Dynamic revetment implementation

[christavanijzendoorn]

• New runup method included
• z0 can be defined based on grid
• shear module can handle spatially varying z0
• implementation of sand infilling within cobble
• sediment trapping implemented based on roughness density
• constants added where needed

[Copilot]

Pull Request Overview

This PR implements dynamic revetment functionality for coastal modeling, introducing composite beach handling with sand-cobble interactions, new runup calculation methods, and enhanced roughness-based sediment trapping capabilities.

Key changes include:

• Implementation of spatially varying roughness length (z0) from grid data
• Addition of Ruggiero runup method as alternative to existing Stockdon method
• New sediment trapping mechanism based on roughness density (lambda) for larger scale elements
• Comprehensive composite beach bed update algorithm handling sand infilling within cobble layers

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
aeolis/wind.py	Adds z0_grid method for spatially varying roughness and fixes shear stress array handling
aeolis/threshold.py	Implements new sediment trapping threshold modification based on roughness density
aeolis/shear.py	Enhances shear module to handle spatially varying stress values and removes unused whitespace
aeolis/hydro.py	Adds Ruggiero runup method option alongside existing Stockdon method
aeolis/constants.py	Defines new constants and configuration parameters for composite beach processes
aeolis/bed.py	Implements comprehensive composite beach bed update algorithm with sand-cobble interactions

Comments suppressed due to low confidence (2)

[Copilot]

Use isinstance(p['lambda'], (int, float)) instead of separate isinstance checks for better readability and performance.

Suggested change

	if isinstance(p['lambda'], int) or isinstance(p['lambda'], float):
	if isinstance(p['lambda'], (int, float)):

[Copilot]

Documentation should include proper citation format and parameter descriptions. The docstring is incomplete compared to the existing calc_runup_stockdon function.

Suggested change

	Calculate runup according to /Ruggiero et al 2004.
	Calculate runup according to Ruggiero et al. (2004).
	This function calculates the runup for dissipative conditions based on
	the significant wave height (Ho). The formula is derived from the work
	of Ruggiero et al. (2004).
	Parameters
	----------
	Ho : float
	Significant wave height (in meters).
	Returns
	-------
	eta : float
	Mean water level (set to 0 for this method).
	sigma_s : float
	Standard deviation of swash oscillations (set to 0 for this method).
	R : float
	Total runup height (in meters).
	References
	----------
	Ruggiero, P., Komar, P. D., McDougal, W. G., Marra, J. J., & Beach, R. A. (2004).
	Wave runup, extreme water levels and the erosion of properties backing beaches.
	Journal of Coastal Research, 20(3), 1018-1026.

[Copilot]

Placeholder text 'XX by YYY' should be replaced with actual description of what the function updates.

Suggested change

	Update XX by YYY
	layers.
	Updates the sand level, cobble thickness, and related parameters
	for composite beaches. This includes adjusting the bathymetry
	based on changes in sand cover and managing the overlap and
	distribution of cobbles and sand layers.

[Copilot]

Long line with many arguments makes code hard to read. Consider breaking this into multiple lines or using a list comprehension.

Suggested change

	ix_steps = np.vstack((ix_nocob[1,:], ix_step0[1,:], ix_step1[1,:], ix_step2[1,:], ix_step3[1,:], ix_step4[1,:], ix_step5[1,:], ix_step6[1,:], ix_step7[1,:], ix_step8[1,:]))
	ix_steps_list = [
	ix_nocob[1,:],
	ix_step0[1,:],
	ix_step1[1,:],
	ix_step2[1,:],
	ix_step3[1,:],
	ix_step4[1,:],
	ix_step5[1,:],
	ix_step6[1,:],
	ix_step7[1,:],
	ix_step8[1,:]
	]
	ix_steps = np.vstack(ix_steps_list)

[Copilot]

Use proper logging instead of print statements. Consider using logger.debug() or logger.warning() for debugging information.

Suggested change

	print(check)
	logger.debug(check)