SLiM 3.6 released

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Ben Haller

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Mar 3, 2021, 8:44:53 PMMar 3
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Hi everyone.  SLiM 3.6 is a major release, with some important bug fixes; it is strongly recommended over SLiM 3.5.  It preserves backward compatibility/reproducibility with SLiM 3.5 (apart from bug fixes).  Below are the most high-profile changes in SLiM 3.6; complete release notes are in the manual, chapter 29.

- Improvements to tree-sequence recording, including: the ability to "retain" individuals (different from "remembering" them), with permanent=F passed to treeSeqRememberIndividuals(); the ability to keep "retained" individuals across simplification even when they are not a coalescence point, with retainCoalescentOnly=F passed to initializeTreeSeq(); and the ability to attach user-defined metadata to .trees files, with metadata= passed to treeSeqOutput()

- SLiMgui has some nice new features, including: "debug points" that can be set to obtain debugging output on specific lines of your script as it runs (see section 19.6 in the new SLiM manual); support for dark mode on macOS (automatic) and Linux (chosen in the preferences panel)

- Eidos adds some nice things including: better support for sending output to stderr (or to the debugging output window, in SLiMgui); extensions to the Dictionary class to support dataframe/struct/tuple-like usage patterns; support for Unicode characters in variable names, including accents, Chinese characters, and even emojis (use wisely)

- Major bug fixes.  (1) Using takeMigrants() could cause data corruption or crashes, in very unusual circumstances.  This was introduced in SLiM 3.5.  It is unlikely to bite most users, but if you use takeMigrants() you should not use SLiM 3.5, period.  (2) The "reproductive output" property added in SLiM 3.5 would be incorrect when takeMigrants() is used; again, do not use this method in SLiM 3.5.  (3) Several other bugs that could cause a crash, a runtime error, or a large memory leak, but that would not cause data corruption; see the full release notes for details on these.

If you are on Fedora, RedHat, CentOS, Debian, or Ubuntu, the SLiM installer for your Linux platform has already been updated (see the manual, chapter 2).  The installer for Arch should be updated soon.  If you are on macOS, download the double-click installer from the SLiM home page at http://messerlab.org/slim/.  Everyone else can download the SLiM.zip source archive from the SLiM home page and build it themselves.  The manuals, recipes, and reference sheets have also undergone revisions, so you should re-download those too.  Note that the manuals now have PDF "document outlines", i.e. tables of contents visible in your PDF reader, for easier navigation.

If you're a beginner in SLiM, you might want to check out our recent paper "Evolutionary modeling in SLiM 3 for beginners" (http://dx.doi.org/10.1093/molbev/msy237).  Beyond that, a complete SLiM Workshop is available online at http://benhaller.com/workshops/workshops.html, and is highly recommended for new users.

If you have any questions, comments, etc., please use the slim-discuss group for that.  Thanks, and happy modeling!
Cheers,

Benjamin C. Haller
Messer Lab
Cornell University

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