SLiMSuite Servers out of action

Following a move out of academia and lack of ongoing funding, the SLiMSuite website and servers at UNSW are currently out of action. It is not clear at this point whether they will be restored, replaced, or permanently retired. SLiMSuite programs and code are still available from GitHub. Please get in touch if you have any questions during this transition period.

Odd blog behaviour

For some reason, the Download blog page is not working properly. Until rectified, please check the downloads tag if a link to SLiMSuite downloads breaks.

Update: this should be fixed now!

New MAJOR.MINOR.PATCH version numbers

One of the changes in the last release was the introduction of three component X.Y.Z version numbers in place of the old X.Y numbers. These are slowly being rolled out across all the modules in an effort to approach proper semantic versioning for SLiMSuite. (Due to the somewhat organic nature of its development, it may never reach full semantic versioning.)

From release 2015-01-07 onwards, therefore, version number changes should indicate the nature of the change following MAJOR.MINOR.PATCH version numbering:

1. MAJOR version increments when a backwards-incompatible change is made. Typically a major change to input/output or core module/class structure.

2. MINOR version increments when functionality is added in a backwards-compatible manner.

3. PATCH version increments when bugs are fixed or minor functionality added in a backwards-compatible manner.

Under the old MAJOR.MINOR version numbers, PATCH changes were treated as MINOR changes.

Regrettably, due to modular structure of SLiMSuite, the main program modules will not always have MINOR and PATCH version increments when the underlying modules are changed. The plan is to make sure that the main SLiMSuite and SeqSuite modules do increment with a new release to reflect changes. In the meantime, please contact the author if you have any questions or unexpected behaviour.

Blog switchover

Posts and pages from the old SLiMSuite and SeqSuite blog have now been imported and this blog will take over as the main source of ongoing news, tips, documentation and updates.

Coming soon...

This blog will replace the current SeqSuite and SLiMSuite blog. For now, please see the existing blog.

Documentation

SLiMSuite and SeqSuite have grown into rather unwieldy beasts since their origins as individual programs and the documentation has struggled to keep up. In particular, the original plan of a single PDF manual per program is getting creaky. Because of the shared reliance on common modules, multiple programs make use of the same sets of options for alignments and conservation scoring etc. and propagating tweaks and modifications through all the manuals can be a bit head-wrecking.

As a result of all of this, the documentation currently undergoing a bit of a review and rethink. I am still keen to keep the PDF manuals (as I think they are useful) but will be working through an intermediate phase of online Markdown/HTML documentation of some kind. The current plan is to trickle out draft copies via the blog and then probably release a Git repository once sufficiently populated.

In the meantime, I would be interested to hear any thoughts regarding favoured documentation styles etc. (e.g. HTML vs PDF, large files vs small chunks) as well as bits that are particularly unclear or in need of attention.

Welcome!

Welcome to the new blog for, SLiMSuite, SeqSuite and associated open-source python gubbins. Due to a recent overhaul of file organisation, the blog, web page and documentation are likely to take a bit of time to get polished up but please feel free to post comments and questions in the meantime!