Kevin R. Thornton
Kevin R. Thornton
With Cython 0.25.2, GCC5.2, and Ubuntu, I'm getting the following unit test failure: test_gsl_vector_view_array_with_stride (cython_gsl.test.test_vector.VectorTest) ... *** stack smashing detected ***: /usr/bin/python terminated
The genic selection model is not giving the correct output when the starting frequency is high. The code to reproduce the plot below is [here](https://github.com/molpopgen/msprime_discoal_comparison), and the README discusses the...
(This is related to #2024) The docs for `recombination_rate` under `sim_ancestry` state: ``` See the [Recombination](https://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-recombination) section for usage examples for this parameter and how it interacts with other parameters....
The firsts symptoms of the error in #1966 were a Jupyter notebook kernel repeatedly dying. This behavior is due to the use of `tsk_bug_assert` , which calls `abort`, preventing any...
This issue is motivated by #1762 The current class for modeling the [structured coalescent](https://pubmed.ncbi.nlm.nih.gov/3066685/) is `msprime.SweepGenicSelection`. This class handles the following scenario: * Given a start/end frequency (e.g., moving backwards...
Related to #1762, `verification.py` only considers sweep models with initial frequencies of 1/2N.
The docs for `msprime.sim_ancestry` say that ploidy defaults to 2, yet the function defaults to `None`. It would be preferable if the function default were acutally 2, especially for people...
It'd be handy for the cell magic to support something like this: ``` %%pybind11 -I=`gsl-config --cflags` -I=`python -c "import numpy;print(numpy.get_include())"` ``` When using other Python packages that provide headers, it'd...
## 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...
When the output dimension of a statistic is large, so is the memory consumption. The following example calculates the pairwise distance matrix for all samples from a single tree and...