Improves epireview signals & moves to cli package

tristan-myles commented 2 months ago

Pull Request

Moves all epireview messages, warnings, and errors to cli package. Addresses #57 by added check_column_types function which will now cause load_epidata to fail if the input csv column types are incorrect (rather than outputting the opaque vroom package warning). Additionally, improves clarity of warnings for load_epireview.
Addresses #21 by outputting the columns and the number of rows per column that will epireview will attempt to convert from hours/weeks to days.

Checklist:

[x] I have added new dependencies in DESCRIPTION
[x] I have bumped the version number in DESCRIPTION
[x] I have updated the NEWS.md
[x] I have added unit tests using testthat
[x] I have checked that the package can install locally using devtools::install_local("<path-to-epireview>")
[x] I have added documentation where required
[ ] My documentation includes examples of how to use the function
[ ] If necessary, I have updated priority-pathogens

tristan-myles commented 2 months ago

A big PR which should have likely been separated into three different pieces of work. Sorry!

tristan-myles commented 2 months ago

The use of cli makes the testthat output a bit messy - I'm sure there is a way to improve this, but I haven't addressed it in this PR .

mrc-ide / epireview

Improves epireview signals & moves to cli package #101