Add deterministic explicit morphology locations

[ilkilic]

Summary

Implement #769

Add deterministic morphology targeting through a new ExplicitMorphologyLocations block.

Locations are represented as a non-empty collection of:

MorphologyLocationPoint(section_id=1, offset=0.5)

The block supports both single and multiple explicit locations.

Implementation

• Add MorphologyLocationPoint as a nested model.
• Add ExplicitMorphologyLocations as the only new user-facing block.
• Validate:
  • section_id is a non-negative integer.
  • offset is between 0.0 and 1.0.
  • At least one location is provided.
  • Referenced neurite sections exist when points_on() is called.
• Update the morphology locations example notebook.

Section ID convention

Locations use SONATA global section IDs:

• 0: soma
• 1..N: neurite sections in MorphIO nrn_order

Therefore, SONATA neurite section ID N maps to MorphIO section N - 1.

The generated dataframe is compatible with existing random morphology locations and contains section_id and normalized_section_offset for compartment-set materialization.

Additional fix

Fix normalized section-offset/path-distance calculations for random morphology locations

Tests

Added coverage for:

• Single neurite location
• Soma location
• Multiple locations
• Invalid section IDs and offsets
• Empty location lists
• Missing morphology sections

Compartment-set materialization is provided by the dependent infrastructure in PR #498.

[codecov]

Codecov Report

❌ Patch coverage is 89.28571% with 6 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...scientific/blocks/morphology_locations/explicit.py	88.00%	4 Missing and 2 partials ⚠️

Flag	Coverage Δ
pytest	75.59% <89.28%> (+0.33%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
obi_one/__init__.py	100.00% <100.00%> (ø)
obi_one/scientific/library/morphology_locations.py	60.17% <100.00%> (+32.49%)	⬆️
...ific/unions_and_references/morphology_locations.py	100.00% <100.00%> (ø)
...scientific/blocks/morphology_locations/explicit.py	88.00% <88.00%> (ø)

... and 2 files with indirect coverage changes

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[james-isbister]

Looks good. Just one suggestion

[james-isbister]

Probably we can reuse path_distance_all_segments_from in the library for calculating the path distance

[ilkilic]

Good point, I reused path_distances directly since we only need the distance for one segment here.