phase1-05: Dynamics Visualization and Ground Truth Validation

[anibalrojosan]

Issue: phase1-05: Dynamics Visualization and Ground Truth Validation
Branch: feat/streamlit-dashboard
Type: frontend
Priority: Medium
Dependencies: phase1-04

Description

Develop the visualization layer. While UI testing is lighter, ensure that the data processing for plots is robust and exports are consistent.

Mathematical Context

• Reference: See @docs/MATH_MODEL.md.
• Core Logic: Visualize the interaction between biological rates ($\rho$) and chemical states (pH, $DO$).
• Validation: Compare outputs against Figure 2 & 3 of Casagli et al. (2021).

Tasks

• Test: Verify data transformation logic for visualization (e.g., unit conversions).
• Code: Develop src/utils/visualization.py and src/main.py (Streamlit).
• Test: Ensure exported "Ground Truth" data matches simulation outputs.
• Run quality checks: uv run ruff check src/
• Format code: uv run ruff format src/

Acceptance Criteria

• Dashboard displays diel cycles (day/night) for $O_2$ and pH correctly.
• Exported data is valid and ready for PINN training (Phase 2).
• All utility functions pass unit tests.
• Code passes Ruff validation.