Merge pull request #3 from nlmixr2/update-ci

Update continuous integration and pkgdown building
nlmixr2 · Apr 5, 2023 · 396a72a · 396a72a
2 parents 8f33876 + c912b4f
commit 396a72a
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,48 +1,46 @@
+# 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
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,9 +29,10 @@ Description: Datasets for 'nlmixr2' and 'rxode2'. 'nlmixr2' is used for fitting
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 2.10)
 LazyData: true
 BugReports: https://github.com/nlmixr2/nlmixr2data/issues/
-URL: https://nlmixr2.github.io/nlmixr2data/, https://github.com/nlmixr2/nlmixr2data/
+URL: https://nlmixr2.github.io/nlmixr2data/,
+    https://github.com/nlmixr2/nlmixr2data/
diff --git a/README.Rmd b/README.Rmd
@@ -16,26 +16,27 @@ knitr::opts_chunk$set(
 # nlmixr2data
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/nlmixr2/nlmixr2data/workflows/R-CMD-check/badge.svg)](https://github.com/nlmixr2/nlmixr2data/actions)
+[![R-CMD-check](https://github.com/nlmixr2/nlmixr2data/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/nlmixr2data/actions/workflows/R-CMD-check.yaml)
 [![CodeFactor](https://www.codefactor.io/repository/github/nlmixr2/nlmixr2data/badge)](https://www.codefactor.io/repository/github/nlmixr2/nlmixr2data)
 <!-- badges: end -->
 
-The goal of nlmixr2data is to include all the example dataset from the nlmixr2 project in one place
+The goal of nlmixr2data is to include all the example datasets from the nlmixr2
+project in one place.
 
 ## Example
 
-This shows the `theo_sd` dataset, the hello world for nlmixr2
+This shows the `theo_sd` dataset, the hello world for nlmixr2.
 
 ```{r example}
 library(nlmixr2data)
 head(theo_sd)
 ```
 ## Installation
 
-You can install the development version of nlmixr2data from [GitHub](https://github.com/) with:
+You can install the development version of nlmixr2data from
+[GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("nlmixr2/nlmixr2data")
+# install.packages("remotes")
+remotes::install_github("nlmixr2/nlmixr2data")
 ```
-
diff --git a/README.md b/README.md
@@ -5,16 +5,16 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/nlmixr2/nlmixr2data/workflows/R-CMD-check/badge.svg)](https://github.com/nlmixr2/nlmixr2data/actions)
+[![R-CMD-check](https://github.com/nlmixr2/nlmixr2data/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/nlmixr2data/actions/workflows/R-CMD-check.yaml)
 [![CodeFactor](https://www.codefactor.io/repository/github/nlmixr2/nlmixr2data/badge)](https://www.codefactor.io/repository/github/nlmixr2/nlmixr2data)
 <!-- badges: end -->
 
-The goal of nlmixr2data is to include all the example dataset from the
-nlmixr2 project in one place
+The goal of nlmixr2data is to include all the example datasets from the
+nlmixr2 project in one place.
 
 ## Example
 
-This shows the `theo_sd` dataset, the hello world for nlmixr2
+This shows the `theo_sd` dataset, the hello world for nlmixr2.
 
 ``` r
 library(nlmixr2data)
@@ -34,6 +34,6 @@ You can install the development version of nlmixr2data from
 [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("nlmixr2/nlmixr2data")
+# install.packages("remotes")
+remotes::install_github("nlmixr2/nlmixr2data")
 ```
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: https://nlmixr2.github.io/nlmixr2data
+url: https://nlmixr2.github.io/nlmixr2data/
 template:
   bootstrap: 5
   params: