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Bioconductor / BiocClassesWorkingGroup

Notes and Discussion concerning recommended classes for Bioconductor
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Participation #1

Closed llrs closed 1 year ago

llrs commented 1 year ago

I'd like to participate! Not sure if I should send a PR for the README and/or the working groups' book.

Here are some ideas on this topic:

The development guide only has one line encouraging reusing classes and much more on how to write them. It would be nice if it included some guidance about:  - which situations would benefit from a new class and which wouldn't  - which other low level classes could be built upon (BiocGenerics or other useful packages & classes)  - when it is useful to create new classes  - object oriented system (S3, S4, RC, R6, R7, ...)

It would be nice if the group could develop:  - normative material on why the classes were designed  - Procedures to recommended classes in package reviews and teaching materials.  - Procedures to select classes from already existing packages to recommend.

Perhaps I am splitting hairs here but I particularly want to distinguish between common used classes and promoted classes. Currently the development guide mentions common classes, there are some that I don't feel comfortable promoting as common-classes and to my knowledge are not used by many packages. In addition, when a class is superseded by another promoting a popular class is not the best for the developers (or users), thinking now about the SummarizedExperiment and the ExpressionSet classes.

Full disclosure: part of my interest is that I have/had some conflicts about a class implemented & promoted.

drighelli commented 1 year ago

I'm interested in participate to this WG, no comments at the moment, but I'll comment here in case I have some.

Thanks!