Graham Gower

Exercises

1

Thanks for the amazing resource! It's greatly apreciated, and I'm learning a lot. One thing that is lacking is a concrete set of exercises that follow the content. Any recommendations...

docs for Demography.add_population_split() (and others) parameters are unclear

1

Docs for the following `Demography` methods: [`add_population_split()`](https://tskit.dev/msprime/docs/latest/api.html#msprime.Demography.add_population_split), `add_admixture()`, `add_mass_migration()`, `add_migration_rate_change()`, `add_simple_bottleneck()`, `add_instantaneous_bottleneck()`; all have problematic formatting of types in the parameters section. In addition, they all accept either an integer...

mspms slow compared with ms

7

Here's a small three population example without recombination. ```sh # ms.sh $MS 2 1 \ -t 1.0 \ -I 3 1 0 1 \ -em 0.0 3 2 1.0 \...

`nn.tabulate()` unexpectedly prints to the jupyter console

2

### System information flax 0.5.3 rich 11.2.0 ### Problem you have encountered: The new `tabulate()` function returns a string. It doesn't print the tabulation to the terminal. However, if the...

--- Supercedes #36294

incorrect line number in warning

1

In contrast to errors, warnings print line numbers starting from 0 and appear to correspond to the line of the clause head rather than a more specific line inside the...

exception tracebacks in `run:` blocks are sent to /dev/null, making rules hard to debug

14

**Snakemake version** 7.8.1 **Describe the bug** When calling python code in a `run:` block, an uncaught exception will cause the job to fail. As it should. However, the stack trace...

"mk" autocorrelation calculation

4

Hi @minaskar, I looked at the autocorrelation stuff you've just added, and it looks really useful. Thanks! https://github.com/minaskar/zeus/blob/658ad948b6f2e6edff88af8632b064b651e234fc/zeus/autocorr.py#L54-L65 I had a question/comment about the "mk" calculation. It looks like you're...

specify random seed?

1

Unless I missed something, it doesn't seem like there's an option to supply a seed for the random number generator. If possible, I'd like to make my analyses reproducible. While...