From 55489bcbaf1939fe99294f8a55924eb0f7adcbd3 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Thu, 12 Sep 2024 15:44:02 -0700 Subject: [PATCH 1/3] use_github_action() --- .github/.gitignore | 1 + .github/workflows/R-CMD-check-old.yaml | 86 ++++++++++++++++++++++++++ .github/workflows/R-CMD-check.yaml | 82 +++++++----------------- README.md | 2 +- 4 files changed, 112 insertions(+), 59 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check-old.yaml diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check-old.yaml b/.github/workflows/R-CMD-check-old.yaml new file mode 100644 index 0000000..4b910a1 --- /dev/null +++ b/.github/workflows/R-CMD-check-old.yaml @@ -0,0 +1,86 @@ +# # 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 +# on: +# push: +# branches: +# - main +# - master +# pull_request: +# branches: +# - main +# - master +# +# name: R-CMD-check +# +# jobs: +# R-CMD-check: +# runs-on: ${{ matrix.config.os }} +# +# name: ${{ matrix.config.os }} (${{ matrix.config.r }}) +# +# strategy: +# fail-fast: false +# matrix: +# config: +# - {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"} +# +# env: +# R_REMOTES_NO_ERRORS_FROM_WARNINGS: true +# RSPM: ${{ matrix.config.rspm }} +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# +# steps: +# - uses: actions/checkout@v2 +# +# - uses: r-lib/actions/setup-r@v1 +# with: +# r-version: ${{ matrix.config.r }} +# +# - uses: r-lib/actions/setup-pandoc@v1 +# +# - name: Query dependencies +# run: | +# install.packages('remotes') +# saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) +# writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") +# shell: Rscript {0} +# +# - name: Restore R package cache +# if: runner.os != 'Windows' +# uses: actions/cache@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 +# env: +# _R_CHECK_CRAN_INCOMING_REMOTE_: false +# run: | +# options(crayon.enabled = TRUE) +# rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", 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 diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index fb7b370..d46a617 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,16 +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 on: push: - branches: - - main - - master + branches: [main, master] pull_request: - branches: - - main - - master + branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -22,65 +20,33 @@ 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"} + - {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: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - if: runner.os != 'Windows' - 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 - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: | - options(crayon.enabled = TRUE) - 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@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/README.md b/README.md index ae65472..daa2f10 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # amerifluxr -[![R-CMD-check](https://github.com/chuhousen/amerifluxr/workflows/R-CMD-check/badge.svg)](https://github.com/chuhousen/amerifluxr/actions) +[![R-CMD-check](https://github.com/chuhousen/amerifluxr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/chuhousen/amerifluxr/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/chuhousen/amerifluxr/branch/master/graph/badge.svg)](https://codecov.io/gh/chuhousen/amerifluxr) [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/amerifluxr)](https://cran.r-project.org/package=amerifluxr) ![CRAN\_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/amerifluxr) From f46208314756662dbd5a05ce4490e648be928bfc Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Thu, 12 Sep 2024 17:06:07 -0700 Subject: [PATCH 2/3] update test-coverage.yaml with use_github_action() --- .github/workflows/test-coverage.yaml | 71 ++++++++++++++++------------ README.md | 2 +- 2 files changed, 43 insertions(+), 30 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index ba1f94f..9882260 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,48 +1,61 @@ +# 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 - - master + branches: [main, master] pull_request: - branches: - - main - - master + branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage - - name: Query dependencies + - name: Test coverage run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) shell: Rscript {0} - - name: Restore R package cache - uses: actions/cache@v2 + - uses: codecov/codecov-action@v4 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 dependencies + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() run: | - install.packages(c("remotes")) - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("covr") - shell: Rscript {0} + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/README.md b/README.md index daa2f10..d7f0283 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # amerifluxr [![R-CMD-check](https://github.com/chuhousen/amerifluxr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/chuhousen/amerifluxr/actions/workflows/R-CMD-check.yaml) -[![codecov](https://codecov.io/gh/chuhousen/amerifluxr/branch/master/graph/badge.svg)](https://codecov.io/gh/chuhousen/amerifluxr) + [![Codecov test coverage](https://codecov.io/gh/chuhousen/amerifluxr/graph/badge.svg)](https://app.codecov.io/gh/chuhousen/amerifluxr) [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/amerifluxr)](https://cran.r-project.org/package=amerifluxr) ![CRAN\_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/amerifluxr) From f68001ddb70f7b0bfe9d50402b2ef6e65c9fda12 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Thu, 12 Sep 2024 17:06:29 -0700 Subject: [PATCH 3/3] remove old .yaml --- .github/workflows/R-CMD-check-old.yaml | 86 -------------------------- 1 file changed, 86 deletions(-) delete mode 100644 .github/workflows/R-CMD-check-old.yaml diff --git a/.github/workflows/R-CMD-check-old.yaml b/.github/workflows/R-CMD-check-old.yaml deleted file mode 100644 index 4b910a1..0000000 --- a/.github/workflows/R-CMD-check-old.yaml +++ /dev/null @@ -1,86 +0,0 @@ -# # 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 -# on: -# push: -# branches: -# - main -# - master -# pull_request: -# branches: -# - main -# - master -# -# name: R-CMD-check -# -# jobs: -# R-CMD-check: -# runs-on: ${{ matrix.config.os }} -# -# name: ${{ matrix.config.os }} (${{ matrix.config.r }}) -# -# strategy: -# fail-fast: false -# matrix: -# config: -# - {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"} -# -# env: -# R_REMOTES_NO_ERRORS_FROM_WARNINGS: true -# RSPM: ${{ matrix.config.rspm }} -# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} -# -# steps: -# - uses: actions/checkout@v2 -# -# - uses: r-lib/actions/setup-r@v1 -# with: -# r-version: ${{ matrix.config.r }} -# -# - uses: r-lib/actions/setup-pandoc@v1 -# -# - name: Query dependencies -# run: | -# install.packages('remotes') -# saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) -# writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") -# shell: Rscript {0} -# -# - name: Restore R package cache -# if: runner.os != 'Windows' -# uses: actions/cache@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 -# env: -# _R_CHECK_CRAN_INCOMING_REMOTE_: false -# run: | -# options(crayon.enabled = TRUE) -# rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", 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