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Annolid Docs

Annolid is a practical toolkit for annotation, segmentation, tracking, behavior analysis, and model-assisted workflows in real research settings.

The current codebase includes:

  • the desktop GUI launched with annolid,
  • the plugin-based CLI launched with annolid-run,
  • Annolid Bot in the GUI, including multimodal chat and optional background integrations,
  • deployment pipelines for the landing page, docs portal, and notebook-style tutorial book.

Start Here

  • Installation: choose the right install path for your platform.
  • uv Setup: create a local development environment with .venv.
  • Workflows: follow the main GUI, CLI, and analysis flows.
  • Tutorials: jump to practical notebooks, videos, and focused guides.
  • MCP: extend Annolid Bot with Model Context Protocol servers.
  • Codex and ACP: choose between cloud Codex, local Codex CLI, and long-lived ACP coding sessions.
  • Agent Calendar: configure Google Calendar auth, cached tokens, and token renewal.
  • Agent Secrets: keep agent/provider credentials out of plaintext config.json.
  • Agent Security: audit session scope, tool policy, channel exposure, and local agent state.
  • SAM 3D: configure the optional 3D reconstruction integration.
  • Reference: commands, config files, and operational paths.
  • Deployment: understand how docs and the website are published.

Current Documentation Surfaces

  • README.md: repository overview and quick-start guidance.
  • docs/: canonical MkDocs content published to the docs portal and mirrored root routes.
  • website/: the landing page source for annolid.com/.
  • docs/tutorials/: notebook tutorials tracked in the repository.

Current Product Status

  • Python support in the package metadata is >=3.10; current docs and CI focus on Python 3.10 to 3.13.
  • The primary entry points are annolid for the GUI and annolid-run for model/plugin workflows.
  • Annolid Bot is an active part of the GUI and now includes a Zulip draft/send workflow in the bot dock when Zulip is configured.
  • Agent/provider credentials can now be managed through annolid-run agent-secrets-audit, agent-secrets-set, and agent-secrets-migrate so config.json can reference environment or local private secrets instead of storing plaintext.
  • Agent security posture can now be reviewed through annolid-run agent-security-check and annolid-run agent-security-audit, with --fix available for safe local permission repairs.
  • Docs are built with MkDocs in strict mode through the docs-quality and docs-pages GitHub Actions workflows.