Initialize renv and image workflow

.Rprofile

@@ -1 +1,46 @@
+# Set renv profile base on R version.
+.get_dependencies <- function(project_dir) {
+  dependencies <- renv::dependencies("DESCRIPTION", dev = TRUE)$Package
+
+  c(
+    project_dir,
+    dependencies
+  ) |>
+    unique() |>
+    renv:::renv_package_dependencies() |>
+    names()
+}
+
+options(renv.snapshot.filter = .get_dependencies)
+
+if (Sys.getenv("GITHUB_ACTIONS") != "") {
+  options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest"))
+  Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE)
+}
+Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE)
+Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE)
+
+# Do not load renv by default
+
+if (identical(Sys.getenv("RENV_AUTOLOADER_ENABLED"), "")) {
+  Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE)
+}
+
+if (!isFALSE(Sys.getenv("RENV_AUTOLOADER_ENABLED"))) {
+  .renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
+  if (!file.exists("./renv/profile")) {
+    if (.renv_profile %in% c("4.1", "4.2", "4.3")) {
+      message("Set renv profile to `", .renv_profile, "`")
+      Sys.setenv("RENV_PROFILE" = .renv_profile)
+    } else {
+      message("This repository do not contains the renv profile for your R version.")
+    }
+  } else {
+    message(
+      "Using renv profile from `renv/profile` file.\n",
+      "The `", readLines("./renv/profile"), "` profile will be used."
+    )
+  }
+}
+
 source("renv/activate.R")

.github/CONTRIBUTING.md

@@ -25,7 +25,7 @@ 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).
 
- * All newly [created issues](https://github.com/pharmaverse/aok/issues) will be
+ * All newly [created issues](https://github.com/pharmaverse/oak/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

.github/workflows/build_docker_image.yml

@@ -0,0 +1,98 @@
+---
+name: Deploy Docker Image
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'renv/profiles/**/renv.lock'
+  workflow_dispatch: # give possibility to run it manually
+
+permissions: write-all
+env:
+  REGISTRY: ghcr.io
+
+concurrency:
+  group: deploy-docker-image-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  get_renv_list:
+    runs-on: ubuntu-latest
+    outputs:
+        matrix: ${{ steps.matrix.outputs.renv }}
+
+    steps:
+
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 2 # "2" -> To retrieve the preceding commit.
+
+      - name: Get changed files in renv/profiles
+        id: changed-files
+        uses: tj-actions/changed-files@v35
+        with:
+          files: renv/profiles/**/renv.lock
+
+      # TODO: what to do with renv_legacy ?
+      - name: Get Updated renv # note: for case schedules job, we update every docker images, and for renv.lock files updates we only update modified renv.lock versions
+        id: matrix
+        run: |
+          if [[ "${{github.event_name}}" == "schedule" || "${{github.event_name}}" == "workflow_dispatch" ]]
+          then
+            renv_list=$(find renv/profiles | grep renv.lock )
+          else
+            renv_list="${{ steps.changed-files.outputs.all_changed_files }}"
+          fi
+          renv_list=$(echo $renv_list | sed 's/ /", "/g')
+          echo "renv=[\"$renv_list\"]" >> $GITHUB_OUTPUT
+
+  deploy-image:
+    needs: [ get_renv_list ]
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false # if one of the job "deploy-image" fails, the other parallel jobs will just continue
+      matrix:
+        value: ${{ fromJson(needs.get_renv_list.outputs.matrix) }}
+
+    # Token permissions
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Print message
+        run: |
+          echo "updating docker image for renv ${{ matrix.value }}"
+
+      - name: Set image specs
+        id: image_specs
+        run: |
+          package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}')
+          r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?)
+          echo "r_version=$r_version" >> $GITHUB_OUTPUT
+          echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT
+          renv=$(echo "${{ matrix.value }}" | tr -d '"')
+          echo "renv_lock_path=$renv" >> $GITHUB_OUTPUT
+
+      - name: Call deploy docker image action for every renv
+        uses: insightsengineering/r-image-creator@v1
+        with:
+          image-name: "${{ steps.image_specs.outputs.image_name }}"
+          tag-latest: true
+          base-image: "rocker/rstudio:${{ steps.image_specs.outputs.r_version }}"
+          sysdeps: qpdf,libxt-dev,curl,npm,libicu-dev,libcurl4-openssl-dev,libssl-dev,make,zlib1g-dev,libfontconfig1-dev,libfreetype6-dev,libfribidi-dev,libharfbuzz-dev,libjpeg-dev,libpng-dev,libtiff-dev,pandoc,libxml2-dev,libgit2-dev,libgit2-dev,jq
+          renv-lock-file: "${{ steps.image_specs.outputs.renv_lock_path }}"
+          repository-owner: ${{ github.repository_owner }}
+          repo-user: ${{ github.actor }}
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+
+# note: in case of 403 error when pushing to ghcr : link current repo to the given package registry - https://github.com/docker/build-push-action/issues/687
+# (got to https://github.com/<user name>?tab=packages to go to packages settings) and there https://github.com/users/<user name>/packages/container/admiralci-4.0/settings

.github/workflows/common.yml

@@ -92,11 +92,11 @@ jobs:
     if: >
       github.event_name != 'release'
     with:
-      r-version: "4.3"
+      r-version: "4.1"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
-      skip-coverage-badges: false
+      skip-coverage-badges: true
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main

.github/workflows/r-renv-lock.yml

@@ -0,0 +1,141 @@
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .github/workflows/r-renv-lock.yml
+      - DESCRIPTION
+
+name: Generate renv.lock
+
+concurrency:
+  group: r-renv-lock-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  r-renv-lock-gen:
+    if: github.event.pull_request.draft == false
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    strategy:
+      max-parallel: 1
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-20.04, r: '4.1', repos: 'https://packagemanager.posit.co/cran/2022-03-10/'}
+          - {os: ubuntu-20.04, r: '4.2', repos: 'https://packagemanager.posit.co/cran/2023-03-15/'}
+          - {os: ubuntu-20.04, r: '4.3', repos: 'https://packagemanager.posit.co/cran/2023-04-20/'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_CRAN_REPO: ${{ matrix.config.repos }}
+      RENV_PROFILE_NAME: ${{ matrix.config.r }}
+      R_RELEASE_LAGACY: ${{ matrix.config.legacy || false }}
+
+    steps:
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/[email protected]
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v3
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install system dependencies
+        run: sudo apt update && sudo apt install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libgit2-dev -y
+
+      - name: Collect dependencies
+        run: |
+          Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE)
+          Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE)
+          source("renv/activate.R")
+          lock_gen_version <- "0.1.0"
+          legacy <- identical(Sys.getenv("R_RELEASE_LAGACY"), "true")
+          renv_profile <- Sys.getenv("RENV_PROFILE_NAME", "dev")
+          if (legacy) renv_profile <- paste0(renv_profile, "_legacy")
+          cran_r_release <- Sys.getenv("R_CRAN_REPO", "https://packagemanager.posit.co/cran/2023-03-15/")
+          cran_latest <- Sys.getenv("CRAN_R_LATEST", "https://packagemanager.posit.co/cran/latest")
+          unlink(file.path("renv", "profiles", renv_profile), recursive = TRUE)
+
+          cat("\n==================================\n")
+          cat("Create renv.lock files\n")
+          cat(paste("renv_profile: \"", renv_profile, "\"\n", sep = ""))
+          cat(paste("cran_r_release: \"", cran_r_release, "\"\n", sep = ""))
+          cat(paste("cran_latest: \"", cran_latest, "\"\n", sep = ""))
+          cat("==================================\n")
+
+
+          renv::activate(profile = renv_profile)
+
+          renv::settings$snapshot.type("custom")
+          .get_dependencies <- function(project_dir) {
+            dependencies <- renv::dependencies("DESCRIPTION", dev = TRUE)$Package
+
+            c(
+              project_dir,
+              dependencies
+            ) |>
+              unique() |>
+              renv:::renv_package_dependencies() |>
+              names()
+          }
+
+          options(renv.snapshot.filter = .get_dependencies)
+
+          # CRAN repo from R release
+          options("repos" = c("RSPM" = cran_r_release))
+
+          renv::install("openpharma/staged.dependencies", repos = options("repos"))
+          renv::install("devtools")
+
+          # Packages from stage dependencies to ignore
+          renv::settings$ignored.packages(c("admiraldev"))
+
+          # Install dependencies
+          renv::settings$snapshot.type("explicit")
+          renv::install(repos = options("repos"))
+
+          # Set newest CRAN for few packages upgrade
+          options("repos" = c(
+            "CRAN" = cran_latest,
+            "RSPM" = cran_r_release
+          ))
+
+          # Install latest remotes version
+          renv::install("remotes", repos = cran_latest)
+
+          renv::install("[email protected]", dependencies = "none")
+          renv::install("[email protected]", dependencies = "none")
+
+          renv::settings$snapshot.type("custom")
+          renv::snapshot(force = TRUE, prompt = FALSE)
+          renv::record("[email protected]")
+          renv::record("devtools")
+          renv::record("[email protected]")
+          renv::record("openpharma/staged.dependencies")
+
+          if (identical(renv_profile, "4.3")) {
+            file.copy(renv::paths$lockfile(), "renv.lock", overwrite = TRUE)
+          }
+        shell: Rscript --vanilla {0}
+
+      - name: Commit and push changes
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: Automatic renv profile update.
+          file_pattern: 'renv.lock renv/profiles/*'
+          commit_user_name: pharmaverse-bot
+          commit_user_email: [email protected]
+          create_branch: true

.lintr

@@ -2,7 +2,6 @@ linters: linters_with_defaults(
     any_duplicated_linter(),
     any_is_na_linter(),
     backport_linter("oldrel-4"),
-    consecutive_assertion_linter(),
     expect_comparison_linter(),
     expect_identical_linter(),
     expect_length_linter(),

.lycheeignore

@@ -0,0 +1 @@
+https://cran.r-project.org/package=sdtm.oak

DESCRIPTION

@@ -21,7 +21,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Depends: R (>= 4.1)
 Imports: 
-    rlang
+    rlang (>= 1.0.0)
 Suggests:
     knitr,
     rmarkdown,

renv/.gitignore

@@ -5,3 +5,4 @@ lock/
 python/
 sandbox/
 staging/
+profile