[Bioc-devel] Updates to basilisk on BioC-devel

[Aaron Lun]

basilisk 1.9.6 on BioC-devel now uses an updated version of the
Miniconda installer, in order to support the new Arm-based Macs. The
update of the conda version is accompanied by a change in the default
Python version, which is now 3.8 as opposed to 3.7.

For developers of basilisk client packages, there are a few things to
watch out for:

1) If you didn't pin the Python version in your BasiliskEnvironment
manifest, you may be encountering BioC build system failures due to
version resolution failures, specifically between Python 3.8 and your
requested Python packages. There are two solutions:

- Pin the Python version to 3.7 in the manifest.
- Update your manifest to use 3.8-compatible versions of requested
Python packages.

Either of these would be fine, depending on how conservative you want to be.

2) basiliskStart and basiliskRun provide a new testload= option to
catch GLIBCXX errors from mismatches with the system shared libraries.
Upon error, basilisk will fall back to an internal copy of R to run
the requested function. Typical usage is to set something like
'testload="scipy.optimize"' in your basiliskStart/Run calls to catch
common scipy loading errors. See ?basiliskStart and
https://github.com/LTLA/basilisk/issues/20 for more details.

3) basiliskRun provides a new persist= option to more robustly persist
variables across calls for the same process. This avoids
inefficiencies from continually transferring data/results between
processes for multi-step workflows. See the BioC-devel vignette for
more details.

-A