docs: Add comprehensive documentation for configuration system #447
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Add documentation for the YAML-based configuration system introduced in PRs #417 and #441: - configuration-system.md: Main guide covering architecture, machine configs (illumination, confocal, camera mappings), user profiles (general.yaml, objective.yaml), merge logic, and best practices - configuration-api.md: Developer reference for ConfigRepository API, Pydantic models, utility functions, and access patterns - configuration-migration.md: Migration guide from legacy XML/JSON format including auto-migration, manual migration script usage, and troubleshooting - Update automation.md to reference new configuration docs Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Fix has_legacy_configs_to_migrate() signature (takes profile and base_path) - Clarify confocal_config.yaml structure matches Pydantic model - Add note about .example file format difference Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The method signature is get_channels(objective), not get_channels(). Updated the widget example to show correct usage. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Mark camera_mappings.yaml as optional (for multi-camera setups) - Mark intensity_calibrations/ as optional in directory diagram - Mark illumination_channel_config.yaml as required Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Pull request overview
This PR adds comprehensive documentation for Squid's YAML-based configuration system, covering user guides, developer API reference, and migration procedures for upgrading from the legacy XML format.
Changes:
- Three new documentation files (
configuration-system.md,configuration-api.md,configuration-migration.md) providing complete coverage of the configuration architecture - Updated cross-reference in
automation.mdto point to the new configuration documentation
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
software/docs/configuration-system.md |
Main user guide covering architecture, machine configs, user profiles, merge logic, and best practices |
software/docs/configuration-api.md |
Developer reference documenting ConfigRepository API, Pydantic models, and code integration patterns |
software/docs/configuration-migration.md |
Migration guide for transitioning from legacy XML/JSON format to YAML |
software/docs/automation.md |
Updated cross-reference to point to new configuration system documentation |
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| | `public_properties` | Properties available in `general.yaml` | | ||
| | `objective_specific_properties` | Properties only in objective-specific files | | ||
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| > **Note**: The `confocal_config.yaml.example` file in `machine_configs/` uses a simplified format for reference. When creating your actual config, use the structure shown above which matches the Pydantic model. |
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This note refers to a confocal_config.yaml.example file but doesn't explain what the simplified format looks like or why it differs from the actual format. Consider adding a brief explanation of the differences or removing the reference if the example file uses the same format.
Suggested change
| > **Note**: The `confocal_config.yaml.example` file in `machine_configs/` uses a simplified format for reference. When creating your actual config, use the structure shown above which matches the Pydantic model. | |
| > **Note**: The `confocal_config.yaml.example` file in `machine_configs/` is a minimal example: it only includes a small subset of filter-wheel mappings and properties to keep the file easy to read. Your actual `confocal_config.yaml` must follow the full structure documented above (including `version`, `filter_wheel_mappings`, `public_properties`, and `objective_specific_properties`); you can copy the example as a starting point and then extend it to match your hardware. |
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Summary
New Documentation
configuration-system.md(Main Guide)configuration-api.md(Developer Reference)configuration-migration.md(Migration Guide)tools/migrate_acquisition_configs.pyTest plan
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