Add rdocx package

.Rbuildignore

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+^rdocx\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
+.gitlab-ci.yml
+_pkgdown.yml
+^\.github$

.github/.gitignore

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+*.html

.github/workflows/check_package.yml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+  branches: [main, master]
+pull_request:
+  branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+  runs-on: ${{ matrix.config.os }}
+
+name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+strategy:
+  fail-fast: false
+matrix:
+  config:
+  - {os: macos-latest,   r: 'release'}
+- {os: windows-latest, r: 'release'}
+- {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+- {os: ubuntu-latest,   r: 'release'}
+- {os: ubuntu-latest,   r: 'oldrel-1'}
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+R_KEEP_PKG_SOURCE: yes
+
+steps:
+  - uses: actions/checkout@v4
+
+- uses: r-lib/actions/setup-pandoc@v2
+
+- uses: r-lib/actions/setup-r@v2
+with:
+  r-version: ${{ matrix.config.r }}
+http-user-agent: ${{ matrix.config.http-user-agent }}
+use-public-rspm: true
+
+- uses: r-lib/actions/setup-r-dependencies@v2
+with:
+  extra-packages: any::rcmdcheck
+needs: check
+
+- uses: r-lib/actions/check-r-package@v2
+with:
+  upload-snapshots: true
+build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/coverage_and_build.yml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+# From {cards} actions
+on:
+    push:
+      branches: [main, master]
+    pull_request:
+      branches: [main, master]
+    workflow_dispatch:
+
+name: Test and build pages
+
+permissions: read-all
+
+jobs:
+    coverage_and_build:
+      runs-on: ubuntu-latest
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      permissions:
+        contents: write
+      concurrency:
+          group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+
+      steps:
+        - uses: actions/checkout@v4
+
+        - uses: r-lib/actions/setup-pandoc@v2
+
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::covr, any::pkgdown, local::.
+            needs: coverage, check, website
+
+        - name: Test coverage
+          run: |
+            cov <- covr::package_coverage(
+              quiet = FALSE,
+              clean = FALSE,
+              install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+            )
+            covr::to_cobertura(cov)
+          shell: Rscript {0}
+
+        - uses: codecov/codecov-action@v4
+          with:
+            fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+            file: ./cobertura.xml
+            plugin: noop
+            disable_search: true
+            token: ${{ secrets.CODECOV_TOKEN }}
+
+        - name: Show testthat output
+          if: always()
+          run: |
+            ## --------------------------------------------------------------------
+            find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+          shell: bash
+
+        - name: Upload test results
+          if: failure()
+          uses: actions/upload-artifact@v4
+          with:
+            name: coverage-test-failures
+            path: ${{ runner.temp }}/package
+        - name: Build site
+          run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          shell: Rscript {0}
+
+        - name: Deploy to GitHub pages 🚀
+          if: github.event_name != 'pull_request'
+          uses: JamesIves/[email protected]
+          with:
+            clean: false
+            branch: gh-pages
+            folder: docs

DESCRIPTION

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+Package: rdocx
+Title: rdocx
+Description: The `rdocx` package streamlines clinical trial reporting 
+    by enabling R-driven, end-to-end workflows that produce reports in 
+    Microsoft Word format for interdisciplinary collaboration. Built with 
+    an object-oriented design, `rdocx` provides classes for creating 
+    structured report items (tables, figures, etc.) with a comprehensive 
+    suite of tests for quality assurance. The package allows rendering 
+    reports in a customizable Word template, promoting seamless 
+    integration into GxP-compliant environments. Two main use cases are 
+    supported, a generic RMarkdown report template for standardized 
+    document creation, and an automated reporting tool for selective 
+    updates to tables and figures in existing Word files.
+Version: 1.0.0
+Authors@R: c(
+  person("Janina", "Linnik", email = "[email protected]", role = c("aut", "cre")),
+  person("Orla", "Doyle", email = "[email protected]", role = c("aut")),
+  person("Ines", "Gimeno Molina", email = "[email protected]", role = c("aut")),
+  person("Jack", "Talboys", email = "[email protected]", role = c("ctb")))
+Maintainer: Janina Linnik <[email protected]>, Orla Doyle <[email protected]>, Ines Gimeno Molina <[email protected]> 
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Imports:
+    rmarkdown,
+    dplyr,
+    flextable,
+    knitr,
+    lgr,
+    officer,
+    R6,
+    checkmate,
+    jpeg,
+    magick,
+    magrittr,
+    png,
+    stats,
+    stringr,
+    tools,
+    utils,
+    xml2,
+    yaml,
+    cowplot,
+    ggplot2,
+    kableExtra,
+    testthat
+VignetteBuilder: knitr
+Collate: 
+    'ActivityTable.R'
+    'ChangelogTable.R'
+    'ReplaceOutputs.R'
+    'SignaturesTable.R'
+    'TitlePage.R'
+    'rdocx_global.R'
+    'rmd_render.R'
+    'utils.R'
+    'utils_checks.R'

LICENSE

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-MIT License
+# MIT License
 
-Copyright (c) 2024 Novartis
+Copyright (c) 2023-2024 Novartis, rdocx authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023-2024 Novartis, rdocx authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(ActivityTable)
+export(ChangelogTable)
+export(ChangelogTableRow)
+export(ReplaceOutputs)
+export(SignaturesTable)
+export(SignaturesTableRow)
+export(TitlePage)
+export(generic_report_template)
+export(rmd_render)
+import(R6)
+import(checkmate)
+import(dplyr)
+import(flextable)
+import(jpeg)
+import(lgr)
+import(magick)
+import(officer)
+import(png)
+import(rmarkdown)
+import(stats)
+import(stringr)
+import(tools)
+import(utils)
+import(xml2)
+import(yaml)
+importFrom(magrittr,`%>%`)