Catch patch up to v1.0.0

.Rbuildignore

@@ -29,3 +29,5 @@
 ^staged_dependencies.yaml$
 ^inst/dev_dependencies.R$
 ^\.devcontainer$
+^vignettes/articles$
+^inst/cheatsheet$

.github/CONTRIBUTING.md

@@ -1,34 +1,98 @@
 # Contribution to {admiral} 
 
-This outlines how to propose a change to the admiral package. For more detailed info about contributing to {admiral}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [development process guide](https://pharmaverse.github.io/admiraldev/main/articles/development_process.html) as well as other Developer Guides in the Articles section of the [{admiral} website](https://pharmaverse.github.io/admiral/cran-release/index.html)
+This outlines how to propose a change to the admiral package. For more detailed info about contributing to {admiral}, and other [pharmaverse packages](https://pharmaverse.org/), please see the [Contribution Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) as well as other Developer Guides in the Articles section of the [{admiraldev} website](https://pharmaverse.github.io/admiraldev/).
 
-# Basics
- * For each new contribution, the user creates an issue on the issue tab on [GitHub](https://github.com/pharmaverse/admiral/issues) to put it in our backlog. The issues can range from bug identification and/or fixes, enhancements to functions, documentation, tests or new features.   
+Please note that we try to align to best practices used in other R packages' development processes - so veteran developers should be familiar with our processes. However, we do deviate slightly from some best practices and we advise all new contributors to review our package documentation accordingly.
 
- * We advise you to contact us when an [issue](https://github.com/pharmaverse/admiral/issues) is created via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) (If you don't have access, use this [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A) to join).  We can discuss details or align expectations if you are not familiar with the `{admiral}` philosophy and programming strategy. The team will try to review the issues within the next backlog meeting and give some initial feedback. Since we are not a 100% fully resourced software development team it might be that some issues will take longer to respond to depending on the amount of overall issues. 
 
- * Familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/main/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/main/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/main/articles/unit_test_guidance.html).
+# Basics of Contribution
+ 🦋 For each new contribution, the user creates an issue on the issue tab on [GitHub](https://github.com/pharmaverse/admiral/issues) to put it in our backlog. The issues can range from bug identification and/or fixes, enhancements to functions, documentation, tests or new features.   
 
- * All newly [created issues](https://github.com/pharmaverse/admiral/issues) will be reviewed within the next backlog meeting and the creator will receive an initial feedback via a comment. Someone from the core development team will then triage new issues by assigning the appropriate labels (such as “user request” so we can easily identify new requests).
+ 🦋 We advise you to contact us when an [issue](https://github.com/pharmaverse/admiral/issues) is created via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) (If you don't have access, use this [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A) to join).  We can discuss details or align expectations if you are not familiar with the `{admiral}` philosophy and programming strategy. The team will try to review the issues within the next backlog meeting and give some initial feedback. Since we are not a 100% fully resourced software development team it might be that some issues will take longer to respond to depending on the amount of overall issues. 
+
+ 🦋 We advise you to familiarize yourself with our [programming strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html), guidance for [GitHub usage](https://pharmaverse.github.io/admiraldev/articles/git_usage.html) and [unit testing](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html).
+
+ 🦋 All newly [created issues](https://github.com/pharmaverse/admiral/issues) will be reviewed within the next backlog meeting and the creator will receive an initial feedback via a comment. Someone from the core development team will then triage new issues by assigning the appropriate labels (such as “user request” so we can easily identify new requests).
 
- * Issues are meant to be taken on by users from the Pharma programming community and not exclusively by the `{admiral}` team from GSK and Roche.
+ 🦋 Issues are meant to be taken on by users from the Pharma programming community and not exclusively by the `{admiral}` team from GSK and Roche.
 
 # Contribution Model
 
+## Type 1: Contribution without Code 
 
-## Type 1 Contribution with Code: 
-
- * First, the user creates an issue or comments on an existing issue to notify that they’d like to contribute code.
- * Follow our development process step-by-step guide.
- * We advise to contact an `{admiral}` core development team directly via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) before submitting code for complex functionality.
+  🦋  User creates an issue and ideally contacts an `{admiral}` team member via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269).
+
+  🦋  The `{admiral}` core development team will contact the issue creator as soon as possible to discuss further details.
+
 
+## Type 2: Contribution with Code
 
-## Type 2 Contribution without Code: 
+  🦋  First, the user creates an issue or comments on an existing issue to notify that they’d like to contribute code.
+
+  🦋  Follow our development process step-by-step guide.
+
+  🦋  We advise to contact an `{admiral}` core development team directly via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269) before submitting code for complex functionality.
 
- * User creates an issue and ideally contacts an `{admiral}` team member via [Slack](https://app.slack.com/client/T028PB489D3/C02M8KN8269).
- * The `{admiral}` core development team will contact the issue creator as soon as possible to discuss further details.
+## Detailed Development Process
 
+If you decide to contribute with code and you're ready to make your first code contribution, this detailed development process step-by-step guide will help tie all the other detailed vignettes together to give you the simplest experience of helping to grow and enhance our codebase.
 
-See [Contribution to {admiral}](https://pharmaverse.github.io/admiral/cran-release/articles/contribution_model.html) for additional details.
-
+1.  Create a new feature branch from the development branch `main`
+    following the naming convention and pull the latest changes - as
+    detailed on the [GitHub
+    usage](https://pharmaverse.github.io/admiraldev/articles/git_usage.html#working-with-feature-branches-1) guide.
+2.  Familiarize yourself with the `{admiral}` [programming
+    strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html), and then make the required
+    code updates.
+3.  Before making a pull request, check the [Pull Request Review
+    Guidance](https://pharmaverse.github.io/admiraldev/articles/pr_review_guidance.html) & the following checklist of
+    common things developers miss:
+    a.  Is all your code formatted according to the
+        [tidyverse](https://style.tidyverse.org/) style guide?
+    b.  Did you create/add appropriate [unit
+        tests](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#writing-unit-tests-in-admiral)?
+    c.  If you removed/replaced any function and/or function parameters,
+        did you fully follow the [deprecation
+        guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
+    d.  Did you update the
+        [documentation]https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#function-header-documentation)?
+        If so, remember to run `devtools::document()` and include the
+        updated `NAMESPACE` and `.Rd` files in `man/`.
+    e.  Does your code update have any impact on the [ADaM
+        template](https://pharmaverse.github.io/admiral/articles/admiral.html#starting-a-script)
+        R scripts stored in `inst/templates`?
+    f.  Does your code update have any impact on the vignettes stored in
+        vignettes?
+    g.  Did you update the Changelog `NEWS.md`?
+    h.  Did you build `{admiral}` site `pkgdown::build_site()` and check
+        that all affected examples are displayed correctly and that all
+        new functions occur on the
+        "[Reference](https://pharmaverse.github.io/admiral/reference/)" page?
+4.  Once happy with all the updates, make a [pull
+    request](https://pharmaverse.github.io/admiraldev/articles/git_usage.html#pull-request) to merge to the `main` branch
+    and link the issue so that it closes after successful merging.
+5.  Check that there are no merge conflicts. If there are any, fix them
+    before requesting review. See [solving merge
+    conflicts](https://pharmaverse.github.io/admiraldev/articles/git_usage.html#solving-merge-conflicts-in-the-terminal-on-rstudio)
+    guidance.
+6.  Check the results of the automated `R-CMD check` and `lintr` checks
+    and if any issues consult this
+    [guide](https://pharmaverse.github.io/admiraldev/articles/pr_review_guidance.html#common-r-cmd-check-issues).
+7.  Assign a reviewer from the `{admiral}` core development team - this
+    could be anyone you discussed the issue with previously via Slack or
+    GitHub. If unsure, add a comment that the pull request is ready for
+    review and add the `@pharmaverse/admiral` tag to it.
+8.  Once the review is completed, the reviewer will merge the PR and
+    this will then automatically delete the feature branch.
 
+Finally, just a note to say from the core developers that we hugely
+appreciate you taking the time to contribute to `{admiral}`. Don't be
+offended if during review we send requests back to you, as the
+expectations are high so that we can ensure the `{admiral}` codebase
+remains robust and consistent. The best way to learn here is always to
+jump in and get involved, so please don't be afraid you'll make mistakes
+along the way -- we all have and continue to do so, and that's what the
+reviews are for. Also if ever you get stuck don't hesitate to reach out
+for support via the [Slack
+channel](https://app.slack.com/client/T028PB489D3/C02M8KN8269).
+ ***Welcome to our `{admiral}` community!***

.github/pull_request_template.md

@@ -1,16 +1,17 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.   
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.   
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
 
 - [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
-- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/devel/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#deprecation)?
-- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
+- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
+- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
+- [ ] Review the [Cheat Sheet](https://github.com/pharmaverse/admiral/blob/main/inst/cheatsheet/admiral_cheatsheet.pdf). Make any required updates to it by editing the file `inst/cheatsheet/admiral_cheatsheet.pptx` and re-upload a PDF version of it to the same folder.
+- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates
 - [ ] Update `NEWS.md` under the header `# admiral (development version)` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
-- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/cran-release/reference/index.html)" page. 
+- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiral/reference/index.html)" page. 
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
 - [ ] Link the issue in the Development Section on the right hand side.

.github/workflows/common.yml

@@ -33,31 +33,48 @@ concurrency:
   group: admiral-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  R_VERSION: "4.1"
+
 jobs:
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
   style:
     name: Code Style
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -68,22 +85,19 @@ jobs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/v')
+    needs: get_r_version
     with:
-      r-version: "4.1"
-      # Whether to skip multiversion docs
-      # Note that if you have multiple versions of docs,
-      # your URL links are likely to break due to path changes
-      skip-multiversion-docs: false
-      latest-tag-alt-name: cran-release
-      multiversion-docs-landing-page: cran-release
-      branches-or-tags-to-list: >-
-        ^cran-release$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
+      r-version: "4.3"
+      skip-multiversion-docs: true
+    secrets:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    needs: get_r_version
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -93,8 +107,9 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
     if: >
       github.event_name != 'release'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -103,5 +118,20 @@ jobs:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  templates:
+    name: Check Templates
+    uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
+    secrets: inherit
+    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
+    needs: get_r_version
     with:
-      r-version: "4.1"
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  vbump:
+    name: Version Bump 🤜🤛
+    if: github.event_name == 'push'
+    uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}

.github/workflows/cran-status.yml → .github/workflows/cran-status.yml.paused

@@ -17,7 +17,7 @@ jobs:
     with:
       # Whom should the issue be assigned to if errors are encountered
       # in the CRAN status checks?
-      issue-assignees: "bundfussr,esimms999-gsk,manciniedoardo,bms63"
+      issue-assignees: "bundfussr,zdz2101,manciniedoardo,bms63"
       # Create an issue if one or more of the following
       # statuses are reported on the check report.
       statuses: "WARN,ERROR,NOTE"

.lycheeignore

@@ -3,3 +3,4 @@ https://github.com/pharmaverse/admiral/blob/main/
 https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adxx.R
 irongut/[email protected]
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+https://raw.githubusercontent.com/pharmaverse/admiral/main/inst/cheatsheet/cheatsheet_image.png