NEWS.md

In facilebio/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

Cleanup Branch

This includes changes that:

1. Lays some groundwork down for factoring out the "FacileData API" from the FacileDataSet.
2. Largely fills out documentation needed to placate R CMD check [WIP]
3. Fills out some vignettes [WIP]
4. pkgdown [not started]
5. Addresses unit test failures introduced by code changes in this branch [not started]

Introduction of FacileDataStore

Introduced a FacileDataStore "abstract class" in anticipation of refactoring out the "FacileData API" into a top-level FacileData package.

The idea is that:

1. Any object that implements the "FacileData API" must include "FacileDataStore" in its class hierarchy (at the root(?)). For instance, class(exampleFacileDataSet()) returns "ExampleFacileTCGADataSet" "FacileDataSet" "FacileDataStore"

2. The S3 methods that will be factored out of this package to define the "FacileData API" will effectively use *.FacileDataStore as their "default" methods. *.default FacileData API S3 methods should either (i) not be defined; or (ii) throw an error.

Note that the names of the to-be-factored-out base package name ("FacileData", here) and "FacileData API" are up for discussion. I'm just using them here as placeholders to reference the concept we are all working towards.

Random notes in this orbit:

• I added @family API roxygen tags to methods that I (loosely) think should make up the "FacileData API". I'm pretty sure

• @family API methods should probably assert_facile_data_store() instead of assert_facile_data_set()

FacileDataSet validity checking

This is currently split across many functions:

• (assert|check|test)_facile_data_set() are checkmate-esque
• The FacileDataSet() constructor calls validate.facile.dirs() which is a workhorse-of a function.
• is.FacileDataSet() now delegates to assert_facile_data_set()

ASK: Should check_facile_data_set() do all of the checking that validate.facile.dirs() does? The downside is that assert_facile_data_set() is likely called a lot, and validate.facile.dirs() may be doing too much all of the time?

Minor Changes

• Enables roxygen markdown parsing as default in DESCRIPTION.
• Most ##' documentation blocks are changed to #'

facilebio/FacileData documentation built on Feb. 23, 2024, 9:14 a.m.