Merge with main (2024-05-23)

.Rbuildignore

@@ -0,0 +1,22 @@
+^add_docs
+^doc$
+^docs$
+^pkgdown$
+^TrialSPSS
+^TrialOMV
+^TrialOther
+^LICENSE$
+^Meta$
+^README\.Rmd$
+^jmvReadWrite.svg$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^\.lintr$
+^.prepare4CRAN$
+^_pkgdown\.yml$
+^CONTRIBUTING.md$
+^cran-comments\.md$
+^CRAN-RELEASE$
+^CRAN-SUBMISSION$
+^codemeta\.json$

.github/FUNDING.yml

@@ -0,0 +1,2 @@
+# If you find this module useful, please donate to the jamovi project.
+patreon: jamovi

.github/workflows/ci.yml → .github/workflows/CI.yml

@@ -1,6 +1,6 @@
 # Run CI for R using https://eddelbuettel.github.io/r-ci/
 
-name: ci
+name: CI
 
 on:
   push:

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

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main]
+    branches: ['**']
   pull_request:
-    branches: [main]
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,7 +22,7 @@ jobs:
           - {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: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -45,9 +45,13 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::XML, any::roxygen2, github::jamovi/jmvcore
           needs: check
 
+      - name: Document
+        run: roxygen2::roxygenise(roclets = "rd")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

.github/workflows/pkgcheck.yaml

@@ -0,0 +1,28 @@
+name: pkgcheck
+
+# This will cancel running jobs once a new run is triggered
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  # Manually trigger the Action under Actions/pkgcheck
+  workflow_dispatch:
+  # Run on every push to main
+  push:
+    branches:
+      - main
+env:
+    ACTIONS_RUNNER_DEBUG: true
+    ACTIONS_STEP_DEBUG: true
+    NO_CHKDIR: true
+
+jobs:
+  pkgcheck:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - uses: ropensci-review-tools/pkgcheck-action@main
+        with:
+          post-to-issue: false

.github/workflows/rhub.yaml

@@ -0,0 +1,97 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos,macos-arm64'
+      name:
+        description: 'Run name.'
+        type: string
+        default: 'manually started run'
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+        default: 'rhub'
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -42,7 +42,6 @@ pkgdown/
 
 # R Environment Variables
 .Renviron
-.Rbuildignore
 
 # pkgdown site
 docs/

.lintr

@@ -1 +1 @@
-linters: lintr::linters_with_defaults(line_length_linter = NULL, object_name_linter = NULL, commented_code_linter = NULL, indentation_linter = NULL)
+linters: lintr::linters_with_defaults(line_length_linter = NULL, object_name_linter = NULL, commented_code_linter = NULL, indentation_linter = NULL, cyclocomp_linter(complexity_limit = 30L))

.prepare4CRAN

@@ -4,11 +4,11 @@ OR
 devtools::load_all()
 
 for (blnAtt in c(TRUE, FALSE)) {
-    for (crrOMV in list.files('inst/extdata/')) {
+    for (crrOMV in list.files('inst/extdata/', '*.omv')) {
+        cat(sprintf('\n%s\n\n%s\n\n', strrep("=", 100), crrOMV))
         data <- read_omv(file.path('inst/extdata/', crrOMV), sveAtt = blnAtt)
         write_omv(data, "~/Trial.omv")
         data2 <- read_omv("~/Trial.omv", sveAtt = blnAtt)
-        cat(sprintf('\n%s\n\n%s\n\n', strrep("=", 100), crrOMV))
         suppressWarnings(print(diffdf::diffdf(data, data2)))
         unlink("~/Trial.omv")
         rm("data", "data2")
@@ -19,8 +19,7 @@ rm('blnAtt', 'crrOMV')
 
 # checks the requirements (all dependencies up-to-date, etc.)
 # use devtools::update_packages("devtools") and devtools::install_dev_deps() if required
-# NB: there might be an error when updating the tidyverse-packages: remove the APA-style
-#     formatting in .Rprofile, restart R and put it back afterwards
+# NB: there might be an error when updating the tidyverse-packages: start R with R --no-init-file
 devtools::dev_sitrep()
 
 # do some initial checks
@@ -37,14 +36,15 @@ devtools::lint()
 devtools::test()
 devtools::test_coverage()
 # once happy with the coverage, it can be uploaded using
-covr::codecov(token = "2f521d97-d1e2-4baf-b05b-0b569a7c6f0f")
+covr::codecov(token = "2f521d97-d1e2-4baf-b05b-0b569a7c6f0f")  # jmvReadWrite
+covr::codecov(token = "821f2b2f-e305-49b2-ab96-7f328530f6ed")  # jTransform
 
 # ================================================================================================================================================
 # REMEMBER: error messages from R are not always pointing to the place where the error occurs - especially when using commands like build_readme()
 # ================================================================================================================================================
 
-# update version number in DESCRIPTION and NEWS.md (and changes in NEWS.md)
-system("gedit DESCRIPTION NEWS.md inst/CITATION")
+# update version number in DESCRIPTION and NEWS.md (and changes in NEWS.md)$(git log --date=format:'%Y-%m-%d' | grep -m1 "^Date" | sed 's/Date:\s*//')"
+system("gedit DESCRIPTION NEWS.md inst/CITATION")  # jmvReadWrite
 
 # building / updating README, PDF manual, and the HTML documentation
 # add new functions to _pkgdown.yaml and to vignettes/jmvReadWrite.Rmd if required
@@ -64,17 +64,20 @@ devtools::check(force_suggests = TRUE, incoming = TRUE, remote = TRUE, env_vars
 devtools::check_win_devel()
 
 # the next stage of ping-pong, either build on the standard platforms
-devtools::check_rhub()
-# or builds it the package on rhub using all major platforms R is supported on
-devtools::check_rhub(pkg = ".", platforms = rhub::platforms()$name, env_vars = c("_R_CHECK_FORCE_SUGGESTS_" = "false"))
-# or, if there are known errors (e.g., on rhub), exclude certain platforms explicitly
-crrPlt = rhub::platforms()
-crrPlt = crrPlt[-c(x, ...), ]
-devtools::check_rhub(pkg = ".", platforms = crrPlt$name, env_vars = c("_R_CHECK_FORCE_SUGGESTS_" = "false"))
+#rhub::rc_submit(platforms=c("linux", "windows", "macos", "macos-arm64"))
+rhub::rhub_check(platforms=c("linux", "windows", "macos", "macos-arm64"))
+# running github actions requires a personal access token: https://github.com/settings/profile
+# → Developer options → Personal access token → Tokens (classic) → tick “repo”
+# the token is valid for a limited time period and can be regenerated; to update the
+# token, the following function can be used (choose 2 and copy the token when requested)
+gitcreds::gitcreds_set()
 
 # update version number and comments in cran-comments.md (and perhaps NEWS.md)
 system("gedit cran-comments.md NEWS.md")
 
+# update codemeta.json (devtools::release() asks for it)
+codemetar::write_codemeta()
+
 # now, we are ready to release the package onto CRAN
 devtools::release()
 

CONTRIBUTING.md

@@ -0,0 +1,24 @@
+# Contributing to jmvReadWrite
+
+## Opening issues
+
+The easiest way to note any behavioural curiosities or to request new features
+is by opening an [issue](https://github.com/sjentsch/jmvReadWrite/issues).
+
+
+## Development guidelines
+
+If you'd like to contribute changes to `jmvReadWrite`, the  [GitHub
+flow](https://docs.github.com/en/get-started/quickstart/github-flow) is used
+for proposing, submitting, reviewing, and accepting changes. If you haven't
+done this before, there's a nice [overview of
+git](https://r-pkgs.org/git.html), as well as [best practices for submitting
+pull requests](http://r-pkgs.org/git.html#pr-make) in the R packages book by
+Hadley Wickham and Jenny Bryan.
+
+You are also welcome to contribute further checks / tests to `jmvReadWrite`.
+Please discuss any proposed new checks by opening an issue on the GitHub
+repository.
+
+The `jmvReadWrite` coding style follows the commonly used [tidyverse style
+guide](https://style.tidyverse.org/syntax.html#spacing).

DESCRIPTION

@@ -1,10 +1,9 @@
 Package: jmvReadWrite
 Title: Read and Write 'jamovi' Files ('.omv')
-Version: 0.4.0
-Author: Sebastian Jentschke [aut, cre]
-    (<https://orcid.org/0000-0003-2576-5432>)
+Version: 0.4.6
+Author: Sebastian Jentschke [aut, cre, cph] (<https://orcid.org/0000-0003-2576-5432>)
 Authors@R:
-    person(given = "Sebastian", family = "Jentschke", role = c("aut", "cre"), email = "sebastian.jentschke@uib.no", comment = c(ORCID = "0000-0003-2576-5432"))
+    person(given = "Sebastian", family = "Jentschke", role = c("aut", "cre", "cph"), email = "sebastian.jentschke@uib.no", comment = c(ORCID = "0000-0003-2576-5432"))
 Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
 Description: The free and open a statistical spreadsheet 'jamovi'
     (<https://www.jamovi.org>) aims to make statistical analyses easy and
@@ -13,12 +12,12 @@ Description: The free and open a statistical spreadsheet 'jamovi'
     the data files 'jamovi' produces ('.omv') permits an easy transfer of
     data and analyses between 'jamovi' and R.
 License: AGPL-3
+Language: en-GB
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
-Language: en-GB
 URL: https://sjentsch.github.io/jmvReadWrite/
 BugReports: https://github.com/sjentsch/jmvReadWrite/issues
 Depends: R (>= 3.5.0)

NAMESPACE

@@ -3,6 +3,7 @@
 export(arrange_cols_omv)
 export(convert_to_omv)
 export(describe_omv)
+export(label_vars_omv)
 export(long2wide_omv)
 export(merge_cols_omv)
 export(merge_rows_omv)