Update continuous integration

nlmixr2 · Apr 19, 2023 · 38b6bc4 · 38b6bc4
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commit 38b6bc4
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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'}
@@ -29,63 +29,29 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - name: Install X11 dependencies on MacOS
-        if: runner.os == 'macOS'
-        run: brew install --cask xquartz
-        shell: bash
-
       - name: Install deps on MacOS
         if: runner.os == 'macOS'
         run: |
+          brew install --cask xquartz
           brew install cairo
-          brew install libgit2
           brew install udunits
         shell: bash
 
-      - name: Link gfortran on MacOS
-        if: runner.os == 'macOS'
-        run: |
-          sudo ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran
-          sudo mkdir /usr/local/gfortran
-          sudo ln -s /usr/local/gfortran-10 /usr/local/gfortran
-        shell: bash
+      - uses: actions/checkout@v3
 
-      - name: Create Makevars for Fortran linking options on macOS
-        if: runner.os == 'macOS'
-        run: |
-          try(dir.create("~/.R"))
-          writeLines(c("GCCBASE:=$(shell brew --prefix gcc)","FLIBS=-L$(GCCBASE)/lib/gcc/10/lib -lm",""),"~/.R/Makevars")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Install Symengine from source for MacOS
-        if: runner.os == 'macOS'
-        run: install.packages("symengine", type="source")
-        shell: Rscript {0}
-
-      - 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
-
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - 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/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: ${{ runner.temp }}/package
diff --git a/README.Rmd b/README.Rmd
@@ -19,7 +19,7 @@ knitr::opts_chunk$set(
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN status](https://www.r-pkg.org/badges/version/nlmixr2targets)](https://CRAN.R-project.org/package=nlmixr2targets)
 [![R Targetopia](https://img.shields.io/badge/R_Targetopia-member-blue?style=flat&labelColor=gray)](https://wlandau.github.io/targetopia/)
-[![R-CMD-check](https://github.com/nlmixr2/nlmixr2targets/workflows/R-CMD-check/badge.svg)](https://github.com/nlmixr2/nlmixr2targets/actions)
+[![R-CMD-check](https://github.com/nlmixr2/nlmixr2targets/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/nlmixr2targets/actions/workflows/R-CMD-check.yaml)
 [![Code_Coverage_Badge](http://codecov.io/github/nlmixr2/nlmixr2targets/coverage.svg?branch=main)](http://codecov.io/github/nlmixr2/nlmixr2targets?branch=main)
 <!-- badges: end -->