Remove unused code in forecasting pipeline

[ma595]

The unused code removal can be separated into three distinct categories.

Unused optimization code

• Remove src/nemo_spinup_forecast/optimization.py

Deletions relating to restart (relevant parts will be moved to another repo)

• src/nemo_spinup_forecast/restart.py
• restart_toolbox.sh
• standalone/restarter.py
• standalone/restarter_V2.py

Unused tools

• CMIP_to_xarray.sh
• xarray_to_CMIP.sh
• rename.sh

Fixes #79 #80

[Copilot]

Pull Request Overview

This pull request restructures the package from a lib/ directory-based approach to a proper Python package structure under src/nemo_spinup_forecast/, while removing unused code and updating configuration files for modern Python packaging practices.

Key Changes:

• Migrated code from lib/ to src/nemo_spinup_forecast/ package structure
• Removed unused utility scripts (shell scripts in tools/) and standalone Python files
• Replaced setup.py + requirements.txt + pytest.ini with modern pyproject.toml
• Added new test infrastructure (download_test_data.sh) and expanded test coverage

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tools/xarray_to_CMIP.sh	Deleted unused shell script for coordinate renaming
tools/rename.sh	Deleted unused shell script for directory reorganization
tools/CMIP_to_xarray.sh	Deleted unused shell script for coordinate transformation
standalone/restarter_V2.py	Deleted unused standalone restart file manipulation script
standalone/restarter.py	Deleted unused standalone restart file manipulation script
lib/restart.py	Deleted old library file (functionality not migrated to new package)
lib/optimization.py	Deleted unused optimization utilities
setup.py	Deleted legacy setup file in favor of pyproject.toml
requirements.txt	Deleted in favor of pyproject.toml dependencies
pytest.ini	Deleted in favor of pyproject.toml test configuration
main_restart.py	Deleted unused restart processing script
pyproject.toml	Added modern Python package configuration with build system, dependencies, and dev tools
tests/download_test_data.sh	Added script to download test data from GitHub releases
tests/test_forecast.py	Expanded with new NetCDF file creation and testing functions
tests/*.py	Updated imports from lib.* to src.nemo_spinup_forecast.*
src/nemo_spinup_forecast/forecast_method.py	New file containing forecaster base classes and implementations
src/nemo_spinup_forecast/dimensionality_reduction.py	New file with PCA and Kernel PCA implementations
src/nemo_spinup_forecast/density.py	Migrated from lib/, cleaned up numpy imports and added grav constant
src/nemo_spinup_forecast/utils.py	Updated import path for Simulation class
src/nemo_spinup_forecast/forecast.py	Removed unnecessary noqa comment
main.py	Updated imports to use new package structure
ruff.toml	Updated file exclusions to match new structure

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[ma595]

We want the forecast library to consist of code relating to the forecast step only. We intend to create a separate restart repo containing the necessary steps for modifying a pre-existing restart based on the ML hop or forecast.
@GuillaumeGACHON can you check if the remaining deletions make sense?

[GuillaumeGACHON]

Everything seems good to me !

[isaacaka]

Also remove Notebooks/Restart.ipynb

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[isaacaka]

Good to merge