refactor cargo-processx functions

[kbvernon]

This PR tries to bring consistency to how functions call processx::run(). The main goal is to unburden this package by letting processx do the heavy lifting wherever possible. Changes include:

• setting error_on_status = TRUE everywhere
• adding an echo parameter and passing it to echo_cmd = echo (print cargo command to console) and echo = echo (print stdout to console). The default is TRUE to ensure that maximum information is printed to the console.
• setting env = get_cargo_envvars(). I'm not sure this one is strictly necessary. I believe the function was originally written to handle issues with rtools and windows, but functions that don't use this still pass CI on all OS.
• standardize logic for defining wd. This is now done with a single call to rprojroot::find_package_root_file().
• using jsonlite::parse_json(simplifyDataFrame = TRUE) whenever cargo command returns json formatted strings in stdout. If we can always assume data.frames rather than lists, I think this will simplify future maintenance.

At the same time, I took the liberty of adding standalone type checks, reformatting to ensure scripts past lintr tests, removing magrittr pipes, and replacing redundant code.

Right now, there are seven files with calls to processx::run(), but I only updated four of them:

• clean.R
• cran-compliance.R
• license_note.R
• read_cargo_metadata.R
• source.R
• use_crate.R
• utils.R

I'm ignoring cran-compliance.R because I think Josiah's recent work will make that code obsolete. I think the myriad issues in source.R are substantial enough that they call for their own PR. And the call in utils.R is only really there to check for third party cargo tools, so maybe not worth messing with.

[JosiahParry]

codcov is being a bit extreme here. We can address the coverage later on. It is actually penalizing this PR for adding more checks funnily enough.

Good work @kbvernon

[codecov]

Codecov Report

Attention: Patch coverage is 52.80899% with 84 lines in your changes missing coverage. Please review.

Project coverage is 80.31%. Comparing base (d8689d9) to head (d46ee51).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
R/license_note.R	0.00%	69 Missing ⚠️
R/run_cargo.R	72.22%	10 Missing ⚠️
R/clean.R	88.46%	3 Missing ⚠️
R/read_cargo_metadata.R	94.44%	1 Missing ⚠️
R/use_crate.R	95.45%	1 Missing ⚠️

Additional details and impacted files

Files with missing lines	Coverage Δ
R/find_extendr.R	100.00% <ø> (ø)
R/utils.R	100.00% <100.00%> (ø)
R/read_cargo_metadata.R	95.23% <94.44%> (-4.77%)	⬇️
R/use_crate.R	97.61% <95.45%> (-2.39%)	⬇️
R/clean.R	82.50% <88.46%> (+12.32%)	⬆️
R/run_cargo.R	72.22% <72.22%> (ø)
R/license_note.R	0.00% <0.00%> (ø)

... and 1 file with indirect coverage changes

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