Merge remote-tracking branch 'origin/main' into refactor

.github/ISSUE_TEMPLATE/release.yaml

@@ -0,0 +1,107 @@
+---
+name: 🚀 Release
+description: Template for package release
+title: "[Release]: <version>"
+labels: ["release"]
+assignees:
+  - KlaudiaBB
+  - cicdguy
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ⚠️ Please do not link or mention any internal references in this issue. This includes internal URLs, intellectual property and references.
+  - type: textarea
+    id: blocked-by
+    attributes:
+      label: Blocked by
+      description: Any PRs or issues that this release is blocked by.
+      placeholder: Add a list of blocking PRs or issues here.
+      value: |
+        ### PRs
+
+        - [ ] PR 1
+
+        ### Issues
+
+        - [ ] Issue 1
+    validations:
+      required: true
+  - type: textarea
+    id: pre-requisites
+    attributes:
+      label: Pre-requisites
+      description: Pre-requisites that must be fulfilled before initiating the release process.
+      placeholder: Add your list of pre-requisites here.
+      value: |
+        - [ ] Make sure that high priority bugs (label "priority" + "bug") have been resolved before going into the release.
+        - [ ] Review old/hanging PRs before going into the release.
+        - [ ] Revisit R-package's lifecycle badges (Optional).
+        - [ ] Discuss package dependencies before going into release activities.
+        - [ ] Create a plan to sequentially close release activities and submit groups of packages for internal validation (Applicable only for regulatory release).
+        - [ ] Make sure all relevant integration tests are green 2-3 days before the release. Look carefully through logs (check for warnings and notes).
+        - [ ] Check if a package is installable on our supported internal systems (Optional).
+        - [ ] Inform about the soft code freeze, decide what gets merged in before starting release activities.
+  - type: textarea
+    id: release-checklist
+    attributes:
+      label: Release Checklist
+      description: The steps to be taken in order to create a release.
+      placeholder: Steps to create a release.
+      value: |
+        - [ ] Recurring tasks: Execute the manual tests on Shiny apps that are deployed on various hosting providers (Posit connect and shinyapps.io) - track the results in GitHub issue (Applicable only for frameworks that use Shiny).
+        - [ ] Recurring tasks: Monitor integration tests, if integration fails, create priority issues on the board.
+        - [ ] Sanity checks for Shiny applications e.g. checking if Shiny apps are deployable and making sure there are no errors/warnings.
+        - [ ] Update NEWS.md file: make sure it reflects a holistic summary of what has changed in the package, check README.
+        - [ ] Remove the additional fields (`Remotes` and `Config/Needs/*`) from the DESCRIPTION file where applicable.
+        - [ ] Make sure that the minimum dependency versions are updated in the DESCRIPTION file for the package.
+        - [ ] Increase versioned dependency on {package name} to >=X.X.X.
+        - [ ] Create a pull request to make necessary bug fixes/changes (add "[skip vbump]" in the PR title), and after merging the PR, tag the update(s) as a release candidate v < intended release version > -rc < release candidate iteration > on the main branch. Note that tags are created in GitHub and synchronized with GitLab automatically.
+        - [ ] The package is submitted for internal validation by Release Coordinator (Applicable only for regulatory release).
+        - [ ] Address any feedback (internal validation/user testing), retag the package as a release candidate vX.X.X-rc(n+1). Repeat the submission for internal validation if necessary.
+        - [ ] Get the package validated (Applicable only for regulatory release).
+        - [ ] If the additional fields were removed, add them back in a separate PR, and then merge the PR back to main (add "[skip vbump]" in the PR title).
+        - [ ] Create a git tag with the final version set to X.X.X on the main branch.
+        - [ ] Update downstream package dependencies to (>=X.X.X) in {package name}.
+  - type: textarea
+    id: testing
+    attributes:
+      label: Testing
+      description: Summary of testing activities - integration tests, UAT, other.
+      placeholder: Tests results
+      value: |
+        - [ ] Integration tests results - accepted.
+        - [ ] UAT results - accepted.
+        - [ ] Shiny apps test results - accepted (Applicable only for Shiny apps).
+        - [ ] Necessary testing on target environment - performed (up to ETL).
+  - type: textarea
+    id: feedback
+    attributes:
+      label: Release Feedback
+      description: Feedback received from internal validation/UAT testers.
+      placeholder: Feedback to be implemented after submission for internal validation/testing.
+      value: |
+        - [ ] Fix 1
+        - [ ] Enhancement 1
+        - [ ] Defect 1
+  - type: textarea
+    id: post-release
+    attributes:
+      label: Post-release Checklist
+      description: The list of activities to be completed after the release.
+      placeholder: The steps that must be taken after the release.
+      value: |
+        - [ ] Make sure that the package is published to internal repositories (Validated and/or Non-Validated repository).
+        - [ ] Review and update installation instructions for the package if needed.
+        - [ ] Verify if a new dev version (.9XXX) has been added to the NEWS.md file and DESCRIPTION file as a placeholder for release notes by automation.
+        - [ ] Make sure internal documentation/documentation catalogs are up to date.
+        - [ ] Notify the IDR team to start post-release/clean-up activities.
+        - [ ] Announce the release on ________.
+  - type: textarea
+    id: decision-tree
+    attributes:
+      label: Decision tree
+      description: Any decision tree(s) that would aid release management
+      placeholder: Any decision tree(s) that would aid release management.
+      value: |
+        Click [here](https://github.com/insightsengineering/.github/blob/main/.github/ISSUE_TEMPLATE/RELEASE_DECISION_TREE.md) to see the release decision tree.

.github/workflows/check.yaml

@@ -15,13 +15,6 @@ on:
       - main
   workflow_dispatch:
 
-  # Rerun workflows once pkgdown has finished running, to add coverage
-  # and unit test report to gh-pages branch.
-  workflow_run:
-    workflows: ["Docs 📚"]
-    types:
-      - completed
-
 jobs:
   audit:
     name: Audit Dependencies 🕵️‍♂️
@@ -41,6 +34,9 @@ jobs:
         checking R code for possible problems .* NOTE
         checking examples .* NOTE
         checking Rd line widths .* NOTE
+        checking S3 generic/method consistency .* NOTE
+        checking Rd .usage sections .* NOTE
+        checking for unstated dependencies in vignettes .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
   coverage:
@@ -63,9 +59,10 @@ jobs:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main
   spelling:
-    if: github.event_name != 'push'
     name: Spell Check 🆎
     uses: insightsengineering/r.pkg.template/.github/workflows/spelling.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   links:
     if: github.event_name != 'push'
     name: Check URLs 🌐

.pre-commit-config.yaml

@@ -16,25 +16,20 @@ repos:
         name: Regenerate package documentation
         additional_dependencies:
           - checkmate
-          - digest
-          - dplyr
-          - ggplot2
-          - glue
-          - grDevices
           - lifecycle
           - logger
           - magrittr
-          - methods
-          - bioc::MultiAssayExperiment
-          - R6
           - rlang
-          - rtables
+          - shiny
           - shinyjs
-          - shinyWidgets
           - stats
-          - bioc::SummarizedExperiment
+          - insightsengineering/teal.data
+          - insightsengineering/teal.logger
+          - insightsengineering/teal.reporter
+          - insightsengineering/teal.slice
+          - insightsengineering/teal.transform
+          - insightsengineering/teal.widgets
           - utils
-          - yaml
       - id: spell-check
         name: Check spelling with `spelling`
         exclude: >

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal
 Title: Exploratory Web Apps for Analyzing Clinical Trials Data
-Version: 0.14.0.9000
-Date: 2023-08-14
+Version: 0.14.0.9004
+Date: 2023-08-24
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,4 +1,8 @@
-# teal 0.14.0.9000
+# teal 0.14.0.9004
+
+### Miscellaneous
+
+* Enhance a `module` validation checks so that it won't throw messages about `data` argument unnecessarily.
 
 # teal 0.14.0
 
@@ -17,6 +21,7 @@
 ### Miscellaneous
 
 * Removed `scda` package dependency from examples.
+* Updated the header tag style to enhance element containment.
 
 # teal 0.13.0
 

R/modules.R

@@ -232,7 +232,7 @@ module <- function(label = "module",
     )
   }
 
-  if (!is.element("data", server_formals)) {
+  if (!is.element("data", server_formals) && !is.null(datanames)) {
     message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
     datanames <- NULL
   }

inst/WORDLIST

@@ -4,8 +4,10 @@ TLG
 UI
 UIs
 UX
+cloneable
 funder
 omics
+pharmaverse
 preselected
 programmatically
 repo
@@ -14,5 +16,3 @@ tabsetted
 themer
 theming
 uncheck
-cloneable
-pharmaverse

inst/css/custom.css

@@ -54,6 +54,10 @@
   flex-wrap: wrap;
 }
 
+header {
+  display: flow-root;
+}
+
 footer {
   text-align: left;
   padding: 5px;