Merge pull request #165 from atorus-research/devel

0.3.0 Release to CRAN

.Rbuildignore

@@ -1,5 +1,6 @@
 ^renv$
 ^renv\.lock$
+.lintr
 ^xportr\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
@@ -21,3 +22,6 @@
 ^advs\.xpt$
 ^advs_Define-Excel-Spec_match_admiral\.xlsx
 ^cran-comments\.md$
+^example_data_specs$
+
+^\.devcontainer$

.Rprofile

@@ -1,5 +1,3 @@
-if (Sys.getenv("GITHUB_ACTIONS") == "") {
-  source("renv/activate.R")
-} else {
+if (Sys.getenv("GITHUB_ACTIONS") != "") {
   options(repos = c(CRAN = "https://cran.rstudio.com"))
 }

.devcontainer/devcontainer.json

@@ -0,0 +1,9 @@
+{
+  "image": "mcr.microsoft.com/devcontainers/universal:2",
+"features": {
+    "ghcr.io/rocker-org/devcontainer-features/r-rig:1": {},
+     "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
+       "packages": "dplyr,purrr,stringr,magrittr,glue,rlang,cli,tidyselect,readr,janitor,tm,haven,lifecycle,testthat,withr,knitr,rmarkdown,readxl,DT,labelled,admiral,devtools,spelling,usethis,lintr,metacore"
+     }
+ }
+}

.github/workflows/check-links.yml

@@ -0,0 +1,36 @@
+name: Check URLs 🔗
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, devel]
+
+jobs:
+  links:
+    name: Validate Links 🕸️
+    runs-on: ubuntu-latest
+    if: >
+      !contains(github.event.commits[0].message, '[skip links]')
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Check URLs in docs 📑
+        uses: lycheeverse/[email protected]
+        with:
+          fail: true
+          jobSummary: true
+          format: markdown
+          output: links-results.md
+          args: >-
+            --exclude-private
+            --exclude "https://github.com.*.git|lycheeverse.*"
+            --verbose
+            --no-progress
+            **/*.md
+            **/*.html
+            **/*.Rmd
+            **/*.yaml
+            **/*.yml
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/check-standard.yaml

@@ -1,13 +1,13 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: R-CMD-check 📦
+
 on:
   push:
     branches: [main, devel]
   pull_request:
     branches: [main, devel]
 
-name: R-CMD-check
-
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# 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
+name: Check Lint 🧹
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, devel]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -1,18 +1,18 @@
+name: Deploy pkgdown site 📜
+
 on:
   push:
     branches:
       - main
       - master
 
-name: pkgdown
-
 jobs:
   pkgdown:
     runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
 

.github/workflows/spellcheck.yml

@@ -1,5 +1,4 @@
----
-name: Spelling 🆎
+name: Check Spelling 🆎
 
 on:
   workflow_dispatch:
@@ -27,7 +26,7 @@ jobs:
         && github.event.pull_request.draft == false
     steps:
       - name: Checkout repo 🛎
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -62,5 +61,5 @@ jobs:
       - name: Run Spellcheck 👟
         uses: insightsengineering/r-spellcheck-action@v3
         with:
-          exclude: data/*,**/*.Rd,**/*.Rmd,**/*.md,*.md
+          exclude: data/*,**/*.Rd,**/*.md,*.md
           additional_options: ""

.github/workflows/style.yml

@@ -0,0 +1,45 @@
+name: Check Style 🎨
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, devel]
+
+concurrency:
+  group: style-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  style:
+    name: Check code style 🧑‍🎨
+    runs-on: ubuntu-latest
+    if: >
+      !contains(github.event.commits[0].message, '[skip stylecheck]')
+        && github.event.pull_request.draft == false
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          path: ${{ github.event.repository.name }}
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install styler 🖌️
+        run: install.packages(c("styler", "knitr", "roxygen2"), repos = "https://cloud.r-project.org")
+        shell: Rscript {0}
+
+      - name: Run styler 🖼️
+        run: |
+          detect <- styler::style_pkg(dry = "on")
+          if (TRUE %in% detect$changed) {
+            problems <- subset(detect$file, detect$changed == T)
+            cat(paste("Styling errors found in", length(problems), "files\n"))
+            cat("Please run `styler::style_pkg()` to fix the style\n")
+            quit(status = 1)
+          }
+        shell: Rscript {0}
+        working-directory: ${{ github.event.repository.name }}

.github/workflows/test-coverage.yaml

@@ -1,3 +1,5 @@
+name: Check Test Coverage 🧪
+
 on:
   push:
     branches:
@@ -8,15 +10,13 @@ on:
       - main
       - master
 
-name: test-coverage
-
 jobs:
   test-coverage:
     runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
 

.gitignore

@@ -2,19 +2,16 @@
 .Rhistory
 .RData
 .Ruserdata
-xportr.Rproj
 .gitattributes
-xptr.Rproj
 /archive
 /.idea
 scratch_check.R
 inst/doc
 adsl.xpt
 demo.R
-/doc/
 /Meta/
-docs
+docs/
 xportr.Rcheck/
 xportr*.tar.gz
 xportr*.tgz
-docs/*
+local

.lintr

@@ -0,0 +1,8 @@
+linters: linters_with_defaults(
+  line_length_linter(120),
+  object_usage_linter = NULL,
+  object_name_linter = NULL,
+  trailing_whitespace_linter(allow_empty_lines = TRUE, allow_in_strings = TRUE)
+  )
+encoding: "UTF-8"
+exclusions: list()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: xportr
 Title: Utilities to Output CDISC SDTM/ADaM XPT Files
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: 
     c(
     person(given = "Eli",
@@ -10,23 +10,39 @@ Authors@R:
            comment = c(ORCID = "0000-0002-2127-9456")),
     person(given = "Vignesh ",
            family = "Thanikachalam",
-           role = c("aut"),
-           email = "[email protected]"),
+           role = c("aut")),
     person(given = "Ben", 
            family = "Straub",
-           email = "[email protected]", 
-           role = "aut"),
+           role = ("aut")),
     person(given = "Ross",
            family = "Didenko",
-           email = "[email protected]",
-           role = "aut"),
+           role = ("aut")),
     person(given = "Zelos",
            family = "Zhu",
-           email = "[email protected]",
-           role = "aut"),
+           role = ("aut")),
+    person(given = "Ethan",
+           family = "Brockmann",
+           role = ("aut")),
+    person(given = "Vedha",
+           family = "Viyash",
+           role = ("aut")),
+    person(given = "Andre",
+           family = "Verissimo",
+           role = ("aut")),
+    person(given = "Sophie",
+           family = "Shapcott",
+           role = ("aut")),
+    person(given = "Celine",
+           family = "Piraux",
+           role = ("aut")),
+    person(given = "Adrian",
+           family = "Chan",
+           role = ("aut")),
+   person(given = "Sadchla",
+           family = "Mascary",
+           role = ("aut")),
     person(given = "Atorus/GSK JPT",
-           role = "cph")
-    )
+           role = "cph"))
 Description: Tools to build CDISC compliant data sets and check for CDISC compliance.
 URL: https://github.com/atorus-research/xportr
 BugReports: https://github.com/atorus-research/xportr/issues
@@ -42,7 +58,8 @@ Imports:
     readr,
     janitor,
     tm,
-    haven (>= 2.5.0)
+    haven (>= 2.5.0),
+    lifecycle
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -61,6 +78,8 @@ Suggests:
     spelling,
     usethis,
     lintr,
-    styler
+    metacore
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+Depends: 
+    R (>= 3.5)

NAMESPACE

@@ -10,11 +10,13 @@ export(xportr_format)
 export(xportr_label)
 export(xportr_length)
 export(xportr_logger)
+export(xportr_metadata)
 export(xportr_order)
 export(xportr_type)
 export(xportr_write)
 import(haven)
 import(rlang)
+importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
 importFrom(cli,cli_div)
@@ -27,24 +29,29 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,if_else)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(dplyr,summarize)
+importFrom(dplyr,tribble)
 importFrom(dplyr,ungroup)
 importFrom(glue,glue)
 importFrom(glue,glue_collapse)
 importFrom(graphics,stem)
 importFrom(janitor,make_clean_names)
+importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,extract2)
 importFrom(purrr,map)
 importFrom(purrr,map2_chr)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
+importFrom(purrr,pluck)
+importFrom(purrr,walk)
 importFrom(purrr,walk2)
 importFrom(readr,parse_number)
 importFrom(stringr,str_detect)