{
  "markdown": "# CyVerse User Guide (UNM CARC)\n\nHow to use [CyVerse](https://cyverse.org) cyberinfrastructure: accounts, the\nData Store (GoCommands, iCommands, SFTP, WebDAV), the Discovery Environment\nand VICE interactive apps, cloud services, and AI tools. Published by the\n[UNM Center for Advanced Research Computing (CARC)](https://carc.unm.edu) at\n**<https://unm-carc.github.io/cyverse/>**, built with\n[Zensical](https://zensical.org), styled after the\n[CARC documentation](https://carc.unm.edu/docs/), and structured as an\n[Open Knowledge Format (OKF) v0.2](https://github.com/GoogleCloudPlatform/open-knowledge-format)\nknowledge bundle so the content is first-class for both humans and AI agents.\n\nThe content is adapted from the CyVerse Learning Center user guide\n([CyVerse-learning-materials/learning-materials-home](https://github.com/CyVerse-learning-materials/learning-materials-home),\nformerly at learning.cyverse.org) under CC BY 4.0 — see [Credits](#credits).\n\n## Quick start\n\n```bash\npython3 -m venv .venv && source .venv/bin/activate\npip install -r requirements.txt   # zensical + pyyaml (Python 3.11+)\nzensical serve                    # live preview at http://localhost:8000\nzensical build --clean            # static site in ./site\n```\n\n## Repository layout\n\n```\n├── zensical.toml              # Site configuration (theme, full nav, extensions)\n├── docs/                      # The OKF knowledge bundle + site content\n│   ├── index.md               # Landing page (declares okf_version: \"0.2\")\n│   ├── log.md                 # OKF update log (reserved filename)\n│   ├── getting-started/       # What CyVerse is, accounts, subscriptions, help\n│   ├── data-store/            # Data Store: DE, GoCommands, iCommands, SFTP, WebDAV\n│   ├── discovery-environment/ # Apps, analyses, app integration, vice/ interactive apps\n│   ├── cloud/  ai/            # CACAO, DataWatch, Harbor; AI Verde and MCP servers\n│   ├── education/  developers/\n│   ├── about/                 # Credits, contributing, For AI agents\n│   ├── llms.txt, llms-full.txt  # Generated agent indexes (CI checks drift)\n│   ├── assets/                # Images and logos\n│   └── stylesheets/extra.css  # UNM cherry + turquoise theme\n├── scripts/                   # OKF validation, link check, llms.txt, agent surface\n├── MIGRATION.md               # Old learning.cyverse.org URL -> new URL map\n├── AGENTS.md / CLAUDE.md      # Rules for coding agents working in this repo\n└── .github/workflows/docs.yml # Validation + GitHub Pages deployment\n```\n\nEvery section folder has an `index.md` listing (OKF §8, no frontmatter); every\nother page carries OKF frontmatter and must appear in the `nav` of\n`zensical.toml`.\n\n## Machine readability (OKF)\n\nEvery content page carries YAML frontmatter with:\n\n- `type` — `Guide`, `Tutorial`, `Reference`, or `Policy` (required by OKF)\n- `title`, `description`, `tags` — used by search, indexes, and agents\n- `generated: { by, at }` — who or what produced the current content\n- `sources` — the exact upstream CyVerse file and commit, with `last_modified`\n  from its git history\n- `status` / `stale_after` — lifecycle markers when needed\n\nPages migrated by an agent are intentionally **unverified** (no `verified`\nkey). When a reviewer confirms a page, they add\n`verified: { by: \"human:<netid>\", at: \"<ISO 8601>\" }`.\n\n```bash\npython3 scripts/okf_validate.py docs      # OKF conformance (CI-enforced)\npython3 scripts/check_links.py docs       # links, images, nav coverage (CI-enforced)\npython3 scripts/gen_llms_txt.py           # regenerate llms.txt indexes (CI checks drift)\nzensical build --clean && python3 scripts/postbuild_agent_surface.py site\npython3 scripts/externalize_links.py      # add {target=_blank} to external links\n```\n\nThe deployed site is directly consumable by AI agents: `/llms.txt` (linked\noutline), `/llms-full.txt` (full corpus with frontmatter), a Markdown mirror\nat any page URL + `index.md`, `okf:*` meta tags and\n`<link rel=\"alternate\" type=\"text/markdown\">` on every page, and a\n`robots.txt` that advertises all of it. See `docs/about/ai-agents.md`.\n\n## Credits\n\nAdapted from the CyVerse Learning Center documentation by the CyVerse Science\nTeam, Copyright © The Arizona Board of Regents (CyVerse), licensed under\n[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) (see `LICENSE`).\nCyVerse is supported by the National Science Foundation (DBI-0735191,\nDBI-1265383, DBI-1743442). Each page's `sources` frontmatter and footer link\nthe original file; `docs/about/credits.md` has the full attribution and\ncitation guidance, and `MIGRATION.md` maps every old page to its new home.\nThis adaptation is not endorsed by CyVerse.\n\n## Deployment\n\nPushing to `main` on [UNM-CARC/cyverse](https://github.com/UNM-CARC/cyverse)\nruns OKF validation and the link check, verifies the llms.txt indexes, builds\nthe site, adds the agent surface, and deploys to GitHub Pages at\n<https://unm-carc.github.io/cyverse/> via `.github/workflows/docs.yml`. If the\nfirst deploy fails on permissions, set Settings → Pages → Source to\n\"GitHub Actions\" once.\n",
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