ci: update ci workflows

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

@@ -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'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pkgdown.yaml

@@ -14,8 +14,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -34,7 +36,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,5 +27,10 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
         shell: Rscript {0}

README.Rmd

@@ -22,7 +22,7 @@ knitr::opts_chunk$set(
 [![CRAN](https://www.r-pkg.org/badges/version-ago/mapsf)](https://cran.r-project.org/package=mapsf)
 [![R-CMD-check](https://github.com/riatelab/mapsf/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/riatelab/mapsf/actions/workflows/R-CMD-check.yaml)
 [![downloads](https://cranlogs.r-pkg.org/badges/mapsf?color=brightgreen)](https://cran.r-project.org/package=mapsf)
-[![codecov](https://codecov.io/gh/riatelab/mapsf/branch/master/graph/badge.svg?token=TPK6HZOLWH)](https://app.codecov.io/gh/riatelab/mapsf)
+[![Codecov test coverage](https://codecov.io/gh/riatelab/mapsf/branch/master/graph/badge.svg)](https://app.codecov.io/gh/riatelab/mapsf?branch=master)
 [![status](https://tinyverse.netlify.com/badge/mapsf)](https://CRAN.R-project.org/package=mapsf)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 <!-- badges: end -->

README.md

@@ -8,7 +8,8 @@
 [![CRAN](https://www.r-pkg.org/badges/version-ago/mapsf)](https://cran.r-project.org/package=mapsf)
 [![R-CMD-check](https://github.com/riatelab/mapsf/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/riatelab/mapsf/actions/workflows/R-CMD-check.yaml)
 [![downloads](https://cranlogs.r-pkg.org/badges/mapsf?color=brightgreen)](https://cran.r-project.org/package=mapsf)
-[![codecov](https://codecov.io/gh/riatelab/mapsf/branch/master/graph/badge.svg?token=TPK6HZOLWH)](https://app.codecov.io/gh/riatelab/mapsf)
+[![Codecov test
+coverage](https://codecov.io/gh/riatelab/mapsf/branch/master/graph/badge.svg)](https://app.codecov.io/gh/riatelab/mapsf?branch=master)
 [![status](https://tinyverse.netlify.com/badge/mapsf)](https://CRAN.R-project.org/package=mapsf)
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively

codecov.yml

@@ -1,6 +1,14 @@
+comment: false
+
 coverage:
   status:
     project:
       default:
         target: 80%
         threshold: 10%
+        informational: true
+    patch:
+      default:
+        target: 80%
+        threshold: 10%
+        informational: true