zensical.toml

# ============================================================================
# MESA Documentation site — Zensical configuration
#
# Built with Zensical (https://zensical.org/), a static site generator from
# the Material for MkDocs team. Run `zensical serve` to preview locally and
# `zensical build` to render to ./site/. GitHub Actions publishes ./site/ to
# GitHub Pages on every push to main (see .github/workflows/docs.yml).
# ============================================================================

[project]

site_name = "MESA — Metadata-Enabled Scientific Agents"
site_description = """
MESA is an NSF IDSS-funded prototype combining an open-source Data Lakehouse, \
a federated iRODS Data Mesh, and Agentic AI orchestration on leveraged NSF \
cyberinfrastructure. This site is the user and developer documentation hub \
for early adopters and project contributors.
"""
site_author = "MESA Project — University of Arizona & RENCI / UNC Chapel Hill"
site_url = "https://cyverse.github.io/mesa/"

copyright = """
Copyright © 2026 The Arizona Board of Regents on behalf of the
University of Arizona. MESA is supported by the NSF IDSS program.
Content licensed under CC BY 4.0; code under Apache 2.0.
"""

repo_name = "cyverse/mesa"
repo_url = "https://github.com/cyverse/mesa"
edit_uri = "edit/main/docs/"

nav = [
  { "Home" = "index.md" },
  { "Getting Started" = [
      { "Overview" = "getting-started/index.md" },
      { "For Early Adopters" = "getting-started/early-adopters.md" },
      { "Accessing MESA" = "getting-started/access.md" },
      { "First Analysis" = "getting-started/first-analysis.md" },
  ] },
  { "Project" = [
      { "Mission and Scope" = "project/index.md" },
      { "Innovation Goals" = "project/goals.md" },
      { "Work Breakdown Structure" = "project/wbs.md" },
      { "Organization & Governance" = "project/organization.md" },
      { "Schedule & Milestones" = "project/schedule.md" },
      { "Sustainability" = "project/sustainability.md" },
  ] },
  { "Components" = [
      { "Architecture Overview" = "components/index.md" },
      { "Data Lakehouse (DuckLake)" = "components/lakehouse.md" },
      { "iRODS Data Mesh" = "components/data-mesh.md" },
      { "Agentic AI & MCP" = "components/agentic-ai.md" },
      { "MCP Servers" = [
          { "Overview" = "components/mcp-servers/index.md" },
          { "mesa-mcp" = "components/mcp-servers/mesa-mcp.md" },
          { "mesa-ducklake" = "components/mcp-servers/mesa-ducklake.md" },
          { "irods-mcp-server" = "components/mcp-servers/irods-mcp-server.md" },
          { "formation-mcp" = "components/mcp-servers/formation-mcp.md" },
          { "terrain-mcp" = "components/mcp-servers/terrain-mcp.md" },
      ] },
  ] },
  { "Use Cases" = [
      { "Overview" = "use-cases/index.md" },
      { "UC1 — Agentic Discovery + Multi-Omics" = "use-cases/uc1-agentic-discovery.md" },
      { "UC2 — Geospatial + EHT" = "use-cases/uc2-geospatial-eht.md" },
      { "UC3 — IoT / Edge" = "use-cases/uc3-iot-edge.md" },
  ] },
  { "User Guide" = [
      { "Installing an MCP Client" = "user-guide/mcp-clients.md" },
      { "Connecting to CyVerse" = "user-guide/cyverse-auth.md" },
      { "Metadata with Ontologies" = "user-guide/metadata-ontologies.md" },
      { "Time-Travel Queries" = "user-guide/time-travel.md" },
      { "Troubleshooting" = "user-guide/troubleshooting.md" },
  ] },
  { "Developer Guide" = [
      { "Contributing" = "developer-guide/contributing.md" },
      { "Repository Layout" = "developer-guide/repos.md" },
      { "Local Development" = "developer-guide/local-dev.md" },
      { "Testing & CI" = "developer-guide/testing.md" },
      { "Security Review" = "developer-guide/security.md" },
  ] },
  { "Community" = [
      { "Early Adopter Program" = "community/index.md" },
      { "Workshops" = "community/workshops.md" },
      { "Educator Fellows" = "community/educator-fellows.md" },
      { "AI Ethics Advisory Board" = "community/ethics-board.md" },
      { "Contact & Support" = "community/contact.md" },
  ] },
  { "Policies" = [
      { "Data Governance" = "policies/data-governance.md" },
      { "AI Safety" = "policies/ai-safety.md" },
      { "Security & Compliance" = "policies/security.md" },
      { "License & Attribution" = "policies/license.md" },
  ] },
]

extra_css = ["stylesheets/extra.css"]

# ----------------------------------------------------------------------------
# Theme configuration
# ----------------------------------------------------------------------------
[project.theme]

language = "en"

features = [
  "announce.dismiss",
  "content.action.edit",
  "content.action.view",
  "content.code.annotate",
  "content.code.copy",
  "content.code.select",
  "content.footnote.tooltips",
  "content.tabs.link",
  "content.tooltips",
  "navigation.footer",
  "navigation.indexes",
  "navigation.instant",
  "navigation.instant.prefetch",
  "navigation.path",
  "navigation.sections",
  "navigation.tabs",
  "navigation.tabs.sticky",
  "navigation.top",
  "navigation.tracking",
  "search.highlight",
  "toc.follow",
]

[project.theme.icon]
logo = "lucide/database"

# University of Arizona-leaning palette — red (UA cardinal) light, navy slate dark
[[project.theme.palette]]
scheme = "default"
primary = "red"
accent = "blue"
toggle.icon = "lucide/sun"
toggle.name = "Switch to dark mode"

[[project.theme.palette]]
scheme = "slate"
primary = "red"
accent = "blue"
toggle.icon = "lucide/moon"
toggle.name = "Switch to light mode"

# ----------------------------------------------------------------------------
# Social links shown in the footer
# ----------------------------------------------------------------------------
[[project.extra.social]]
icon = "fontawesome/brands/github"
link = "https://github.com/cyverse/mesa"
name = "MESA on GitHub"

[[project.extra.social]]
icon = "fontawesome/brands/python"
link = "https://pypi.org/project/mesa-mcp/"
name = "mesa-mcp on PyPI"

# ----------------------------------------------------------------------------
# Markdown extensions (carried over from Zensical defaults)
# ----------------------------------------------------------------------------
[project.markdown_extensions.abbr]
[project.markdown_extensions.admonition]
[project.markdown_extensions.attr_list]
[project.markdown_extensions.def_list]
[project.markdown_extensions.footnotes]
[project.markdown_extensions.md_in_html]
[project.markdown_extensions.toc]
permalink = true
[project.markdown_extensions.pymdownx.arithmatex]
generic = true
[project.markdown_extensions.pymdownx.betterem]
[project.markdown_extensions.pymdownx.caret]
[project.markdown_extensions.pymdownx.details]
[project.markdown_extensions.pymdownx.emoji]
emoji_generator = "zensical.extensions.emoji.to_svg"
emoji_index = "zensical.extensions.emoji.twemoji"
[project.markdown_extensions.pymdownx.highlight]
anchor_linenums = true
line_spans = "__span"
pygments_lang_class = true
[project.markdown_extensions.pymdownx.inlinehilite]
[project.markdown_extensions.pymdownx.keys]
[project.markdown_extensions.pymdownx.magiclink]
[project.markdown_extensions.pymdownx.mark]
[project.markdown_extensions.pymdownx.smartsymbols]
[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
combine_header_slug = true
[project.markdown_extensions.pymdownx.tasklist]
custom_checkbox = true
[project.markdown_extensions.pymdownx.tilde]