Split Conformational Analysis into Explicit Serial Phases

[harryswift01]

Summary

This PR refactors the existing serial conformational analysis into explicit phases without changing execution behaviour. The current two-pass conformational workflow is preserved, but the logic is now separated into clearer steps for angle collection, peak construction, state assignment, flexible-dihedral counting, and final output merging. This prepares the conformational analysis for a future chunked map-reduce implementation.

Changes

Split peak-identification workflow into explicit phases:

• Extracted selected-frame dihedral angle collection into _collect_dihedral_angle_data(...).
• Extracted histogram and peak construction into _build_peak_data(...).
• Kept _identify_peaks(...) as a serial orchestration wrapper around the new phase helpers.
• Added DihedralAngleData and DihedralPeakData containers to make intermediate phase outputs explicit.

Split state-assignment workflow into explicit phases:

• Extracted group-level conformational state calculation into _calculate_group_state_data(...).
• Extracted final accumulator merging into _merge_group_state_data(...).
• Kept _assign_states(...) as a serial orchestration wrapper around the new phase helpers.
• Added ConformationStateData to represent state labels and flexible-dihedral counts before final output construction.

Update atomic unit tests:

• Updated dihedral unit tests to cover the new explicit serial phase boundaries.
• Added tests for angle collection, peak construction, group state calculation, and final output merging.
• Preserved existing behaviour tests for negative-angle wrapping, histogram peak detection, state assignment, progress handling, and frame-selection bounds.
• Confirmed that unit and regression tests pass.

Impact

• Makes the conformational analysis workflow easier to reason about and maintain.
• Preserves the existing serial execution behaviour and scientific output.
• Keeps the MDAnalysis frame-index contract unchanged: Dihedral.run(...) uses analysis-universe frame bounds, while results.angles is indexed locally from zero.
• Creates clear internal phase boundaries that can later be mapped onto chunked serial execution and Dask-based map-reduce.
• Avoids introducing chunking, Dask, scheduler logic, or public API changes in this PR.

[jimboid]

More prep for further work on the parallel implementation. I will approve this on the basis that the cyclohexane regression test is looked at, since I will be at a conference the next two days and won't respond as quickly.