Support H5 morphology container and individual H5 morphologies#57
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darshanmandge wants to merge 11 commits intomainfrom
Open
Support H5 morphology container and individual H5 morphologies#57darshanmandge wants to merge 11 commits intomainfrom
darshanmandge wants to merge 11 commits intomainfrom
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ilkilic
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Feb 10, 2026
…for Cell simualtion and SONATA circuit simulations
…ore adding build/
- Add test for _is_valid_morphology_path method covering regular files and H5 containers - Add tests for type2name and mksubset class methods - Improve test coverage for new H5 morphology features This addresses codecov coverage gaps in the H5 morphology implementation.
- Fix W293 linting errors in test files - Remove trailing whitespace from blank lines in docstrings - Ensure all linting checks pass
- Add test for corrupted H5 container exception handling - Add test for SectionName dataclass functionality - Improve coverage from 92.34% to 92.39% (above HEAD's 92.36%) - Cover exception paths in template.py and morphio_wrapper.py - All tests passing (25 H5-related tests) This brings the branch coverage above HEAD and ensures all new H5 morphology functionality is thoroughly tested.
- Add test to verify soma conversion functions work correctly - Improves test coverage for morphology wrapper - Tests morph_as_hoc() output for soma sections Note: Codecov shows 81.36% patch coverage because it measures coverage of only the NEW lines added in the PR (403 lines in morphio_wrapper.py). Overall project coverage is 92.39% which is above HEAD's 92.36%. Some uncovered lines are edge cases (specific soma types, exception paths) that require rare morphology scenarios to trigger.
- Add test for make_convex with non-monotonic data (covers line 97) - Add test for _to_sphere function (covers lines 150-158) - Add test for single_point_sphere_to_circular_contour (covers lines 164-167) - Improves morphio_wrapper.py coverage from 90.80% to 97.70% - Overall project coverage improved to 93% Remaining uncovered lines (234, 235, 245, 247) are exception paths for invalid soma types that require malformed morphologies to trigger.
- Remove trailing whitespace from blank lines - Add noqa comment for morphio import availability check - All linting checks now pass
- Add test for split_morphology_path error condition (empty path) - Add test for H5 container path with cell name parsing - Add tests for contourcenter, get_sides, contour2centroid functions - Add integration test for nested H5 path validation - Add integration test for split_morphology_path with nested directories
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- add get_target_cell_ids tests for population and non-population node_set paths - add morph_filepath tests for h5v1, asc fallback, and wrapped error branches - add emodel_path fallback tests for hoc model_template and failure path
- make h5 integration path-validation tests self-contained with temp H5 files - remove conditional branches that skipped coverage in morphology wrapper tests - mark script-only __main__ block as no-cover - keep assertions deterministic for container/nested path parsing
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Description
Adds support for H5 morphology containers and individual H5 morphology files to BlueCelluLab, aligning the implementation with Neurodamus. It also fixes critical issues with node set resolution in multi-population circuits that were causing "Invalid range: 0-0" errors.
H5 Morphology Support
Core Implementation Changes
Bug Fixes
Examples and Tests
Dependencies
Added: morphio (required for H5 morphology support)