Merge pull request #59 from atorus-research/development

CRAN Prep steps

.Rbuildignore

@@ -11,4 +11,6 @@
 ^archive$
 ^data\-raw$
 ^scratch\.R$
-^demos$
+^demos$
+^cran_comments\.md$
+^NEWS\.md$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,59 @@
+# 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
+        - dev
+    pull_request:
+      branches:
+        - main
+        - master
+        - dev
+
+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: windows-latest, r: 'release'}
+            - {os: macOS-latest, r: 'release'}
+            - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+            - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
+            - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+            - {os: ubuntu-latest,  r: 'release'}
+
+      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/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinify
 Type: Package
-Title: flextable and officer extensions for clinical outputs
+Title: Clinical Table Styling Tools and Utilities
 Version: 0.1.0
 Authors@R: c(
     person(given = "Mike",
@@ -11,7 +11,10 @@ Authors@R: c(
     person("Ross", "Didenko", email = "[email protected]", role = c("aut")),
     person("Yevhenii", "Boiko", email = "[email protected]", role = c("aut")),
     person("Marat", "Zakirov", email = "[email protected]", role = "ctb"),
-    person("Roman", "Rogoza", email = "[email protected]", role = "ctb"))
+    person("Roman", "Rogoza", email = "[email protected]", role = "ctb"),
+    person(given = "Atorus Research, Inc.",
+           role = "cph"),
+    person(given = "Incyte Corporation", role="cph"))
 Depends:
     R (>= 4.2)
 Imports: 

NEWS.md

@@ -0,0 +1,3 @@
+# clinify 0.1.0
+
+* Initial CRAN submission.

README.Rmd

@@ -27,6 +27,8 @@ knitr::opts_chunk$set(
 You can install the development version of **{clinify}** like so:
 
 ```{r, eval=FALSE}
+install.packages("clinify")
+
 # Install the development version:
 devtools::install_github("https://github.com/atorus-research/clinify.git", ref="development")
 ```

README.md

@@ -20,6 +20,8 @@ the creation of clinical tables, listings and figures.
 You can install the development version of **{clinify}** like so:
 
 ``` r
+install.packages("clinify")
+
 # Install the development version:
 devtools::install_github("https://github.com/atorus-research/clinify.git", ref="development")
 ```

cran_comments.md

@@ -0,0 +1,3 @@
+# clinify 0.1.0 
+
+Initial CRAN submission