Zensical - #16
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Replace links to this doc with terrain API doc links.
Remove docs/services/api/schema.md
Added notes about input/output paths inside job Docker containers.
* Updated `agave://data.cyverse.rocks` to `agave://data.iplantcollaborative.org` for consistency. * Clarified line about `notes` fields that are not ignored by the DE. * Clarified phrasing about `notes.semantics.ontology` lists.
CORE-1889 Add Tapis v2 to v3 app migration guide
Added `jq` migration helper docs.
Updated the `jq` migration helper docs with a command to populate `envVariables` fields.
Updated the `jq` migration helper commands handle default values and to use the `BATCH` job type.
Added example Tapis v3 `curl` commands.
Added `System Permission Requirements for App Creators` docs.
Updated `Outputs` section for non Docker runtime apps. Updated the `jq` migration helper command `execSystemId` and `maxMinutes` values.
This major update reorganizes the CyVerse documentation structure to improve discoverability and provide clear pathways for different user personas. Navigation Restructuring: - Migrated from MkDocs to Zensical configuration (zensical.toml) - Reorganized navigation into 7 clear sections with role-based approach - Added all 25 previously orphaned files to navigation (100% coverage vs 72%) - Integrated all 22 filesystem API endpoints into hierarchical structure - Added setup guides (Ansible, Docker, Database) to Deployment Guide - Added ingress-nginx deployment documentation - Included Tapis v2-v3 migration guide in Migration Guides section Homepage Improvements (index.md): - Complete redesign with role-based navigation for 3 personas: * DevOps Engineers - infrastructure deployment pathway * System Administrators - user management and operations pathway * Application Developers - API integration pathway - Added documentation sections summary table - Added CyVerse platform components overview - Added quick links section - Improved visual hierarchy and scanability Getting Started Guide Expansion (services/getting_started.md): - Added detailed prerequisites and infrastructure requirements - Created deployment roadmap with Mermaid diagram showing component dependencies - Added 7-week deployment timeline with phases - Created persona-based quick starts for each user type: * DevOps: 5-step deployment workflow with verification steps * Admins: Common administrative tasks and resources * Developers: API integration patterns and resources - Added technology stack overview - Expanded authentication, security, and platform components sections Developer Guide Creation (development/index.md): - Created comprehensive 550+ line developer guide (was placeholder) - Added development environment setup instructions - Documented CyVerse architecture with ASCII diagrams - Included API integration guide with Python code examples: * OAUTH 2.0 authentication (browser and CLI methods) * Filesystem operations (list, upload, download) * Job submission and monitoring * File uploads including chunked uploads for large files - Added custom application best practices - Documented GitHub contribution workflow - Added testing requirements and standards - Created CyVerse repositories directory - Added community and support resources FAQ Population (guides/faq.md): - Populated FAQ with 40+ questions across 5 categories: * Deployment & Installation (8 questions) * Administration (8 questions) * API & Development (7 questions) * Troubleshooting (5 questions) * Data Management (6 questions) - Each answer includes code examples and links to detailed documentation Bug Fixes: - Fixed 4 broken links in services/api/endpoint-index.md (missing closing parentheses) - Removed duplicate FAQ file (services/faq.md, kept guides/faq.md) Content Updates: - Updated subscriptions.md to remove Phoenix Bioinformatics references - Updated all subscription links to subscribe.cyverse.org - Added subscription benefits and management information Build Verification: - Clean Zensical build in 0.13s with no errors - All 88 pages generated successfully - Verified all previously orphaned files now accessible Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
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Updated documentation build instructions from MkDocs Material to Zensical, including new commands (zensical serve/build), configuration file reference (zensical.toml), and corrected typos. Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
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merging new zensical theme