[Bioc-devel] Updates to SingleCellExperiment class structure - no action required

It sounds to me that the class definition / structure?is updated. You 
should also have an associated updateObject() method to deal with this; 
that's tradition. Of course, you may already have addressed this and 
just not written about it in your email.

On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun 
<infinite.monkeys.with.keyboards at gmail.com 
<mailto:infinite.monkeys.with.keyboards at gmail.com>> wrote:

    Dear list,

    As of version 1.9.2, the SingleCellExperiment class structure has been
    updated so that "sizeFactors()<-" will store values in a "sizeFactor"
    field in the "colData()", rather than the internal metadata. This aims
    to improve interoperability of the SCE size factors with functions that
    retrieve information from the column metadata; see GitHub for details.

    This change occurs under the hood in the "sizeFactors()" getter and
    setter functions, so no action should be required from users who were
    already using those functions to manipulate the SCE size factors.
    Nonetheless, downstream developers should keep an eye on their unit
    tests as some of the more fragile checks may fail, e.g., if they
    hard-coded the expected column names of the "colData" of an SCE.

    Version 1.9.2. also removes a bunch of deprecated functionality from
    the
    package, which may cause unrelated failures; though this was pretty
    esoteric stuff that didn't see a lot of use in the first place.

    Best,

    -A