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@bhaller bhaller released this 30 Apr 12:47
· 113 commits to master since this release
v4.2.1
1f0b162

Hi folks! SLiM 4.2.1 has just been released. This is a bug fix release. It should preserve backward compatibility with SLiM 4.2 in all cases (models that run in 4.2 will continue to run with no changes). Similarly, it preserves backward reproducibility (the same model with the same seed will produce the same results) in all cases. I would recommend that everyone on version 4.2 should upgrade to this version; it has one very important bug fix, and version 4.2 SHOULD NOT BE USED. See the new SLiM manual (chapter 30) and the VERSIONS file for a complete list of changes, which will be summarized here.

[ Note that on 30 April 2024 this release was patched to fix a crash in SLiMgui. Only SLiMgui was affected by this bug, so users of the command-line slim program do not need to update that. Users of SLiMgui should reinstall 4.2.1 once the installer for their platform has been updated. Sorry for the confusion! ]

Recommended python package versions are tskit 0.5.6, msprime 1.3.1 (but back to 1.2.0 should be fine for SLiM), and pyslim 1.0.4.

IMPORTANT BUG FIXES:

  • A bug that could result in a crash or a corrupted run (producing incorrect results) has been fixed. This bug would bite under very specific circumstances: in a nonWF model, with a subpopulation of size 0 (containing no individuals), if and only if a non-zero-size subpopulation had not existed in a previous tick. This usage pattern is somewhat common, so this was a very dangerous bug that unfortunately merited a new release.

INSTALLATION NOTES:

  • If you are on Fedora, RedHat, CentOS, openSUSE, or SUSE Linux Enterprise, the SLiM installer for your Linux platform has already been updated, and installs both the command-line slim binary and the SLiMgui app; see section 2.2.2.

  • If you are on Debian or Ubuntu, there is a Bash script that installs both the command-line slim binary and the SLiMgui app; see section 2.2.2.

  • The manual discusses using another method, AppImage, to install SLiMgui (only – no command-line tools) on Linux platforms, since it is the most difficult target to build. However, AppImage is proving a bit finicky to configure, and is not yet ready to use. PLEASE DISREGARD that manual section until further notice. Hopefully it will be working soon.

  • If you are on macOS, download the double-click installer from the SLiM home page at http://messerlab.org/slim/.

  • If you are on Windows, the pacman installer will be somewhat delayed as usual; a followup post will be made here when it is ready, and in the meantime you can use conda or build from sources.

  • If you are on Arch, the installer is delayed a bit; in the meantime, you can use conda or build from sources.

  • For those using conda, the new version is now available for all platforms (but does not give you SLiMgui, only slim).

Everyone else can download the SLiM.zip source archive from the SLiM home page and build it themselves, or build from sources using the git tag associated with the SLiM 4.2.1 release.

The manuals, recipes, and reference sheets have undergone only version number tweaks, if that, and do not need to be downloaded again if you downloaded them for version 4.2.

SLIM BEGINNERS: Note that a free SLiM Workshop is available online at http://benhaller.com/workshops/workshops.html, and is highly recommended for new users. It has been updated to SLiM 4.2 (and 4.2.1). It is offered occasionally in person, and as of this posting there are a few spaces left in the upcoming Ancona, Italy, workshop on May 27-31; see the slim-discuss list for workshop announcements.

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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