Implement index (#96)

* Refactor encoding tests to catch known warning. * Reorg description for readability Used usethis::use_tidy_description() for standardization. Also updated R4DS to DSLC, added the pkgdown site in the URL field, and added a ".9000" while we work on this version (which will probably be at least 1.1). * Switch most examples to examplesIf Also cleaned up some formatting, and added @export directives for S3 methods. This doesn't REALLY export them, it just registers them for dispatch. Closes #94. * Make R CMD check happy. * Style for consistency. * More coverage. Add explicit # nocov to things we won't check, try to cover as much as we can. Also refactored and repaired some tests while I was at it. The biggest change might be that I renamed the test files to match their associated R files. This makes it much easier to run tests and coverage for that single file. With proper mocking, the order of tests shouldn't matter. I also updated to testtthat 3e for snapshots. At the same time, I change the capture.output tests to snapshots. * Update GHA. Other than general updates, the main thing I did was remove the R 3.6 thing specifically since it's way back at the point. * More test coverage. * 100% coverage!
dslc-io · Aug 21, 2024 · 73e15da · 73e15da
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,5 @@
 # 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
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -12,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -23,13 +21,9 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
-
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -42,7 +36,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -60,3 +54,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
@@ -14,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +53,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -8,43 +8,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - 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
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,62 +1,44 @@
-Package: tidytuesdayR
 Type: Package
+Package: tidytuesdayR
 Title: Access the Weekly 'TidyTuesday' Project Dataset
-Version: 1.0.3
-Authors@R: 
-    c(
-      person(
-        given = "Ellis", 
-        family = "Hughes", 
-        email = "[email protected]", 
-        role = c("aut", "cre")
-      ),
-      person(
-        given = "Jon", 
-        family = "Harmon", 
-        email = "[email protected]", 
-        role = "ctb"
-      ),
-      person(
-        given = "Thomas", 
-        family = "Mock", 
-        email = "[email protected]", 
-        role = "ctb"
-      ),
-      person(
-        given = "R4DS Online Learning Community",
-        email = "[email protected]",
-        role = "dtc"
-      )
-    )
-Description: 
-  'TidyTuesday' is a project by the 'R4DS Online Learning Community' in which they 
-  post a weekly dataset onto post a weekly dataset in a public data repository 
-  (<https://github.com/rfordatascience/tidytuesday>) for people to
-  analyze and visualize. This package provides the tools to easily download this data and the 
-  description of the source.
+Version: 1.0.3.9000
+Authors@R: c(
+    person("Ellis", "Hughes", , "[email protected]", role = c("aut", "cre")),
+    person("Jon", "Harmon", , "[email protected]", role = "ctb"),
+    person("Thomas", "Mock", , "[email protected]", role = "ctb"),
+    person("Data Science Learning Community", , , "[email protected]", role = "dtc")
+  )
+Description: 'TidyTuesday' is a project by the 'Data Science Learning
+    Community' in which they post a weekly dataset in a public data
+    repository (<https://github.com/rfordatascience/tidytuesday>) for
+    people to analyze and visualize. This package provides the tools to
+    easily download this data and the description of the source.
 License: MIT + file LICENSE
-URL: https://github.com/thebioengineer/tidytuesdayR
+URL: https://thebioengineer.github.io/tidytuesdayR/,
+    https://github.com/thebioengineer/tidytuesdayR
 BugReports: https://github.com/thebioengineer/tidytuesdayR/issues
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.1
-Depends: R (>= 3.4.0)
-Suggests: 
-    testthat (>= 2.1.0),
-    covr,
-    pkgdown,
-    tibble,
-    withr
+Depends: 
+    R (>= 3.4.0)
 Imports:
-    readxl (>= 1.0.0),
-    rvest (>= 0.3.2),
-    tools (>= 3.1.0),
+    httr,
+    jsonlite,
     lubridate (>= 1.7.0),
+    magrittr,
     purrr (>= 0.2.5),
     readr (>= 1.0.0),
+    readxl (>= 1.0.0),
+    rlang,
     rstudioapi (>= 0.2),
-    xml2 (>= 1.2.0),
-    httr,
-    jsonlite,
-    magrittr,
-    usethis
+    rvest (>= 0.3.2),
+    tools (>= 3.1.0),
+    usethis,
+    xml2 (>= 1.2.0)
+Suggests: 
+    covr,
+    pkgdown,
+    testthat (>= 3.0.0),
+    tibble,
+    withr
+Encoding: UTF-8
+RoxygenNote: 7.3.2
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,8 @@ S3method(print,tt)
 S3method(print,tt_data)
 S3method(print,tt_dataset_table)
 S3method(print,tt_dataset_table_list)
+S3method(tt_gh_error,response)
+S3method(tt_gh_error,tt_response)
 export("%>%")
 export(github_pat)
 export(last_tuesday)
@@ -35,6 +37,7 @@ importFrom(purrr,walk)
 importFrom(readr,read_delim)
 importFrom(readxl,read_xls)
 importFrom(readxl,read_xlsx)
+importFrom(rlang,"%||%")
 importFrom(rstudioapi,isAvailable)
 importFrom(rstudioapi,viewer)
 importFrom(rvest,html_node)