Archive package-related functionality (#314)

Author: edelarua

.github/ISSUE_TEMPLATE/feature.yml

@@ -1,59 +1,12 @@
 ---
-name: 🔨 New Table Template
-description: Add a new table template
-title: "[New Table]: Table XX"
+name: 🔨 New TLG Template
+description: Add a new TLG template
+title: "[New TLG]: <title>"
 labels: ["new template"]
 projects: ["cardinal"]
 body:
   - type: textarea
-    id: table-layout
     attributes:
-      label: Table Layout & Design
-      description: Take a screenshot of the table and paste it here.
-      value: |
-        [Replace this line with your table screenshot by dragging the file here.]
-
-        Please refer to page XX of the [FDA guideline document](https://github.com/pharmaverse/cardinal/files/10744259/FDA-2022-N-1961-0002_attachment_1.pdf) for more details.
-  - type: textarea
-    id: table-description
-    attributes:
-      label: Table Description
-      description: Full title/description of the table.
-      placeholder: Table title
-  - type: textarea
-    id: analysis-datasets
-    attributes:
-      label: Analysis Datasets
-      description: Datasets that are used to generate the table.
-      value: |
-        [List required datasets here]
-
-        Data from the `random.cdisc.data` package, can be retrieved by `random.cdisc.data::c` followed by your
-        dataset name.
-  - type: textarea
-    id: analysis-filters
-    attributes:
-      label: Analysis Filters
-      description: Filters applied to the data to generate the table.
-      value: |
-        Safety population: `SAFFL == "Y"`
-        [List any additional filters here]
-  - type: textarea
-    id: additional-considerations
-    attributes:
-      label: Additional Information
-      description: Any additional information that the developer should know before creating the table function.
-      placeholder: Additional info
-  - type: textarea
-    id: todo
-    attributes:
-      label: Developer To Dos
-      description: Steps to complete as a developer when creating your pull request.
-      value: |
-        - [ ] **Table Function:** Create `R/fda-table_XX.R` file with your table-generating function.
-          - [ ] **Roxygen Documentation:** title, `@details`, document all parameters, `@return`, `@examples`, `@export`.
-        - [ ] **Tests:** Create `tests/testthat/test-table_XX.R` file with tests for the table function and then run these tests.
-        - [ ] **Quarto Template:** Create `quarto/table-templates/template-table_XX.qmd` file your table template.
-        - [ ] **Screenshot:** Add table screenshot as `table_XX.png` to the `quarto/assets/images/screenshots` folder.
-        - [ ] **_quarto.yml:** Add template to the "Template Library" section of the `_quarto.yml` file.
-        - [ ] **Template Index:** Run `quarto/assets/generate-template_index.R` script to update the template index.
+      label: TLG Title/Description
+      description: Title and/or a description of the TLG.
+      placeholder: TLG title/description

.github/ISSUE_TEMPLATE/new_template.yml

@@ -1,5 +1,26 @@
 # Pull Request
 
+## GitHub Issue
 <!--- Replace `#nnn` with your issue link for reference. -->
-
 Closes #nnn
+
+## Include a Screenshot of the TLG
+
+### Screenshot of TLG template from source document (e.g. FDA integrated guide)
+
+TODO: Add screenshot here
+
+## Developer To-Dos
+<!--- Steps to complete as a developer when creating your pull request. -->
+- [ ] Add quarto file `quarto/catalog/[TLG-ID]/index.qmd` with your TLG template.
+- [ ] Ensure that the _title_, _subtitle_, and _categories_ fields at the top of the TLG template are correct.
+- [ ] Add a screenshot of your TLG named `result.png` to the `quarto/catalog/[TLG-ID]` folder.
+- [ ] Branch has all updates from the `main` branch.
+- [ ] Request a reviewer.
+
+## Reviewer To-Dos
+<!--- Steps to complete as a reviewer when reviewing the pull request. -->
+- [ ] Confirm that all GitHub CI/CD pipelines pass with a ✅.
+- [ ] Confirm that the TLG screenshot above matches the template output screenshot (`result.png`).
+- [ ] Confirm that branch has all updates from the `main` branch.
+- [ ] Approve PR once all of the above have been confirmed.

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,34 +16,10 @@ on:
   workflow_dispatch:
 
 jobs:
-  audit:
-    name: Audit Dependencies 🕵️‍♂️
-    uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main
-  r-cmd:
-    name: R CMD Check 🧬
-    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
-    with:
-      additional-r-cmd-check-params: --as-cran
-      additional-env-vars: |
-        _R_CHECK_CRAN_INCOMING_REMOTE_=false
-  coverage:
-    name: Coverage 📔
-    uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
   linter:
     if: github.event_name == 'pull_request'
     name: SuperLinter 🦸‍♀️
     uses: insightsengineering/r.pkg.template/.github/workflows/linter.yaml@main
-  roxygen:
-    name: Roxygen 🅾
-    uses: insightsengineering/r.pkg.template/.github/workflows/roxygen.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.PHARMAVERSE_BOT }}
-    with:
-      auto-update: true
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main

.github/workflows/check.yaml

@@ -11,29 +11,21 @@ License: Apache License (>= 2)
 URL: https://github.com/pharmaverse/cardinal/
 BugReports: https://github.com/pharmaverse/cardinal/issues
 Depends:
-    R (>= 4.1)
+    R (>= 4.2)
 Imports:
-    admiraldev (>= 1.3.1),
-    cards (>= 0.6.1),
-    cardx (>= 0.2.5),
-    checkmate (>= 2.1.0),
+    cards (>= 0.7.0),
+    cardx (>= 0.3.0),
+    crane (>= 0.1.0),
     cowplot (>= 1.0.0),
     dplyr (>= 1.0.0),
-    formatters (>= 0.5.8),
     ggplot2 (>= 3.5.0),
     ggsurvfit (>= 1.1.0),
     gt (>= 1.0.0),
-    gtsummary (>= 2.3.0),
+    gtsummary (>= 2.4.0),
     lubridate (>= 1.7.10),
-    magrittr (>= 1.5),
     purrr (>= 1.0.1),
     rlang (>= 0.4.11),
-    rlistings (>= 0.2.9),
-    rtables (>= 0.6.9),
-    tern (>= 0.9.5),
-    tfrmt (>= 0.1.1),
-    tidyr (>= 0.8.3),
-    Tplyr (>= 1.2.1)
+    tidyr (>= 0.8.3)
 Suggests:
     knitr (>= 1.42),
     pharmaverseadam (>= 1.1.0),

.github/workflows/release.yaml

@@ -1,41 +1,2 @@
 # Generated by roxygen2: do not edit by hand
 
-export(alt_counts_df_preproc)
-export(basic_table_annot)
-export(make_fig_01)
-export(make_fig_02)
-export(make_fig_03)
-export(make_fig_14)
-export(make_table_22)
-export(split_cols_by_arm)
-import(Tplyr)
-import(cards)
-import(cardx)
-import(checkmate)
-import(dplyr)
-import(ggplot2)
-import(gt)
-import(gtsummary)
-import(rtables)
-import(tern)
-import(tfrmt)
-importFrom(admiraldev,assert_filter_cond)
-importFrom(cowplot,get_legend)
-importFrom(cowplot,plot_grid)
-importFrom(formatters,var_labels)
-importFrom(formatters,var_relabel)
-importFrom(formatters,with_label)
-importFrom(magrittr,"%>%")
-importFrom(purrr,walk)
-importFrom(rlang,":=")
-importFrom(rlang,.data)
-importFrom(rlistings,as_listing)
-importFrom(stats,median)
-importFrom(stats,prop.test)
-importFrom(stats,qt)
-importFrom(stats,quantile)
-importFrom(stats,sd)
-importFrom(stats,setNames)
-importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
-importFrom(tidyr,separate_rows)