update github actions workflows

jasenfinch · Feb 20, 2023 · b81658b · b81658b
1 parent 228b2dc
commit b81658b
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Showing 6 changed files with 62 additions and 28 deletions.
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
@@ -1,8 +1,10 @@
-# 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:
     branches: [main, master]
+  pull_request:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,33 @@ name: pkgdown
 jobs:
   pkgdown:
     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-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - 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/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.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:
@@ -15,16 +15,36 @@ jobs:
       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-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,7 +3,7 @@ Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabo
 Version: 0.15.0
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
-URL: https://jasenfinch.github.io/metabolyseR
+URL: https://jasenfinch.github.io/metabolyseR/
 BugReports: https://github.com/jasenfinch/metabolyseR/issues
 biocViews: Metabolomics
 Depends: R (>= 3.4.0)

diff --git a/README.Rmd b/README.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(collapse = TRUE,
 
 <!-- badges: start -->
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![R-CMD-check](https://github.com/jasenfinch/metabolyseR/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions)
+[![R-CMD-check](https://github.com/jasenfinch/metabolyseR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master) 
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION)
 [![DOI](https://zenodo.org/badge/88983134.svg)](https://zenodo.org/badge/latestdoi/88983134)

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 [![Lifecycle:
 stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![R-CMD-check](https://github.com/jasenfinch/metabolyseR/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions)
+[![R-CMD-check](https://github.com/jasenfinch/metabolyseR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master)
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION)
 [![DOI](https://zenodo.org/badge/88983134.svg)](https://zenodo.org/badge/latestdoi/88983134)