Change to integer intervals, Use "IEdge" rather than "Edge"

[hyanwong]

and rename "TableGroup" to "Tables". We can refer to the tree sequence tables as ts_tables when used in a variable.

Summary by CodeRabbit

• New Features

  • Integrated tskit for enhanced genetic inheritance data handling.
  • Improved representation of genetic inheritance intervals with new table structures.

• Bug Fixes

  • Corrected data types for interval positions to ensure accuracy in genetic data representation.

• Refactor

  • Renamed key components to align with updated genetic data models.
  • Streamlined methods for accessing and manipulating genetic data tables.

• Tests

  • Updated test suite to reflect changes in table structures and naming conventions.
  • Enhanced testing for new data types and table methods.

[coderabbitai[bot]]

Walkthrough

The GeneticInheritanceGraph module underwent a refactor, aligning with updates from the tskit library. Key components like TableGroup and IntervalTable were renamed to Tables and IEdgeTable, respectively. Data types for table columns shifted from float to int, and the handling of tree sequences and sample nodes was updated. This overhaul likely enhances performance and compatibility with tskit.

Changes

File Path	Change Summary
GeneticInheritanceGraph/__init__.py, GeneticInheritanceGraph/constants.py	Updated imports and constants to align with tskit.
GeneticInheritanceGraph/tables.py	Renamed classes, changed column data types, and added methods for handling integer positions and samples.
tests/conftest.py, tests/gigutil.py, tests/test_tables.py	Reflected renaming of classes and methods, updated variable names and method calls to match the new structure.

Poem

🐇✨ In the graph where genes intertwine, A change was made, oh so fine. Floats to ints, names anew, CodeRabbit hopped, and the module flew. 🌟🧬

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[codecov-commenter]

Codecov Report

Attention: 14 lines in your changes are missing coverage. Please review.

Comparison is base (a7f1a14) 94.24% compared to head (c67a70a) 89.30%.

Files	Patch %	Lines
GeneticInheritanceGraph/tables.py	80.00%	1 Missing and 13 partials :warning:

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #43 +/- ## ========================================== - Coverage 94.24% 89.30% -4.94% ========================================== Files 3 4 +1 Lines 139 187 +48 Branches 22 35 +13 ========================================== + Hits 131 167 +36 - Misses 4 5 +1 - Partials 4 15 +11 ```

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[hyanwong]

I also renamed "all_mutation_types_gig" to "all_sv_types_gig": I hope that makes sense @duncanMR (these aren't what we normally call mutations as present in the "mutations" table)

[duncanMR]

That's a good point re: mutations. Thanks for the changes!

[hyanwong]

OK, merging. Fixes #43