Disambiguate the device model from device instance (#5)

* remove DeviceModel

* update changelog

* Introduce DeviceModel and DeviceInstance

* Refactor DeviceInstance and DeviceModel documentation and attributes; add FiberInsertion and LensPositioning definitions

* Rename ObjectiveLens and ObjectiveLensModel to OpticalLens and OpticalLensModel; update related mock functions and tests

* Refactor DeviceInstance and DeviceModel references to use Device as the parent type; update mock functions and tests accordingly

* Update changelog, release notes, and namespace for version 0.2.0;

* Refactor README to categorize neurodata types and update device model and instance descriptions

* Refactor code structure for improved readability and maintainability

* ruff fixes

* Add ExcitationSource and PulsedExcitationSource classes to device instance definitions

* Remove unused code and improve notebook structure for clarity

* ignore ruff check on print statements in the example notebook

* Enhance documentation by marking attributes as optional in README and YAML files

* Update docs/source/description.rst

Co-authored-by: Ryan Ly <[email protected]>

* update __all__

* Update device model addition in documentation

* Update DeviceModel class diagram to reflect correct inheritance from Device

---------

Co-authored-by: Ryan Ly <[email protected]>

Author: alessandratrapani

CHANGELOG.md

@@ -1,3 +1,30 @@
+# v0.2.0 (Upcoming)
+
+## Deprecations and Changes
+### Major Refactoring:
+- Implemented a clear distinction between device models and device instances:
+  - Added ``DeviceModel`` as a base class for all device model classes
+  - Added ``DeviceInstance`` as a base class for all device instance classes
+  - Refactored all device classes into model and instance pairs (e.g., ``OpticalFiberModel`` and ``OpticalFiber``)
+  - Renamed ``ObjectiveLens`` to ``OpticalLens`` for consistency
+
+### New Features:
+- Added new neurodata types:
+  - ``LensPositioning``: Extends ``NWBContainer`` to hold metadata on the positioning of a lens relative to the brain.
+  - ``FiberInsertion``: Extends ``NWBContainer`` to hold metadata on the insertion of a fiber into the brain.
+
+### Changes:
+- Changed ``illumination_type`` to ``source_type`` in ``ExcitationSourceModel`` for better clarity.
+- Removed ``excitation_wavelength_in_nm`` from ``ExcitationSourceModel`` as it's often redundant with filter specifications.
+- Removed ``detected_wavelength_in_nm`` from ``PhotodetectorModel`` as it's often redundant with filter specifications.
+- Added ``wavelength_range_in_nm`` to ``ExcitationSourceModel`` and ``PhotodetectorModel`` to specify the range of wavelengths.
+
+## Bug Fixes
+
+## Features
+
+## Improvements
+
 # v0.1.1 (Feb 25, 2025)
 
 ## Deprecations and Changes