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add modular simplifier

13

## Description WIP related to #2751. This PR adds the basic functionality for a "modular" simplifier along with tests. # PR Checklist: - [ ] Tests that fully cover new/changed...

molpopgen

The documentation for IBD is quite sparse and preliminary. When we have implemented MRCA IBD (#2896) we should flesh it out.

jeromekelleher

Add support for MRCA based IBD

2

The MRCA definition of IBD is useful in some cases, and it would be good for us to support it. From an API perspective, I think all that we need...

jeromekelleher

C API for numpy 2.0

4

Numpy 2.0 is about to land, and might have some consequences for us at the C level. Notes on [C API changes](https://numpy.org/devdocs/numpy_2_0_migration_guide.html#c-api-changes) More importantly, [oldest-supported-numpy](https://github.com/scipy/oldest-supported-numpy) is being deprecated, so we...

jeromekelleher

Numpy 2.0 Python

5

Numpy 2.0 is about to drop: https://github.com/numpy/numpy/issues/24300 - [migration guide](https://numpy.org/devdocs/numpy_2_0_migration_guide.html) There is a ruff plugin which can check this as [lint](https://numpy.org/devdocs/numpy_2_0_migration_guide.html#ruff-plugin) This might be a motivation to switch to ruff...

jeromekelleher

Currently undocumented. See also #2889 Also note the parallelism, this needs some explanation.

jeromekelleher

Currently undocumented. Requires #2888

jeromekelleher

Add direct links to Python and C APIs from README

1

I use these a fair bit

hyanwong

Say we have a true situation like this: ``` p | p | p | | | | | | | a | a | a | / \ |...

petrelharp

Can I get a list of descendants of a branch (edge)?

11

Hi there, thank you for developing a terrific library. I'm trying to perform certain matrix operations using tskit. Suppose that A is a matrix in which the number of rows...

hanbin973