Refactored until second_project.explicit_forward_non_advective

[ray-chew]

Intermediate merge before the last push for the implicit solver.

[Copilot]

Pull Request Overview

This PR refactors the flow-solver and blending interfaces to unify function signatures around a central mem (simulation state) object, standardizes imports, and introduces a FlowSolverCache for performance. Key changes include:

• Standardized API: functions now accept mem and ud parameters instead of multiple positional arguments.
• Performance enhancement: added FlowSolverCache to cache recovery and velocity arrays.
• Cleanup: updated import paths, removed deprecated modules, and split large functions into smaller helpers.

Reviewed Changes

Copilot reviewed 39 out of 39 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/pybella/interfaces/dynamics_blending/schemes.py	Updated blending function signatures to use mem and ud
src/pybella/flow_solver/utils/variable.py	Refactored primitive calculations and added FlowSolverCache
src/pybella/flow_solver/utils/prepare.py	Adjusted imports and injected FlowSolverCache into simulation state
src/pybella/flow_solver/utils/options.py	Removed deprecated options definitions
src/pybella/flow_solver/utils/boundary.py	Updated imports and added scale_wall_node_values helper
src/pybella/flow_solver/physics/low_mach/laplacian.py	Fixed relative import path for options
src/pybella/flow_solver/physics/hydrostatics.py	Cleaned up array concatenations and formatting
src/pybella/flow_solver/physics/gas_dynamics/recovery.py	Major refactor: decoupled functions, added caching hooks
src/pybella/flow_solver/physics/gas_dynamics/numerical_flux.py	Refactored flux logic with utility kernels and njit
src/pybella/flow_solver/physics/gas_dynamics/explicit.py	Simplified advect and explicit_step_and_flux
src/pybella/flow_solver/physics/gas_dynamics/cfl.py	Split CFL logic into helper functions
src/pybella/flow_solver/discretisation/time_update.py	Unified do() signature, updated calls, but missing logging import
src/pybella/flow_solver/discretisation/grid.py	Fixed import path for options
src/pybella/data_assimilation/utils.py	Fixed import paths
src/pybella/data_assimilation/letkf.py	Fixed import paths
src/pybella/data_assimilation/analysis.py	Adjusted unpacking of mem tuple
src/pybella/main.py	Updated time_update invocation, introduced unused prepare import
run_scripts/test_suite.py	Trimmed trailing whitespace
README.md	Updated CI badge to deploy.yml workflow
.coveragerc	Updated omit paths for new package structure

Comments suppressed due to low confidence (3)

src/pybella/interfaces/dynamics_blending/schemes.py:585

• The call to do_psinc_to_comp_conv now passes ud twice due to the updated signature; adjust the arguments to (mem, ud, bld, label, writer, step, tout) so they match the new definition.

do_psinc_to_comp_conv(
                mem,
                ud,
                bld,
                ud,
                label,
                writer,
                step,
                t + dt,
            )

src/pybella/flow_solver/discretisation/time_update.py:72

• The logging module is used here but not imported; add import logging at the top of this file.

logging.info(f"step = {mem.time.step}, window_step = {mem.time.window_step}")

src/pybella/main.py:7

• [nitpick] The prepare import is unused in this module; consider removing it to clean up imports.

from .flow_solver.utils import prepare

[ray-chew]

This is again another big PR:

Will be merging this without review after all tests have passed, and if changes have to be made based on copilot's reviews.