Fix SONATA compartment report mapping

[ilkilic]

Description

Fix the SONATA mapping generated for compartment and compartment_set reports.

Previously, the writer created one node_ids entry per recording location and generated sequential element_ids. This produced duplicated node IDs when multiple locations were recorded from the same cell.

The report mapping now:

• writes each node id once
• groups its recorded elements using index_pointers
• uses the LibSONATA section ID as element_id, matching Neurodamus
• preserves separate traces for multiple offsets on the same section.

For example, 20 recording locations on node 0 are now represented as:

node_ids = [0]
index_pointers = [0, 20]

instead of:

node_ids = [0, 0, ..., 0]
index_pointers = [0, 1, ..., 20]

Changes

• Add the LibSONATA section ID to recording-site metadata.
• Group report elements by node when generating the H5 mapping.
• Use section IDs instead of sequential trace indices for element_ids.

[codecov]

Codecov Report

❌ Patch coverage is 99.21875% with 1 line in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
bluecellulab/cell/core.py	93.75%	1 Missing ⚠️

Files with missing lines	Coverage Δ
bluecellulab/reports/utils.py	94.94% <100.00%> (+0.18%)	⬆️
bluecellulab/reports/writers/compartment.py	86.81% <100.00%> (+3.47%)	⬆️
bluecellulab/type_aliases.py	100.00% <100.00%> (ø)
tests/test_cell/test_core.py	99.46% <100.00%> (+0.01%)	⬆️
tests/test_reports/test_compartment_writer.py	99.43% <100.00%> (+0.26%)	⬆️
tests/test_reports/test_reports_utils.py	98.47% <100.00%> (+0.14%)	⬆️
bluecellulab/cell/core.py	79.40% <93.75%> (+0.47%)	⬆️

... and 2 files with indirect coverage changes

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