Update github actions to r-lib v2

- close #202
DrylandEcology · Jul 29, 2022 · 59901dd · 59901dd
1 parent b6aa18c
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diff --git a/.github/workflows/check-standard.yml b/.github/workflows/check-standard.yml
@@ -1,15 +1,14 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
 
-# script obtained 2021-Aug-13 from `usethis::use_github_action("check-standard")`
-# added step `Test coverage` (copied relevant sections from `usethis::use_github_action("test-coverage")`)
+# workflow derived from "check-standard" workflow
 
 # rSOILWAT2 contains submodules: these need to be checkout separately
 
 # rSOILWAT2 creates pdf vignette: these require a minimal latex setup
 
-# rSOILWAT2 doesn't meet documentation standards (see issues #12 and #105): once these are resolved, reset to
-# `rcmdcheck::rcmdcheck(..., error_on = "warning", ...)`
+# rSOILWAT2 doesn't meet documentation standards (see issues #12 and #105):
+# once these are resolved, reset to default `error-on: '"warning"'`
 
 # frequent failures because suggested package "rSW2exter" cannot be installed
 # (usually GDAL-related problems on GHA)
@@ -22,7 +21,7 @@ on:
   pull_request:
     branches: [main, release/**]
 
-name: R-CMD-check-covr
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
@@ -34,77 +33,43 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {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 }}
+      R_KEEP_PKG_SOURCE: yes
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - name: Checkout repository and submodules
-        uses: actions/checkout@v2
+      - uses: actions/checkout@v2
         with:
           submodules: recursive
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
+      - uses: r-lib/actions/setup-tinytex@v2
+      - run: tlmgr install makeindex
 
-      - uses: r-lib/actions/setup-tinytex@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:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        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-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Test coverage
-        if: ${{ runner.os == 'macOS' && success() }}
-        run: |
-          remotes::install_cran("covr")
-          covr::codecov()
-        shell: Rscript {0}
+          upload-snapshots: true
+          error-on: '"error"'
+
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -1,5 +1,6 @@
-# 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, release/**]
@@ -18,13 +19,14 @@ jobs:
         with:
           submodules: recursive
 
-      - 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: lintr
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
         run: lintr::lint_package()

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,33 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, release/**]
+  pull_request:
+    branches: [main, release/**]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, local::.
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rSOILWAT2
-Version: 5.3.1
+Version: 6.0.0-9000
 Title: An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
 Description: Access to the C-based SOILWAT2 v6.5.1 and functionality for
   SQLite-database of weather data.

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# rSOILWAT2 devel
+* `r-lib` Github Actions updated to `v2`;
+  separate workflows for `R-CMD-check` and `test-coverage` (#202).
+
+
 # rSOILWAT2 v5.3.1
 * This version fixes a bug in soil temperature output that was
   introduced with version `3.5.0` (#194).