Pre-release activities (#240)

part of insightsengineering/nestdevs-tasks#48 - [x] Review and update: - README.md (check example code) - NEWS.md - [x] Run urlchecker::url_check() to identify broken links and fix - [x] Review functions: - @example tag, make sure it runs, fix if otherwise - Make sure functions has @return tag to document the return value - no \dontrun tag, replace with if(interactive()) if needed - [x] Sanity check of all vignettes, make sure there is no typo, no wrong format, etc. - [x] Run R CMD check --as-cran make sure everything pass - [x] Package Title is not duplicated in Package Description in DESCRIPTION file (e.g. this happens in teal.slice currently) - [x] All package names in Title and Description fields of DESCRIPTION file are quoted with ' - [x] You have checked the Package Release Template https://github.com/insightsengineering/teal.reporter/pull/205/files - [x] Make sure there are no ::: in examples - [x] Make sure all teal.* mentions are lower-cased and quoted - [x] Make Sure inst/WORDLIST is minimalized - [x] Make sure non-exported functions do not have examples - [x] Make sure each link to our documentation hosted with pkgdown on github pages do not have /main/ in the address but it has /latest/ instead, so we always expose the documentation of the latest release and not what's currently on main branch but not yet released - [x] Consistent usage of `<xyz>` object/datasets (if any). - [x] switch from title case into sentence case for title and description of functions. - [x] remove old rd syntax --------- Signed-off-by: kartikeya kirar <kirar.kartikeya1@gmail.com> Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com> Signed-off-by: Aleksander Chlebowski <114988527+chlebowa@users.noreply.github.com> Co-authored-by: Aleksander Chlebowski <114988527+chlebowa@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Aleksander Chlebowski <aleksander.chlebowski@contractors.roche.com> Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com> Co-authored-by: go_gonzo <dawid.kaledkowski@gmail.com>
insightsengineering · Jan 13, 2024 · 88786c2 · 88786c2
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diff --git a/.github/ISSUE_TEMPLATE/cran-release.yaml b/.github/ISSUE_TEMPLATE/cran-release.yaml
@@ -0,0 +1,124 @@
+---
+name: 🎉 CRAN Release
+description: Template for release to CRAN
+title: "[Release]: <version>"
+labels: ["release"]
+assignees:
+  - KlaudiaBB
+  - cicdguy
+  - shajoezhu
+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-release
+    attributes:
+      label: Pre-release
+      description: Pre-requisites that must be fulfilled before initiating the release process.
+      placeholder: Add your list of pre-requisites here.
+      value: |
+        - [ ] Make sure you adhere to CRAN submission policy: https://cran.r-project.org/web/packages/submission_checklist.html; https://cran.r-project.org/web/packages/policies.html.
+        - [ ] 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 (Optional).
+        - [ ] Revisit R-package's lifecycle badges (Optional).
+        - [ ] Make sure that all upstream dependencies of this package that need to be submitted to CRAN were accepted before going into release activities.
+        - [ ] Make sure integration tests are green 2-3 days before the release. Look carefully through logs (check for warnings and notes).
+        - [ ] Decide what gets merged in before starting release activities.
+  - type: textarea
+    id: release
+    attributes:
+      label: Release
+      description: The steps to be taken in order to create a release.
+      placeholder: Steps to create a release.
+      value: |
+        ### Prepare the release
+
+        - [ ] Create a new release candidate branch
+          `git checkout -b release-candidate-vX.Y.Z`
+        - [ ] Update NEWS.md file: make sure it reflects a holistic summary of what has changed in the package.
+        - [ ] Remove the additional fields (`Remotes`) from the DESCRIPTION file where applicable.
+        - [ ] Make sure that the minimum dependency versions are updated in the DESCRIPTION file for the package and its reverse dependencies (Optional).
+          - [ ] Increase versioned dependency on {package name} to >=X.Y.Z (Optional).
+        - [ ] Commit your changes and create the PR on GitHub (add "[skip vbump]" in the PR title). Add all updates, commit, and push changes:
+          `# Make the necessary modifications to your files
+          # Stage the changes
+          git add <files your modified>
+          # Commit the changes
+          git commit -m "[skip vbump] <Your commit message>"
+          git push origin release-candidate-vX.Y.Z`
+
+        ### Test the release
+
+        - [ ] 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).
+        - [ ] Monitor integration tests, if integration fails, create priority issues on the board.
+        - [ ] Execute UAT tests (Optional).
+
+        ### CRAN submission
+
+        - [ ] Tag the update(s) as a release candidate vX.Y.Z-rc<iteration-number> (e.g. v0.5.3-rc1) on the release candidate branch (release-candidate-vX.Y.Z).
+          `# Create rc tag for submission for internal validation
+          git tag vX.Y.Z-rc<iteration number>
+          git push origin vX.Y.Z-rc<iteration number>`
+        - [ ] Build the package locally using the command:`R CMD build .` which will generate a .tar.gz file necessary for the CRAN submission.
+        - [ ] Submit the package to https://win-builder.r-project.org/upload.aspx for testing, for more details please see "Building and checking R source packages for Windows": https://win-builder.r-project.org/.
+        - [ ] Once tested, send the package that was built in the previous steps to CRAN via this form: https://cran.r-project.org/submit.html.
+        - [ ] Address CRAN feedback, tag the package vX.Y.Z-rc(n+1) and repeat the submission to CRAN whenever necessary.
+        - [ ] Get the package accepted and published on CRAN.
+
+        ### Tag the 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). If nothing was removed just merge the PR you created in the "Prepare the release" section to 'main'. Note the commit hash of the merged commit. **Note:** additional commits might be added to the `main` branch by a bot or an automation - we do **NOT** want to tag this commit.
+
+        ### Make sure of the following before continuing
+
+        - [ ] CI checks are passing in GH before releasing the package.
+        - [ ] Shiny apps are deployable and there are no errors/warnings (Applicable only for frameworks that use Shiny).
+
+        - [ ] Create a git tag with the final version set to vX.Y.Z on the main branch. In order to do this:
+          1. Checkout the commit hash.
+          `git checkout <commit hash>`
+          2. Tag the hash with the release version (vX.Y.Z).
+          `git tag vX.Y.Z`
+          3. Push the tag to make the final release.
+          `git push origin vX.Y.Z`
+        - [ ] Update downstream package dependencies to (>=X.Y.Z) in {package name}.
+        Note: Once the release tag is created, the package is automatically published to internal repositories.
+  - type: textarea
+    id: post-release
+    attributes:
+      label: Post-release
+      description: The list of activities to be completed after the release.
+      placeholder: The steps that must be taken after the release.
+      value: |
+        - [ ] Ensure that CRAN checks are passing for the package.
+        - [ ] Make sure that the package is published to internal repositories.
+        - [ ] Make sure internal documentation is up to date.
+        - [ ] Review and update installation instructions for the package wherever needed (Optional).
+        - [ ] Update all integration tests to reference the new release.
+        - [ ] 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.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -5,12 +5,17 @@ Version: 0.3.0.9033
 Date: 2024-01-11
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre")),
+    person("Aleksander", "Chlebowski", , "aleksander.chlebowski@contractors.roche.com", role = "aut"),
+    person("Marcin", "Kosinski", , "marcin.kosinski.mk1@roche.com", role = "aut"),
+    person("Andre", "Verissimo", , "andre.verissimo@roche.com", role = "aut"),
     person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "aut"),
     person("Mahmoud", "Hallal", , "mahmoud.hallal@roche.com", role = "aut"),
     person("Nikolas", "Burkoff", role = "aut"),
     person("Maciej", "Nasinski", role = "aut"),
     person("Konrad", "Pagacz", role = "aut"),
     person("Junlue", "Zhao", role = "aut"),
+    person("Chendi", "Liao", , "chendi.liao@roche.com", role = "rev"),
+    person("Dony", "Unardi", , "unardid@gene.com", role = "rev"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
 Description: Utilities for data transformations compatible with 'teal'
@@ -21,7 +26,7 @@ URL: https://insightsengineering.github.io/teal.data/,
 BugReports: https://github.com/insightsengineering/teal.data/issues
 Depends:
     R (>= 4.0),
-    teal.code (>= 0.4.1.9009)
+    teal.code (>= 0.5.0)
 Imports:
     checkmate (>= 2.1.0),
     lifecycle (>= 0.2.0),
@@ -47,3 +52,29 @@ Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+Collate: 
+    'cdisc_data.R'
+    'data.R'
+    'default_cdisc_join_keys.R'
+    'formatters_var_labels.R'
+    'deprecated.R'
+    'dummy_function.R'
+    'join_key.R'
+    'join_keys-c.R'
+    'join_keys-extract.R'
+    'join_keys-names.R'
+    'join_keys-parents.R'
+    'join_keys-print.R'
+    'join_keys-utils.R'
+    'join_keys.R'
+    'teal.data.R'
+    'teal_data-class.R'
+    'teal_data-datanames.R'
+    'teal_data-get_code.R'
+    'teal_data-show.R'
+    'teal_data.R'
+    'testhat-helpers.R'
+    'topological_sort.R'
+    'utils-get_code_dependency.R'
+    'verify.R'
+    'zzz.R'
diff --git a/NEWS.md b/NEWS.md
@@ -41,8 +41,8 @@
 * Transferred data hashing step in `TealDataset` and `MAETealDataset` to `teal`.
 * Removed `CDISCTealData` class and updated `TealData` to account for the removed functionality.
 * Added datasets parents information to `JoinKeys` class.
-* Updated `cdisc_data` and `teal_data` wrappers to handle join_keys creation and updating instead of `CDISCTealData` and `TealData`.
-* Removed join_keys methods from `TealDataset`, `TealDatasetConnector`.
+* Updated `cdisc_data` and `teal_data` wrappers to handle `join_keys` creation and updating instead of `CDISCTealData` and `TealData`.
+* Removed `join_keys` methods from `TealDataset`, `TealDatasetConnector`.
 
 # teal.data 0.1.2
 

diff --git a/R/cdisc_data.R b/R/cdisc_data.R
@@ -1,18 +1,16 @@
-#' Data input for teal app
+#' Data input for `teal` app
 #'
 #' @description `r lifecycle::badge("stable")`
 #' Function is a wrapper around [teal_data()] and guesses `join_keys`
 #' for given datasets whose names match ADAM datasets names.
 #'
 #' @inheritParams teal_data
-#' @param join_keys (`join_keys`) or a single (`join_key_set`)\cr
+#' @param join_keys (`join_keys`) object or a single (`join_key_set`) object\cr
 #'   (optional) object with datasets column names used for joining.
 #'   If empty then it would be automatically derived basing on intersection of datasets primary keys.
 #'   For ADAM datasets it would be automatically derived.
 #'
-#' @return
-#' - a `TealData` object when `TealDataset` `TealDatasetConnector`, `TealDataConnector` is provided,
-#' - a `teal_data` object otherwise.
+#' @return A `teal_data` object.
 #'
 #' @details This function checks if there were keys added to all data sets
 #'
@@ -26,8 +24,8 @@
 #' )
 #'
 #' data <- within(data, {
-#'   ADSL <- teal.data::example_cdisc_data("ADSL")
-#'   ADTTE <- teal.data::example_cdisc_data("ADTTE")
+#'   ADSL <- example_cdisc_data("ADSL")
+#'   ADTTE <- example_cdisc_data("ADTTE")
 #' })
 #'
 cdisc_data <- function(...,

diff --git a/R/data.R b/R/data.R
@@ -1,6 +1,6 @@
 #' Random adverse events
 #'
-#' @description Random adverse events
+#' @description Random adverse events.
 #' @docType data
 #'
 #' @usage rADAE
@@ -11,9 +11,9 @@
 #' @name rADAE
 "rADAE"
 
-#' Random Concomitant Medications
+#' Random concomitant medications
 #'
-#' @description Random Concomitant Medications
+#' @description Random concomitant medications.
 #' @docType data
 #'
 #' @usage rADCM
@@ -26,7 +26,7 @@
 
 #' Random response
 #'
-#' @description Random Exposure
+#' @description Random exposure.
 #' @docType data
 #'
 #' @usage rADEX
@@ -39,7 +39,7 @@
 
 #' Random lab analysis
 #'
-#' @description Random lab analysis
+#' @description Random lab analysis.
 #' @docType data
 #'
 #' @usage rADLB
@@ -52,7 +52,7 @@
 
 #' Random response
 #'
-#' @description Random response
+#' @description Random response.
 #' @docType data
 #'
 #' @usage rADRS
@@ -65,7 +65,7 @@
 
 #' Random patient listing
 #'
-#' @description Random patient listing
+#' @description Random patient listing.
 #' @docType data
 #'
 #' @usage rADSL
@@ -78,7 +78,7 @@
 
 #' Random data `rADTR`
 #'
-#' @description Random data `rADTR`
+#' @description Random data `rADTR`.
 #' @docType data
 #'
 #' @usage rADTR
@@ -89,9 +89,9 @@
 #' @name rADTR
 "rADTR"
 
-#' Random Time to Event Analysis Dataset
+#' Random time to event analysis dataset
 #'
-#' @description Random Time to Event Analysis Dataset
+#' @description Random time to event analysis dataset.
 #' @docType data
 #'
 #' @usage rADTTE
@@ -104,7 +104,7 @@
 
 #' Random data `rADVS`
 #'
-#' @description Random data `rADVS`
+#' @description Random data `rADVS`.
 #' @docType data
 #'
 #' @usage rADVS

diff --git a/R/default_cdisc_join_keys.R b/R/default_cdisc_join_keys.R
@@ -1,4 +1,4 @@
-#' List containing the default `CDISC` join keys
+#' List containing default joining keys for `CDISC` datasets
 #'
 #' @details
 #' This data object is created at loading time from `cdisc_datasets/cdisc_datasets.yaml`.