Add type annotations, docstrings, and comments across codebase

[antoine-frot]

General:

• Added type annotations (: and ->) and one-line docstrings to all functions in src/ and src/libs/.
• Corrected spacing issues throughout.

File-specific:

• config.py: Added comments for all options and paths with sidechains_examples filenames, comments for check_paths, corrected typo for 'soap_lcut' (removed trailing space), renamed paths0/paths1 to input_files/output_bases.
• basis.py: Removed basis_read wrapper, renamed basis_read_full to basis_read, renamed Lmax/Nmax to lmax/nmax for consistency, added main block for standalone use.
• ALL.bash: Refactored to separate training (training.bash) from prediction (extrapolation.bash).

Note: I commented out the variance computation in regression.py I will reintroduce in a future commit.

[briling]

Good work, thank you! Will need some time to merge with the refactored version though...

[briling]

Note: I commented out the variance computation in regression.py I will reintroduce in a future commit.

In principle this should not be in the PR. next time you can add partial changes with git add -p

[antoine-frot]

Note: I commented out the variance computation in regression.py I will reintroduce in a future commit.

In principle this should not be in the PR. next time you can add partial changes with git add -p

Okay thank you I did not know about this interesting feature.