diff --git a/.Rbuildignore b/.Rbuildignore index 59f88159..00f6706b 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$ 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: ${{ runner.os }} diff --git a/DESCRIPTION b/DESCRIPTION index e518d1a6..9f29c865 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Description: Interacts with a suite of web 'APIs' for taxonomic tasks, species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. -Version: 0.9.100 +Version: 0.9.101 License: MIT + file LICENSE URL: https://docs.ropensci.org/taxize/ (website), https://github.com/ropensci/taxize (devel), diff --git a/NEWS.md b/NEWS.md index 2c0059b3..4ed95fe4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ +taxize 0.9.101 + +* Add `rworkflows`. + - Update *.Rbuildignore* for `rworkflows`. + - Remove old workflow: *R-CMD-check.yaml* + - Bump `taxize` version. + - Add `rworkflows` status badge to *README*. + +============= taxize 0.9.100 ============= diff --git a/README.Rmd b/README.Rmd index 79995f5e..74986491 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$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)