Upkeep - improve messages + CI (#299)

* Fix tidyselect 1.2.0 warning
* Use testthat 3rd edition, use snapshot tests to test for messages
  Remove deprecated `expect_that()`,`expect_is()` -> `expect_type()` or `expect_s3_class()`
* Lint test with simpler more recent testthat syntax
* Use latest pkgdwon to add a search bar. Add favicons and move logo to logo.png for pkgdown to recognize it.
redocument()
* Drop crayon and clisymbols for cli and enable color in test (will make it easier in RStudio).
* Update test-03-summarize-rodents.R
* Update CI to latest with `usethis::use_github_action()`

---------

Co-authored-by: henrykironde <henrykironde@gmail.com>

.Rbuildignore

@@ -12,4 +12,6 @@
 ^paper$
 ^.Renviron$
 ^_pkgdown\.yml$
+^pkgdown$
 ^\.github$
+^man/figures/portalr.png$

.github/workflows/check-standard.yaml → .github/workflows/R-CMD-check.yaml

@@ -1,16 +1,14 @@
-# R package checking
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
+    branches: [main]
   pull_request:
-    branches:
-      - main
-  workflow_dispatch:
+    branches: [main]
+
+name: R-CMD-check.yaml
 
-name: R-CMD-check
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,16 +20,17 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: windows-latest,  r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,14 +40,12 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - name: Install Dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - name: R CMD check
-        uses: r-lib/actions/check-r-package@v2
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          error-on: '"error"'
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -1,38 +1,50 @@
-# building website
-
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
+    branches: [main]
+  pull_request:
+    branches: [main]
   release:
     types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
 
-name: pkgdown
+permissions: read-all
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Install Dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, examples = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -19,7 +19,7 @@ doc
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+# OAuth2 token, see https://github.com/r-lib/httr/releases/tag/v0.3
 .httr-oauth
 # knitr and R markdown default cache directories
 /*_cache/

CONTRIBUTING.md

@@ -65,4 +65,4 @@ The suggested workflow is:
 
 If you are also prepping the package as a whole, then you will also want to run `devtools::check()` and/or `devtools::check_cran()` to make sure that the package is complete.
 
-For more info, see the [GitHub repo](https://github.com/hadley/devtools) for the `devtools` package. 
+For more info, see the [GitHub repo](https://github.com/r-lib/devtools) for the `devtools` package. 

DESCRIPTION

@@ -53,9 +53,8 @@ BugReports: https://github.com/weecology/portalr/issues
 Depends: 
     R (>= 3.2.3)
 Imports:
-    clipr, 
-    clisymbols,
-    crayon,
+    cli,
+    clipr,
     dplyr,
     forecast,
     httr,
@@ -64,18 +63,17 @@ Imports:
     magrittr,
     rlang,
     tidyr,
-    tidyselect (>= 1.0.0),
+    tidyselect (>= 1.2.1),
     zoo
 Suggests:
-    covr,
     cowplot,
     ggplot2,
     httptest,
     knitr,
-    pkgdown,
     rmarkdown,
-    testthat
+    testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 RoxygenNote: 7.3.1
+Config/testthat/edition: 3

NEWS.md

@@ -1,9 +1,15 @@
 # portalr
 
+* `portalr` now uses [testthat 3rd edition](https://testthat.r-lib.org/articles/third-edition.html)
+* `portalr` no longer imports clisymbols and crayon. Its messages are gemerated with cli.
+* `format_todo()`, `format_code()`, and `format_value()` can be replaced with
+  [inline markup](https://cli.r-lib.org/articles/usethis-ui.html) (i.e. `{.val}`, `{.code}`, etc.) and
+  may be removed from the package.
+
 Version numbers follow [Semantic Versioning](https://semver.org/).
 
 # [portalr 0.4.1](https://github.com/weecology/portalr/releases/tag/v0.4.1)
-*2023-08-223*
+*2023-08-23*
 
 ### Regional weather filling includes more stations
 
@@ -20,6 +26,6 @@ Version numbers follow [Semantic Versioning](https://semver.org/).
 * now defaulty for number of moons to add is `NULL`  and there is a call to `return_if_null` on it
 
 ### addition of new functions (pulled from portalcasting)
-* `return_if_null` 
-* `rodent_species`: helper function that now operates off of the rodent table, not hard-coded
-* `na_conformer`: makes sure the species abbreviation for Neotoma albigula is a character value
+* `return_if_null()` 
+* `rodent_species()`: helper function that now operates off of the rodent table, not hard-coded
+* `na_conformer()`: makes sure the species abbreviation for Neotoma albigula is a character value

R/download_data.R

@@ -35,6 +35,7 @@ download_observations <- function (path    = get_default_data_path(),
                                    force   = FALSE) {
 
   return_if_null(x = version)
+  latest_requested <- identical(version, "latest")
 
   timeout_backup <- getOption("timeout")
   on.exit(options(timeout = timeout_backup))
@@ -113,17 +114,20 @@ download_observations <- function (path    = get_default_data_path(),
 
     if (existing_version == version) {
 
-      if (!quiet) {
-        message("Existing local version is up-to-date with remote version (", version, ") requested and `force` is FALSE, download is skipped")
+      # Avoid showing message in test (except if latest version is requested)
+      # use rlang::local_interactive() to simulate this message in non-interactive session.
+      if (!quiet && (rlang::is_interactive() || latest_requested)) {
+    	message("Existing local version is up-to-date with remote version (", version, ") requested and `force` is FALSE, download is skipped")
       }
 
       return(invisible())
 
     }
 
   }
-
-  if (!quiet) {
+  # Avoid showing message in test (inform of version if latest is requested)
+  # use rlang::local_interactive() to simulate this message in non-interactive session.
+  if (!quiet && (rlang::is_interactive() || latest_requested)) {
     message("Downloading version `", version, "` of the data...")
   }
 
@@ -246,12 +250,14 @@ check_default_data_path <- function(ENV_VAR = "PORTALR_DATA_PATH",
 {
   if (is.na(get_default_data_path(fallback = NA, ENV_VAR)))
   {
-    MESSAGE_FUN("You don't appear to have a defined location for storing ", DATA_NAME, ".")
-    MESSAGE_FUN(format_todo(" Call ",
-                            format_code('use_default_data_path(\"<path>\")'),
-                            " if you wish to set the default data path."))
-    MESSAGE_FUN(DATA_NAME, " will be downloaded into ",
-                format_code(path.expand("~")), " otherwise.")
+  	msg <- cli::format_message(
+  		c(
+  			"You don't appear to have a defined location for storing {DATA_NAME}.",
+  			"i" = "Call {.code use_default_data_path(\"path\")} if you wish to set the default data path.",
+  			"i" = "{DATA_NAME} will be downloaded into {.path {path.expand('~')}} otherwise."
+  		)
+  	)
+  	MESSAGE_FUN(msg)
     return(FALSE)
   }
   return(TRUE)
@@ -311,14 +317,17 @@ use_default_data_path <- function(path = NULL, ENV_VAR = "PORTALR_DATA_PATH")
 
   # display message and copy new path setting to clipboard
   path_setting_string <- paste0(ENV_VAR, "=", '"', path, '"')
-  message(format_todo("Call ", format_code('usethis::edit_r_environ()'), " to open ",
-               format_value('.Renviron')))
-  message(format_todo("Store your data path with a line like:"))
-  message("  ", format_code(path_setting_string))
+  cli::cli_inform(c(
+    "*" = "Call {.run usethis::edit_r_environ()} to open {.val .Renviron}.",
+    "*" = "Store your data path with a line like:",
+    " " = path_setting_string
+  ))
   if (rlang::is_interactive() && clipr::clipr_available()) {
     clipr::write_clip(path_setting_string)
-    message("  [Copied to clipboard]")
+    cli::cli_inform("  [Copied to clipboard]")
   }
-  message(format_todo("Make sure ", format_value('.Renviron'), " ends with a newline!"))
+  cli::cli_inform(c(
+      "*" = "Make sure {.val .Renviron} ends with a newline!"
+  ))
   return()
 }

R/load_data.R

@@ -219,7 +219,8 @@ load_datafile <- function(datafile, na.strings = "", path = get_default_data_pat
   }
 
   ## output message about data version
-  if (!quiet)
+  # Silence this message in testing.
+  if (!quiet && !identical(Sys.getenv("TESTTHAT"), "true"))
   {
     version_file <- file.path(base_path, "version.txt")
     if (tolower(path) != "repo" && !file.exists(version_file))