From 59901dd5109343199d2b609f2dd1b668cdcef0bd Mon Sep 17 00:00:00 2001 From: Daniel Schlaepfer Date: Fri, 29 Jul 2022 11:05:01 -0400 Subject: [PATCH 1/2] Update github actions to r-lib v2 - close #202 --- .github/workflows/check-standard.yml | 91 +++++++++------------------- .github/workflows/lint.yaml | 10 +-- .github/workflows/test-coverage.yaml | 33 ++++++++++ DESCRIPTION | 2 +- NEWS.md | 5 ++ 5 files changed, 73 insertions(+), 68 deletions(-) create mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/check-standard.yml b/.github/workflows/check-standard.yml index ceb355ad..9634c88a 100644 --- 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 index 687541ad..5bb1d581 100644 --- 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 new file mode 100644 index 00000000..cfc1b71e --- /dev/null +++ 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 index cb486f49..b34e5ee8 100644 --- 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 index 608336ec..bf598358 100644 --- 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). From bbc759b6fa89d2a363b7ed355d50aa23ac94bc76 Mon Sep 17 00:00:00 2001 From: Daniel Schlaepfer Date: Fri, 29 Jul 2022 11:18:10 -0400 Subject: [PATCH 2/2] Don't change R package version number without updating test objects -> no change to test objects on this branch -> keep R package version number (plus 9000 for devel) --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b34e5ee8..ee85cb8c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: rSOILWAT2 -Version: 6.0.0-9000 +Version: 5.3.1-9000 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.