pyslim 1.1 beta release

[Peter Ralph]

Hi all - there's been some changes to how SLiM stores tree sequences with SLiM v5, so I'm updating pyslim. If you'd like to try the new pyslim, install it like

  pip install pyslim==1.1b1

I'd appreciate bug reports, etcetera. If you are running single-chromosome simulations in which everyone is diploid, this should not affect you at all.

If you are running non-diploid simulations (eg sex chromosomes, haploids, etc), then you should be aware that the output contains "vacant" placeholder nodes that can cause errors or incorrect output, and these need to be removed from the sample for most downstream operations. pyslim.recapitate( ) does this automatically; if you don't use this function then you should probably use pyslim.remove_vacant. See https://tskit.dev/pyslim/docs/latest/previous_versions.html (and links therein) for more information.

Finally, if you are really getting into the details: the mechanism by which pyslim.remove_vacant stores information about which nodes were removed from the sample (in top-level metadata) is expected to change, so please don't rely on this. Otherwise, the effects and API are expected to be stable.

happy slimulating,

 Peter

[Philip Wolper]

Hi,

thanks for the update. Does calling ts.simplify() automatically remove vacant nodes as well? Not sure, where to find the docs you mentioned in https://github.com/tskit-dev/pyslim/pull/367, once they are finished?

 

Best,

Philip

[Peter Ralph]

The new docs are at

 https://tskit.dev/pyslim/docs/latest/introduction.html

see in particular

 https://tskit.dev/pyslim/docs/latest/overview.html#sec-overview-vacant-nodes

And no - doing for instance

 ts = tskit.load("sim.trees")

 ts = ts.simplify(keep_input_roots=True)

will not remove the vacant sample nodes, because they are samples. If you do want to use simplify() to remove them, you would need to do something like:

 ts = pyslim.remove_vacant(ts).simplify(keep_input_roots=True)

(Recall that keep_input_roots=True is necessary if you're going to recapitate later.)

-p

---

From: 'Philip Wolper' via slim-discuss <slim-d...@googlegroups.com>
Sent: Tuesday, May 20, 2025 10:13 AM
To: slim-discuss <slim-d...@googlegroups.com>
Subject: Re: pyslim 1.1 beta release

 

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SLiM forward genetic simulation: http://messerlab.org/slim/
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