docs: prepare JOSE review materials

.Rbuildignore

@@ -1,6 +1,9 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^LICENSE-CONTENT\.md$
+^LICENSES\.md$
+^pkgdown$
 ^\.github$
 ^ROADMAP\.md$
 ^docs$
@@ -14,3 +17,7 @@
 ^codemeta\.json$
 ^paper$
 ^SECURITY.md$
+^.*\.Rcheck$
+^\.\.Rcheck$
+^tutorizeR_[0-9.]+\.tar\.gz$
+^CRAN-SUBMISSION$

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Questions and discussion
+    url: https://github.com/AurelienNicosiaULaval/tutorizeR/discussions
+    about: Use discussions for open-ended teaching workflow questions.

.github/ISSUE_TEMPLATE/jose_readiness.md

@@ -0,0 +1,21 @@
+---
+name: JOSE readiness item
+about: Track a task related to JOSE preparation or review
+title: "[JOSE] "
+labels: jose, documentation
+assignees: ''
+---
+
+## Review item
+
+Describe the JOSE readiness issue.
+
+## Evidence
+
+Link to repository files, examples, tests, or documentation that support the item.
+
+## Acceptance criteria
+
+- [ ] Repository evidence is added or updated.
+- [ ] The claim is verifiable from repository contents.
+- [ ] Tests or documentation are updated if needed.

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,13 +2,22 @@
 
 - What this PR changes
 - Why it is needed for teacher workflow reliability
+- Whether this changes generated tutorial output
 
 ## Validation
 
 - [ ] `R CMD check --as-cran --no-manual`
 - [ ] Tests pass (`testthat`)
 - [ ] Lint clean (`lintr::lint_package()`)
 - [ ] Coverage thresholds met (if touching core conversion path)
+- [ ] Example conversion checked with at least one `.Rmd` or `.qmd` fixture
+- [ ] Documentation or vignette updated when user-facing behavior changes
+
+## Educational impact
+
+- What instructor workflow is improved?
+- What student interaction changes, if any?
+- Is any classroom adoption claim supported by repository evidence?
 
 ## Additional notes
 

.github/workflows/r.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
+    branches: [main, release/v0.4.4]
 
 permissions:
   contents: read
@@ -27,6 +27,7 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
           use-public-rspm: true
+          extra-repositories: https://rstudio.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -37,6 +38,27 @@ jobs:
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning")
         shell: Rscript {0}
 
+  testthat:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+          extra-repositories: https://rstudio.r-universe.dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: tests
+          extra-packages: any::testthat
+
+      - name: Run tests
+        run: testthat::test_local(reporter = "summary")
+        shell: Rscript {0}
+
   lintr:
     runs-on: ubuntu-latest
 
@@ -47,6 +69,7 @@ jobs:
         with:
           r-version: 'release'
           use-public-rspm: true
+          extra-repositories: https://rstudio.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -69,6 +92,7 @@ jobs:
         with:
           r-version: 'release'
           use-public-rspm: true
+          extra-repositories: https://rstudio.r-universe.dev
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -78,21 +102,50 @@ jobs:
         run: |
           cov <- covr::package_coverage()
           print(cov)
-          by <- as.data.frame(covr::coverage_to_list(cov))
-          by$file <- rownames(by)
+          cov_list <- covr::coverage_to_list(cov)
+          file_coverage <- cov_list$filecoverage
 
           core_files <- c("R/parser.R", "R/transform.R", "R/validation.R", "R/report.R")
-          missing <- setdiff(core_files, by$file)
+          missing <- setdiff(core_files, names(file_coverage))
           if (length(missing) > 0L) {
             stop(sprintf("Missing core files in coverage table: %s", paste(missing, collapse = ", ")))
           }
 
-          core_pct <- mean(by$filecoverage[match(core_files, by$file)])
-          total_pct <- covr::percent_coverage(cov)
+          core_pct <- mean(unname(file_coverage[core_files]))
+          total_pct <- as.numeric(cov_list$totalcoverage)
           cat(sprintf("Coverage total: %.2f%%\n", total_pct))
           cat(sprintf("Coverage core:  %.2f%%\n", core_pct))
 
           if (core_pct < 80) {
             stop(sprintf("Core coverage threshold not met: %.2f%% < 80%%", core_pct))
           }
         shell: Rscript {0}
+
+  installed-example:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+          extra-repositories: https://rstudio.r-universe.dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: check
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Run installed example module
+        run: |
+          source(system.file(
+            "examples",
+            "example_course_module",
+            "run-example.R",
+            package = "tutorizeR"
+          ))
+        shell: Rscript {0}

.gitignore

@@ -9,3 +9,4 @@
 ..Rcheck
 tutorizeR.Rcheck
 tutorizeR_*.tar.gz
+pkgdown/

CITATION.cff

@@ -11,7 +11,7 @@ version: 0.4.4
 license: MIT
 repository-code: https://github.com/AurelienNicosiaULaval/tutorizeR
 url: https://github.com/AurelienNicosiaULaval/tutorizeR
-date-released: '2026-02-13'
+date-released: '2026-02-14'
 keywords:
   - learnr
   - quarto
@@ -26,5 +26,4 @@ authors:
     email: aurelien.nicosia@mat.ulaval.ca
     affiliation: >-
       Université Laval
-    orcid: null
     role: author

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.4.4
+Date: 2026-05-31 17:07:44 UTC
+SHA: 839f3487567ac6950161c56ebeda225fb8e07373

DESCRIPTION

@@ -17,7 +17,7 @@ Description: Helps teachers convert existing '.Rmd' and '.qmd' teaching
     conversion reports.
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
     R (>= 4.0)
 Imports:
@@ -31,10 +31,13 @@ Imports:
 Suggests:
     commonmark,
     covr,
+    dplyr,
+    ggplot2,
     knitr,
     learnr,
     lintr,
     miniUI,
+    readr,
     shiny,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr

LICENSE-CONTENT.md

@@ -0,0 +1,14 @@
+# Creative Commons Attribution 4.0 International
+
+Educational example materials in `inst/examples/` and graphical documentation assets in `man/figures/` are licensed under the Creative Commons Attribution 4.0 International License unless otherwise specified.
+
+You are free to:
+
+- share, copy, and redistribute the material in any medium or format;
+- adapt, remix, transform, and build upon the material for any purpose, including teaching and research.
+
+You must give appropriate credit, provide a link to the license, and indicate if changes were made.
+
+License text:
+
+https://creativecommons.org/licenses/by/4.0/legalcode

LICENSES.md

@@ -0,0 +1,14 @@
+# License clarification
+
+This file clarifies licensing for reviewers and downstream instructors.
+
+| Repository content | License | Notes |
+|---|---|---|
+| R package code in `R/`, `inst/scripts/`, tests, and package infrastructure | MIT | The CRAN-style license fields are in `DESCRIPTION` and `LICENSE`; the full MIT text is in `LICENSE.md`. |
+| Technical package documentation, including README examples, function documentation, and vignettes | MIT | These files document use of the package and are treated as package documentation. |
+| Educational content in `inst/examples/` | CC-BY 4.0 | This includes the example course module, lesson source, question bank, dataset, and generated expected outputs. |
+| Generated expected outputs in `inst/examples/example_course_module/expected/` | CC-BY 4.0 | These files are educational artifacts derived from the example course module. |
+| Graphical documentation assets in `man/figures/` | CC-BY 4.0 | Includes the logo and workflow figure unless a file-level notice states otherwise. |
+| Reviewer documentation in `docs/` | MIT | These files support package review and release preparation. |
+
+The Creative Commons Attribution 4.0 International license text is available at <https://creativecommons.org/licenses/by/4.0/legalcode>.

NEWS.md

@@ -2,9 +2,17 @@
 
 ## Release finalization
 
-- Finalized JOSS-ready release artifacts and metadata alignment.
+- Finalized JOSE-oriented reviewer artifacts and metadata alignment.
 - Refreshed reproducibility and reviewer guidance docs.
 - Synchronized version fields for release publication.
+- Added JOSE preparation artifacts, educational use-case documentation,
+  expanded vignettes, an example course module, publication-readiness tests,
+  and pkgdown navigation for educational examples.
+- Recentered the review branch on JOSE software-submission requirements,
+  clarified educational evidence boundaries, added CC-BY content licensing,
+  and replaced internal smoke-test paths with installable example workflows.
+- Reworked the README as a package-facing overview and added pkgdown-oriented
+  documentation articles for educational use cases and website maintenance.
 
 # tutorizeR 0.4.3
 

R/transform.R

@@ -703,7 +703,7 @@ transform_setup_chunk <- function(block, format, language, seed, registry) {
     }
 
     body <- block$body_lines
-    required <- c("library(learnr)", "library(gradethis)", "gradethis_setup()")
+    required <- learnr_setup_lines()
 
     for (line in required) {
       if (!any(trimws(body) == line)) {
@@ -738,14 +738,23 @@ build_default_setup_chunk <- function(language, seed = NULL) {
   c(
     "```{r setup, include=FALSE}",
     tr("labels.setup_added", language = language),
-    "library(learnr)",
-    "library(gradethis)",
-    "gradethis_setup()",
+    learnr_setup_lines(),
     seed_line,
     "```"
   )
 }
 
+# Build setup lines required for generated learnr tutorials.
+learnr_setup_lines <- function() {
+  c(
+    "library(learnr)",
+    "if (requireNamespace(\"gradethis\", quietly = TRUE)) {",
+    "  library(gradethis)",
+    "  gradethis_setup()",
+    "}"
+  )
+}
+
 #' Build knitr R chunk header
 #' @keywords internal
 build_r_chunk_header <- function(label = NULL, options = character()) {