feat(num_feat): add NumericalFeature.feature_matrix (#337)

[breimanntools]

Closes #337.

Summary

Adds NumericalFeature.feature_matrix(features, dict_num_parts, df_scales=..., n_jobs=1), the
numerical analog of SequenceFeature.feature_matrix: it turns CPP.run_num-selected features back
into a model matrix X, preserving the per-residue context that per-AA-averaged sequence features
discard.

Details

• Values are reconstructed exactly the way CPP.run_num does — the SPLIT in each feature id is
  re-applied to the part's 0-based residue axis (arange(L_part)), the SCALE selects the column, and
  the selected residues are nanmean-averaged (round 5).
• The df_feat positions column is a JMD-offset display numbering (e.g. 21..30 for a TMD), not a
  tensor index, so it is deliberately not used for value lookup (documented in the method Notes).
  Output is byte-identical to run_num's recompute_feature_matrix (verified for uniform and
  variable-length parts); per-part real lengths are inferred from the NaN padding get_parts emits.
• Heavy lifting lives in NumericalFeature's own _backend/num_feat/feature_matrix.py (reusing the
  shared CPP split/parse helpers). @staticmethod, consistent with the class.
• No __init__.py change (method on an already-exported class).

Ripple

• numpydoc docstring (named Returns / Raises / Examples include)
• executed example notebook examples/nf_feature_matrix.ipynb (every public parameter, display_df tables)
• 27 unit tests (per-parameter positive+negative, golden hand-computed means, run_num consistency, ragged parts)
• release-notes Unreleased entry

Part of epic #336.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 92.04545% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.83%. Comparing base (7dcc8d8) to head (a2d28f9).
⚠️ Report is 9 commits behind head on master.

Files with missing lines	Patch %	Lines
...analysis/feature_engineering/_numerical_feature.py	89.47%	3 Missing and 1 partial ⚠️
...re_engineering/_backend/num_feat/feature_matrix.py	94.00%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##           master     #347    +/-   ##
========================================
  Coverage   94.83%   94.83%            
========================================
  Files         196      197     +1     
  Lines       18767    18870   +103     
  Branches     3175     3196    +21     
========================================
+ Hits        17797    17895    +98     
- Misses        633      637     +4     
- Partials      337      338     +1     

Files with missing lines	Coverage Δ
...re_engineering/_backend/num_feat/feature_matrix.py	94.00% <94.00%> (ø)
...analysis/feature_engineering/_numerical_feature.py	96.26% <89.47%> (-3.74%)	⬇️

... and 9 files with indirect coverage changes

Components	Coverage Δ
cpp_core	94.95% <ø> (ø)

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