update GHA

abichat · Aug 16, 2022 · 58294af · 58294af
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diff --git a/.github/workflows/R-CMD-check-dev.yaml b/.github/workflows/R-CMD-check-dev.yaml
@@ -1,7 +1,6 @@
+# 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:
-      - dev
   pull_request:
     branches:
       - dev
@@ -10,16 +9,20 @@ name: R-CMD-check-dev
 
 jobs:
   R-CMD-check:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@master
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          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
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,16 +1,15 @@
+# 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:
       - master
-  pull_request:
-    branches:
-      - master
+      - dev
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -19,63 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: macOS-latest, r: 'devel'}
-          - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - 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-pandoc@master
-
-      - 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}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - 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-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,42 +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: 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.GH_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: macOS-r-3.6-${{ hashFiles('depends.Rds') }}
-          restore-keys: macOS-r-3.6-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_dev("pkgdown")
+      - 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: pkgdown::deploy_to_branch(new_process = FALSE)
-        shell: Rscript {0}
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/README.Rmd b/README.Rmd
@@ -25,9 +25,7 @@ version <- gsub('-', '.', version)
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![packageversion](https://img.shields.io/badge/package%20version-`r version`-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic)
-[![Codecov test coverage](https://codecov.io/gh/abichat/evabic/branch/master/graph/badge.svg)](https://codecov.io/gh/abichat/evabic?branch=master) 
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/c32dcc4c1c3f40a5950e1c10ea6dfb18)](https://www.codacy.com/app/abichat/evabic?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=abichat/evabic&amp;utm_campaign=Badge_Grade) 
-[![R build status](https://github.com/abichat/evabic/workflows/R-CMD-check/badge.svg)](https://github.com/abichat/evabic/actions)
+[![R-CMD-check](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml)
 [![Documentation](https://img.shields.io/badge/documentation-pkgdown-E91E63.svg)](https://abichat.github.io/evabic/) 
 [![last-commit](https://img.shields.io/github/last-commit/abichat/evabic.svg)](https://github.com/abichat/evabic/commits/master)
 <!-- badges: end -->

diff --git a/README.md b/README.md
@@ -9,12 +9,7 @@
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![packageversion](https://img.shields.io/badge/package%20version-0.0.4.9000-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic)
-[![Codecov test
-coverage](https://codecov.io/gh/abichat/evabic/branch/master/graph/badge.svg)](https://codecov.io/gh/abichat/evabic?branch=master)
-[![Codacy
-Badge](https://api.codacy.com/project/badge/Grade/c32dcc4c1c3f40a5950e1c10ea6dfb18)](https://www.codacy.com/app/abichat/evabic?utm_source=github.com&utm_medium=referral&utm_content=abichat/evabic&utm_campaign=Badge_Grade)
-[![R build
-status](https://github.com/abichat/evabic/workflows/R-CMD-check/badge.svg)](https://github.com/abichat/evabic/actions)
+[![R-CMD-check](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml)
 [![Documentation](https://img.shields.io/badge/documentation-pkgdown-E91E63.svg)](https://abichat.github.io/evabic/)
 [![last-commit](https://img.shields.io/github/last-commit/abichat/evabic.svg)](https://github.com/abichat/evabic/commits/master)
 <!-- badges: end -->
@@ -44,8 +39,8 @@ False Discovery Rate, Accuracy, F1…
 
 ``` r
 evabic::ebc_allmeasures
-#>  [1] "TP"   "FP"   "FN"   "TN"   "TPR"  "TNR"  "PPV"  "NPV"  "FNR"  "FPR"  "FDR" 
-#> [12] "FOR"  "ACC"  "BACC" "F1"   "PLR"  "NLR"  "DOR"
+#>  [1] "TP"   "FP"   "FN"   "TN"   "TPR"  "TNR"  "PPV"  "NPV"  "FNR"  "FPR" 
+#> [11] "FDR"  "FOR"  "ACC"  "BACC" "F1"   "PLR"  "NLR"  "DOR"
 ```
 
 All measures are computed from the confusion matrix:
@@ -114,8 +109,10 @@ summary(model)
 #> F-statistic: 69.99 on 7 and 42 DF,  p-value: < 2.2e-16
 pvalues <- summary(model)$coefficients[-1, 4]
 pvalues
-#>          X1          X2          X3          X4          X5          X6          X7 
-#> 0.004366456 0.829771754 0.003469737 0.491828466 0.581608670 0.887948400 0.449664443
+#>          X1          X2          X3          X4          X5          X6 
+#> 0.004366456 0.829771754 0.003469737 0.491828466 0.581608670 0.887948400 
+#>          X7 
+#> 0.449664443
 detected_var <- names(pvalues[pvalues < 0.05])
 detected_var
 #> [1] "X1" "X3"