Add CI workflows for standard checks, linting, and test coverage

[taylorreiter]

Following https://github.com/r-lib/actions/tree/v2-branch/examples#example-workflows Set up using:

usethis::use_github_action("check-standard")
usethis::use_github_action("test-coverage")

there were LOTS of problems that I didn't know about. First of all, I've been using test() locally to make sure my tests pass before I push something to github. I should have been running check() which runs the tests and lots of other things to look for problems in the code. Some problems that check() found were:

• the use of . in tidyverse pipe functions. I removed a few of these and temporarily kept on for one line of code that was particularly trick to come up with originally and I wasn't sure how to replace yet.
• the use of .data$ to call variables used by tidyverse, or "" when that variable was called by tidyselect().
• missing parameter docs
• use of other global vars
• missing package exports (tibble, stats)

I also switched the majority of examples to not run. eventually I want to add a bunch of data to the package to demonstrate the examples, but I need to learn best practices for that first, so that will be a separate PR.

[taylorreiter]

~I removed lint and test-coverage because they fail with x Failed to build source package 'XML'. I tried adding any::XML but that didn't fix the issue. I'll revisit that after I get the other tests passing.~ See below, I got it working. I re-added tests but left out linting. I'll add linting and fixes in a separate PR later.

https://github.com/r-lib/actions/issues/559

[taylorreiter]

macOS, windows, and ubuntu-lastest (oldrel-1) are all passing, but ubuntu-latest (devel) and (release) both fail with the xml error. Things I'm trying:

• didn't work:

    - uses: r-lib/actions/setup-r-dependencies@v2
      with:
        packages: any::XML
        extra-packages: any::rcmdcheck
        needs: check

• didn't worked:

    - uses: r-lib/actions/setup-r-dependencies@v2
      with:
        extra-packages: any::rcmdcheck, any::XML
        needs: check

• worked 🎉 :

    - uses: r-lib/actions/setup-r-dependencies@v2
      with:
        extra-packages: any::XML, any::rcmdcheck
        needs: check

[taylorreiter]

sourmashconsumr Coverage: 77.97%
R/plot_compare.R: 68.97%
R/metacoder.R: 73.53%
R/plot_signatures.R: 82.28%
R/read_sourmash_outputs.R: 82.35%