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Files that changed from the base of the PR and between 6d15a49b9f2a8ce3802c0da598056d24a968ef1d and 353e6b67752d565f2ee90c7d90643f092ec25d38.
Walkthrough
The recent updates to the GeneticInheritanceGraphLibrary focus on refining data structures and algorithms for better performance and accuracy in genetic inheritance simulations. Key enhancements include the introduction of validation for genetic edges, optimization of interval handling from sets to lists for efficiency, and the addition of functionality to simulate random genetic matching. These changes aim to improve the library's reliability and extend its capabilities in modeling complex genetic inheritance patterns.
Changes
| Files | Change Summary |
|---|---|
graph.py & tables.py |
- Introduced _validated attribute and edges_valid property for validation.- Optimized interval handling with lists. - Added methods for better data integrity and performance. |
README.md |
- Clarified interval inversion handling in GIG library documentation. |
tests/gigutil.py & tests/test_gigutil.py |
- Enhanced simulation classes with new logic and methods. - Added comments and variable renaming for clarity. - Implemented a new test function to validate simulation accuracy. |
tests/test_graph.py |
- Updated assertions to accommodate changes in interval handling. - Added a new test method for validating random matching positions. |
🐇✨
Changes afoot in the code we weave,
Lists over sets, in efficiency we believe.
Validations and tests, to ensure it's right,
Inheritance patterns, in simulated light.
Here's to progress, in our digital grove,
With each update, forward we move.
🌟🐾
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Creates a simple forward simulator with recombination (
DTWF_one_recombination_no_SV_slow_simin gigutils.py)There are no structural variations being created in here yet, but recombination seems to work, hurrah!
Logic is not fully tested yet. One way to do this would be to create an equivalent tree sequence forward simulator using the same RNG calls, and check the outputs are the same.
Summary by CodeRabbit