fix: hydrophobic energy does not return nan when no hydrophobic residues

[jakublala]

Fixes #121

Summary by CodeRabbit

• Bug Fixes

  • Hydrophobic energy now correctly returns 0 when no hydrophobic residues are present in the relevant region.
  • Consistent SASA-based weighting applied across modes (“surface” and “core”) using only relevant hydrophobic atoms.

• Tests

  • Added unit tests for scenarios with no hydrophobic residues across all modes, verifying zero (non-NaN) energies.

• Chores

  • Bumped package version to 0.1.12.

[coderabbitai]

📝 Walkthrough

Walkthrough

Version bumped to 0.1.12. HydrophobicEnergy.compute now intersects relevance and hydrophobic masks, adds early return when no hydrophobics, and adjusts SASA weighting to use the combined mask. New unit test validates zero-energy behavior when no hydrophobic residues are present across modes.

Changes

Cohort / File(s)	Summary
Versioning pyproject.toml	Bumped project version from 0.1.11 to 0.1.12.
Hydrophobic energy logic src/bagel/energies.py	Compute uses combined_mask = relevance_mask & hydrophobic_mask, early-return (0.0, 0.0) if none, and mode-specific SASA means now taken over combined mask.
Unit tests tests/unit_tests/test_energies.py	Added parameterized test ensuring energies are 0.0 when no hydrophobic residues (GLU/ASP-only structure) for modes 'all', 'surface', 'core'.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Binder new #90: Related changes to HydrophobicEnergy’s mode-based SASA weighting; this PR refines masking and adds early-return behavior.

Poem

A nibble of code, a hop in the log,
Masks now align where hydrophobes jog.
If none are found—zero we say,
Tests keep watch in their tidy array.
Version bumps softly—flip of a page,
Carrot-high fives from a coding-stage hare! 🥕🐇

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 25.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the primary change by stating the hydrophobic energy function no longer returns NaN when no hydrophobic residues are present.

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✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/hydrophobic-energy-nan

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