Errors" = "services/api/endpoints/filesystem/errors.md" }
    ]},
    { "Notifications" = "services/api/endpoints/notifications.md" },
    { "Permanent ID Requests" = "services/api/endpoints/permanent-id-requests.md" },
    { "Quick Launches" = "services/api/endpoints/quick-launches.md" },
    { "Terrain vs Apps" = "services/api/endpoints/terrain-v-apps.md" },
    { "Miscellaneous" = "services/api/endpoints/misc.md" }
  ]},
  { "Endpoint Index" = "services/api/endpoint-index.md" },
  { "Error Handling" = "services/api/errors.md" },
  { "Migration Guides" = [
    { "Tapis v2 to v3" = "services/api/tapis-v2-v3-migration.md" }
  ]}
]

[[project.nav]]
"Developer Guide" = "development/index.md"

[[project.nav]]
"System Architecture" = [
  { "Overview" = "services/services_overview.md" },
  { "Products & Services" = [
    { "Discovery Environment" = "services/de.md" },
    { "Data Store" = "services/ds.md" },
    { "Data Commons" = "services/dc.md" },
    { "BisQue" = "services/bisque.md" },
    { "DNA Subway" = "services/dnasubway.md" },
    { "Cloud Services (CACAO)" = "services/cloud.md" },
    { "Authentication (KeyCloak)" = "services/keycloak.md" }
  ]}
]

[[project.nav]]
"Database Reference" = [
  { "Overview" = "database/main.md" },
  { "DE Database" = "database/de-db.md" },
  { "Metadata Database" = "database/metadata-db.md" },
  { "KeyCloak Database" = "database/keycloak-db.md" },
  { "Notifications Database" = "database/notifications-db.md" },
  { "Unleash Database" = "database/unleash-db.md" },
  { "Grouper Database" = "database/grouper-db.md" },
  { "QMS Database" = "database/qms-db.md" },
  { "Portal Database" = "database/portal-db.md" }
]

# Extra configuration
[project.extra]
homepage = "https://docs.cyverse.org"
analytics = { provider = "google", property = "G-6WMK2Y07YW" }

[[project.extra.social]]
icon = "fontawesome/brands/orcid"
link = "https://orcid.org/"

[[project.extra.social]]
icon = "fontawesome/brands/github"
link = "https://github.com/cyverse/"

[[project.extra.social]]
icon = "fontawesome/brands/twitter"
link = "https://twitter.com/cyverseorg"

[[project.extra.social]]
icon = "fontawesome/brands/linkedin"
link = "https://www.linkedin.com/company/cyverse.org"

[[project.extra.social]]
icon = "fontawesome/brands/docker"
link = "https://harbor.cyverse.org/"

[[project.extra.social]]
icon = "fontawesome/brands/youtube"
link = "https://www.youtube.com/c/CyverseOrgProject"

# JavaScript files
extra_javascript = ["javascripts/intercom.js"]

# CSS files
extra_css = ["stylesheets/extra.css"]

# Markdown extensions configuration
# Zensical enables a sensible default set of extensions automatically
# This configuration ensures compatibility with the existing content
[project.markdown_extensions]
# Python Markdown extensions
admonition = {}
abbr = {}
attr_list = {}
def_list = {}
footnotes = {}
md_in_html = {}

[project.markdown_extensions.toc]
permalink = true

# PyMdown Extensions
[project.markdown_extensions.pymdownx]
arithmatex = { generic = true }
betterem = { smart_enable = "all" }
caret = {}
critic = {}
details = {}
highlight = {}
inlinehilite = {}
keys = {}
mark = {}
smartsymbols = {}
tilde = {}

[project.markdown_extensions.pymdownx.emoji]
emoji_index = "material.extensions.emoji.twemoji"
emoji_generator = "material.extensions.emoji.to_svg"

[project.markdown_extensions.pymdownx.magiclink]
repo_url_shorthand = true
user = "squidfunk"
repo = "mkdocs-material"

[project.markdown_extensions.pymdownx.superfences]
custom_fences = [
  { name = "mermaid", class = "mermaid", format = "pymdownx.superfences.fence_code_format" }
]

[project.markdown_extensions.pymdownx.tabbed]
alternate_style = true

[project.markdown_extensions.pymdownx.tasklist]
custom_checkbox = true

# Plugins configuration
[[project.plugins]]
name = "search"