phase1-04e: Beer–Lambert Depth Integration for Light

[anibalrojosan]

Branch: feat/phase1-04e-beer-lambert
Type: backend
Priority: Medium
Dependencies: phase1-04d

Description

Implement $I(z) = I_0 \cdot e^{-\epsilon \cdot \mathrm{TSS} \cdot z}$ and produce an irradiance (or depth-integrated growth proxy) for EnvConditions, with TSS (or a documented proxy) from state/parameters. Aligns with MATH_MODEL / kinetics' use of $I$ for phototrophs. Integrate with 04a surface $I_0(t)$ and the time loop from 04d so a diel run can use a physically motivated light field.

Tasks

• Code + Test (in parallel): Beer–Lambert and unit tests (fixed $I_0$, TSS, depth, $\epsilon$).
• Test: Plug into RHS path: kinetics sees updated $I$ (regression on one or two time points if useful).
• Run Ruff: uv run ruff check src/bioprocess_twin/
• Format: uv run ruff format src/bioprocess_twin/