From 0d9a638e7b63256c90613106dc49a53e4e3309db Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:51:05 +0000 Subject: [PATCH 1/3] add rworkflows --- .Rbuildignore | 4 ++ .github/workflows/R-CMD-check.yaml | 68 ------------------------------ .github/workflows/rworkflows.yml | 52 +++++++++++++++++++++++ DESCRIPTION | 2 +- NEWS.md | 6 +++ 5 files changed, 63 insertions(+), 69 deletions(-) delete mode 100644 .github/workflows/R-CMD-check.yaml create mode 100644 .github/workflows/rworkflows.yml diff --git a/.Rbuildignore b/.Rbuildignore index 59f88159..158ca9da 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -27,3 +27,7 @@ colp_search.R notes-email-question.R log.Rmd ^CRAN-SUBMISSION$ + +node_modules$ +package-lock\.json$ +package\.json$ \ No newline at end of file diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml deleted file mode 100644 index 6847c305..00000000 --- a/.github/workflows/R-CMD-check.yaml +++ /dev/null @@ -1,68 +0,0 @@ -on: [push, pull_request] - -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: 'latest'} - - { os: macOS-latest, r: 'latest'} - - { os: macOS-latest, r: 'devel'} - - { os: ubuntu-16.04, r: 'latest', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - CRAN: ${{ matrix.config.cran }} - VCR_VERBOSE_ERRORS: true - ENTREZ_KEY: ${{ secrets.ENTREZ_KEY }} - IUCN_REDLIST_KEY: ${{ secrets.IUCN_REDLIST_KEY }} - TROPICOS_KEY: ${{ secrets.ENTREZ_KEY }} - - steps: - - uses: actions/checkout@v1 - - - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@master - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v1 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('DESCRIPTION') }} - - - name: Install system dependencies - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "install.packages('remotes')" -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" - - name: Install dependencies - run: Rscript -e "install.packages('remotes')" -e "remotes::install_deps(dependencies = TRUE)" -e "remotes::install_cran('rcmdcheck')" - - - name: Check - run: Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error', check_dir = 'check')" - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check - - - name: Test coverage - if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'latest' - run: | - Rscript -e 'install.packages("covr")' -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")' diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml new file mode 100644 index 00000000..980b6e33 --- /dev/null +++ b/.github/workflows/rworkflows.yml @@ -0,0 +1,52 @@ +name: rworkflows +'on': + push: + branches: + - master + - main + - devel + - RELEASE_** + pull_request: + branches: + - master + - main + - devel + - RELEASE_** +jobs: + rworkflows: + permissions: write-all + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: macOS-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + steps: + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ false }} + run_rcmdcheck: ${{ true }} + as_cran: ${{ true }} + run_vignettes: ${{ true }} + has_testthat: ${{ true }} + run_covr: ${{ true }} + run_pkgdown: ${{ true }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ true }} + runner_os: ${{ runner.os }} diff --git a/DESCRIPTION b/DESCRIPTION index e518d1a6..9f29c865 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Interacts with a suite of web 'APIs' for taxonomic tasks, species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. -Version: 0.9.100 +Version: 0.9.101 License: MIT + file LICENSE URL: https://docs.ropensci.org/taxize/ (website), https://github.com/ropensci/taxize (devel), diff --git a/NEWS.md b/NEWS.md index 2c0059b3..10a2ef4d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +taxize 0.9.101 + +Add `rworkflows`. +Update *.Rbuildignore* for `rworkflows`. + +============= taxize 0.9.100 ============= From ed877c01a5c5bd28da5c7f0aa726d69052c6cbf0 Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Mon, 22 Jan 2024 11:59:12 +0000 Subject: [PATCH 2/3] add rworkflows --- NEWS.md | 7 +++++-- README.Rmd | 2 +- README.md | 18 +++++++++--------- 3 files changed, 15 insertions(+), 12 deletions(-) diff --git a/NEWS.md b/NEWS.md index 10a2ef4d..4ed95fe4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,10 @@ taxize 0.9.101 -Add `rworkflows`. -Update *.Rbuildignore* for `rworkflows`. +* Add `rworkflows`. + - Update *.Rbuildignore* for `rworkflows`. + - Remove old workflow: *R-CMD-check.yaml* + - Bump `taxize` version. + - Add `rworkflows` status badge to *README*. ============= taxize 0.9.100 diff --git a/README.Rmd b/README.Rmd index 79995f5e..74986491 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$set( [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![cran checks](https://badges.cranchecks.info/worst/taxize.svg)](https://cran.r-project.org/web/checks/check_results_taxize.html) -[![R-CMD-check](https://github.com/ropensci/taxize/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/taxize/actions/) +[![rworkflows](https://github.com/ropensci/taxize/workflows/rworkflows/badge.svg)](https://github.com/ropensci/taxize/actions/) [![codecov](https://codecov.io/gh/ropensci/taxize/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/taxize) [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/taxize)](https://github.com/r-hub/cranlogs.app) [![cran version](https://www.r-pkg.org/badges/version/taxize)](https://cran.r-project.org/package=taxize) diff --git a/README.md b/README.md index 53b55982..ece1aa52 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![cran checks](https://badges.cranchecks.info/worst/taxize.svg)](https://cran.r-project.org/web/checks/check_results_taxize.html) -[![R-CMD-check](https://github.com/ropensci/taxize/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/taxize/actions/) +[![rworkflows](https://github.com/ropensci/taxize/workflows/rworkflows/badge.svg)](https://github.com/ropensci/taxize/actions/) [![codecov](https://codecov.io/gh/ropensci/taxize/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/taxize) [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/taxize)](https://github.com/r-hub/cranlogs.app) @@ -193,13 +193,13 @@ we plan to get done for each version. ## Meta -- Please [report any issues or - bugs](https://github.com/ropensci/taxize/issues). -- License: MIT -- Get citation information for `taxize` in R doing - `citation(package = 'taxize')` -- Please note that this package is released with a [Contributor Code - of Conduct](https://ropensci.org/code-of-conduct/). By contributing - to this project, you agree to abide by its terms. +- Please [report any issues or + bugs](https://github.com/ropensci/taxize/issues). +- License: MIT +- Get citation information for `taxize` in R doing + `citation(package = 'taxize')` +- Please note that this package is released with a [Contributor Code of + Conduct](https://ropensci.org/code-of-conduct/). By contributing to + this project, you agree to abide by its terms. [![rofooter](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org) From 465d52b6a388dce8291bf70b9f21b628a3f9bbb5 Mon Sep 17 00:00:00 2001 From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com> Date: Mon, 22 Jan 2024 12:35:29 +0000 Subject: [PATCH 3/3] add newline [skip ci] --- .Rbuildignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 158ca9da..00f6706b 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -30,4 +30,4 @@ log.Rmd node_modules$ package-lock\.json$ -package\.json$ \ No newline at end of file +package\.json$