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Assign numpy structured array to metadata

7

No work has been done on this, there are some easy wins like grouping together calls to `pack` and `unpack` where possible. Maybe after #511

benjeffery

For 1.0 we should do a quick review of these.

benjeffery

Improve docs for modifying metadata

1

From #3140 "Still, it'd be good to have not just "see here" but maybe a warning that in-place modification wont' work. (Also, those docs don't have the simplest use cases...

benjeffery

We should add in a citation from the docstring of `extend_haplotypes` to the published version of https://www.biorxiv.org/content/10.1101/2024.11.30.626138v2, i.e. when it comes out of preprint. This issue is just a reminder...

hyanwong

Setuptools license deprecation

1

Getting this on the current build: ``` /home/benj/projects/tskit/env/lib/python3.12/site-packages/setuptools/dist.py:760: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License ::...

benjeffery

Let's say we have two sets of nodes, `A` and `B`, and let `R` be the `|A| x |B|` matrix that gives relatedness between `A` and `B`. Given a vector...

petrelharp

Documentation/Tutorial for multithreading

4

Continuing from https://github.com/tskit-dev/tskit/pull/3077. I think this link from numpy docs is a good starting point: https://numpy.org/doc/2.2/reference/random/multithreading.html The bottom line is that one can execute multiple computations concurrently with `concurrent.futures.ThreadPoolExecutor` given...

hanbin973

Clarify mutation order in Site() object

5

This is useful to know without having to dive into the order requirements docs. I'm often looking this up to find the inherited state at a node.

hyanwong

`ts.pair_coalescence_rates` can give large or infinite rates

2

Here's an example giving a maximum value of infinity in the returned matrix: ```python L = 10e6 # 10 Mb params = {"sequence_length": L, "population_size":1e4, "recombination_rate": 1e-8, "random_seed": 6} sweep_model...

hyanwong

Chromosome data in VCF

3

Hi, My SLiM simulations include multiple chromosomes (recombination rates are set at 0.5 between them, as described [here](https://github.com/tskit-dev/tskit/issues/176#issuecomment-483839707) ) and I'd like to create a VCF that reflects this structure....

MleGhis