dev/01-setup.md

In CorradoLanera/pkgsetup: Package and Project Setup Workflow

title: "Setup (with {renv})" author: "Corrado Lanera" date: "Thu Jun 25 21:42:57 2020" output: html_document: toc: true toc_float: true keep_md: true

NOTE: For projects which would not use {renv} support, see 01-pkgsetup.R (here, in this gist).

Prerequisites

available::available("pkgsetup")
usethis::create_package("~/Documents/cl/pkgsetup")

usethis::use_directory("dev", ignore = TRUE)
fs::file_create("dev/01-setup.R")
rstudioapi::navigateToFile("dev/01-setup.R")

usethis::use_roxygen_md()
usethis::use_news_md()

Documentiation

DESCRIPTION

usethis::use_gpl3_license("Corrado Lanera")
usethis::use_package_doc()

README

Initialize the README file (ie the package's landing page)

# install.packages("rmarkdown")
usethis::use_readme_rmd()
usethis::use_logo("~/Pictures/pkgsetup_hex.png")
usethis::use_cran_badge()
usethis::use_lifecycle_badge("Maturing")

Our package is not on CRAN, change the README accordingly:

You can install the development version from GitHub with the following procedure:

r # install.packages("devtools") devtools::install_github("CorradoLanera/<package_name>")

Remove everything else that is not necessary and

usethis::use_code_of_conduct()

usethis::use_spell_check()
spelling::spell_check_package()
spelling::update_wordlist()

knit the README

Supporting Folders

Data raw

If raw data are stored inside the main package folder call

usethis::use_data_raw()

and comment the line with usethis::use_data(...) in it until it will be used.

Other folder (eg Analyses)

usethis::use_directory("analysis", ignore = TRUE)
usethis::use_directory("output", ignore = TRUE)

Test suit

usethis::use_testthat()

Create a simple test to check everything works. You can delete it AFTER you have written another test at least.

Check it works:

usethis::use_test("foo") # `test_that("foo works", expect_null(foo()))`
devtools::test()         # see it fails!!
usethis::use_r("foo")    # define `foo <- function() NULL`
devtools::test()         # see it passes!!

delete foo only after have included another function!

Quality assurance

usethis::use_tidy_description()

# install.packages("lintr)
lintr::lint_package()

and fix the spelling script that lint have opened... ;-)

if (requireNamespace("spelling", quietly = TRUE)) {
  spelling::spell_check_test(
    vignettes = TRUE,
    error = FALSE,
    skip_on_cran = TRUE
  )
}

Check again:

lintr::lint_package()

devtools::check_man()
devtools::test()
devtools::check()

Activate Git/GitHub

usethis::use_git()
usethis::git_vaccinate()

Commit everything before to continue!

# remember to open and activate PuTTY
usethis::use_github(
  # "<organization>", # eg, "UBESP-DCTV"
  # private = TRUE # is a private repo?
)

NOTE: If required set the upstream using your preferred GUI^[GitKraken: https://www.gitkraken.com/invite/fas3vkyk is free, multiplatform (Win, Mac, Linux),and super cool :-).], or by command line running (on the Terminal):

git push --set-upstream origin master

usethis::use_tidy_github()

Activate {renv} for reproducibility

We will use "explicit" snapshot whith the intent of capture what is included in the DESCRIPTION file only.

renv::init(settings = list(snapshot.type = "explicit"))
renv::status() # just to check

Package website documentation

Disclaimer (2020-06-22): This and the following actions are mine modification of the ones you can find in https://github.com/r-lib/actions/blob/master/examples/pkgdown.yaml The changes are made to made the action able to be used with {renv} as suggested in https://rstudio.github.io/renv/articles/ci.html#github-actions

As soon/if there will be implemented official Actions, I will substitute these with those ones.

usethis::use_github_action(
  url = "https://raw.githubusercontent.com/CorradoLanera/actions/master/pkgdown.yaml"
)
usethis::use_github_actions_badge("pkgdown")

Bonus:

renv::install("GuangchuangYu/badger")
badger::badge_custom("WEBsite", "click-me", "orange", "http://corradolanera.github.io/pkgsetup/")

And add it between title and logo in the README and knit it.

Continuous Integration

Lint (static code-quality checks)

usethis::use_github_action(
  url = "https://raw.githubusercontent.com/CorradoLanera/actions/master/lint-renv.yaml"
)
usethis::use_github_actions_badge("lint")

WARNING: if you do not use {renv} for your project, call

usethis::use_github_action("lint")
usethis::use_github_actions_badge("lint")

R-CDM-check and coverage

usethis::use_github_action(
  url = "https://raw.githubusercontent.com/CorradoLanera/actions/master/R-CMD-check-renv.yaml"
)
usethis::use_github_actions_badge("R-CMD-check")

usethis::use_github_action(
  url = "https://raw.githubusercontent.com/CorradoLanera/actions/master/covr-renv.yaml"
)
usethis::use_github_actions_badge("test-coverage")

WARNING: if you do not use {renv} for your project, call

usethis::use_github_action("check-full",
  save_as = "R-CMD-check.yaml"
)
usethis::use_github_actions_badge("R-CMD-check")

usethis::use_github_action("test-coverage",
  save_as = "covr.yaml"
)
usethis::use_github_actions_badge("covr")

Bonus:

Automating background continuous tests on RStudio (free command line)

renv::install("CorradoLanera/autotestthat") # {renv} installation

Final checks and update version

usethis::use_tidy_description()
devtools::check_man()

spelling::spell_check_package()
spelling::update_wordlist()

lintr::lint_package()
renv::status()
devtools::check()

Update and knit the README.Rmd

usethis::use_version("dev")

Start to develop

fs::file_create("dev/02-development.R")
rstudioapi::navigateToFile("dev/02-development.R")

commit and push... Happy packaging!

CorradoLanera/pkgsetup documentation built on June 28, 2020, 10:40 a.m.