SLiM 4.0.1 released

[Ben Haller]

Hi everybody!  SLiM 4.0.1 has just been released.  This is a minor release, mostly to fix a couple of bugs.  It should preserve backward compatibility and reproducibility from SLiM 4.0.  If you are on SLiM 4.0 now, upgrading is strongly recommended; if you have chosen to stay back on SLiM 3 for the time being, you can continue to do so if you wish (or if you decide to move to SLiM 4 now, please also read the release notes for SLiM 4.0 for important information).  Recommended python package versions are the same as for SLiM 4.0: at least 0.5.2 for tskit, 1.2.0 for msprime, and 1.0 for pyslim.  See the SLiM manual (chapter 29) and the VERSIONS file for a complete list of changes, which will be summarized here.

NEW FEATURES:

- Individual has a new property, meanParentAge, that makes calculating the generation time of nonWF models easier.  This is useful for adjusting time units when using tree-sequence recording; see the pyslim documentation at https://tskit.dev/pyslim/docs/latest/time_units.html for more information.  (It should be updated to show the use of meanParentAge shortly.)

- DataFrame has a new method, asMatrix(), that converts the target DataFrame into a matrix.  This makes it easy to read a matrix from disk: use readCSV() to read the file in as a DataFrame, and then use asMatrix().  Recipe 16.12 II now provides an example of that.

- DataFrame's subset() method now takes NULL for row/col to get whole rows/columns

- readCSV() now accepts sep="" to use a "whitespace" separator (as in R).

IMPORTANT BUG FIXES:

- Models using tree-sequence recording that read in a saved tree sequence with readFromPopulationFile() could raise an error or leak a large amount of memory; see https://groups.google.com/g/slim-discuss/c/ys4zAQLlXsY/m/VTWbBtO9AAAJ.

NEW/REVISED RECIPES: Recipe 6.1.2 (reading a recombination rate map from a file) now uses readCSV() to read the rate map.

INSTALLATION NOTES:

- If you are on Fedora, RedHat, CentOS, Arch, or the newly supported platforms openSUSE and SUSE Linux Enterprise, the SLiM installer for your Linux platform has already been updated (see chapter 2 of the SLiM manual for details).

- If you are on Debian or Ubuntu, the installation strategy is being overhauled; we will announce when an installer for those platforms is available, but it may take a while (the installation instructions in the manual for those platforms will either not work, or give you version 3.7.1, I imagine); in the meantime Debian and Ubuntu users will need to build from sources, sorry (see chapter 2 for instructions).

- 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 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.

The manuals, recipes, and reference sheets have undergone revisions, so you should re-download those too.

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 not yet been updated to SLiM 4; that should happen fairly soon.

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