diff --git a/.Rbuildignore b/.Rbuildignore index 2b21e287..fea300aa 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,6 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^\.github$ ^man-examples ^man-roxygen diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 00000000..2d19fc76 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml new file mode 100644 index 00000000..3dda13fe --- /dev/null +++ b/.github/workflows/check-standard.yaml @@ -0,0 +1,98 @@ +# 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: + - dev/github-actions + - master + pull_request: + branches: + - 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: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-pandoc@v1 + + - uses: r-lib/actions/setup-tinytex@v1 + + - name: Set up tex in OSX + if: runner.os == 'macOS' + run: tlmgr install placeins cleveref framed + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$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(build_args = "--compact-vignettes", args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + shell: Rscript {0} + continue-on-error: ${{ matrix.config.r == 'devel' }} + + - name: Test coverage + if: runner.os == 'Linux' && matrix.config.r == 'release' + run: | + Rscript -e 'remotes::install_cran("covr")' + Rscript codecov.R + + - 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/README.Rmd b/README.Rmd index aae91907..8749b3ef 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,6 +18,7 @@ knitr::opts_chunk$set( ``` [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/dtwclust)](https://cran.r-project.org/package=dtwclust) +[![R-CMD-check](https://github.com/asardaes/dtwclust/workflows/R-CMD-check/badge.svg)](https://github.com/asardaes/dtwclust/actions) [![Travis-CI Build Status](https://travis-ci.org/asardaes/dtwclust.svg?branch=master)](https://travis-ci.org/asardaes/dtwclust) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/asardaes/dtwclust?branch=master&svg=true)](https://ci.appveyor.com/project/asardaes/dtwclust) [![codecov](https://codecov.io/gh/asardaes/dtwclust/branch/master/graph/badge.svg)](https://codecov.io/gh/asardaes/dtwclust) diff --git a/README.md b/README.md index 46f5d2d2..7e586a5f 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,13 @@ +--- +output: + md_document: + variant: gfm +--- + [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/dtwclust)](https://cran.r-project.org/package=dtwclust) +[![R-CMD-check](https://github.com/asardaes/dtwclust/workflows/R-CMD-check/badge.svg)](https://github.com/asardaes/dtwclust/actions) [![Travis-CI Build Status](https://travis-ci.org/asardaes/dtwclust.svg?branch=master)](https://travis-ci.org/asardaes/dtwclust) [![AppVeyor Build @@ -27,35 +34,35 @@ DTW. For more information: - - [Vignette with +- [Vignette with theory](https://cran.r-project.org/web/packages/dtwclust/vignettes/dtwclust.pdf) (with examples in the appendices) - - [Timing +- [Timing experiments](https://cran.r-project.org/web/packages/dtwclust/vignettes/timing-experiments.html) - - [Parallelization +- [Parallelization considerations](https://cran.r-project.org/web/packages/dtwclust/vignettes/parallelization-considerations.html) - - [Functions’ +- [Functions’ documentation](https://cran.r-project.org/web/packages/dtwclust/dtwclust.pdf) - - [Sample shiny +- [Sample shiny app](https://asardaes.shinyapps.io/dtwclust-tsclust-interactive/) - - [CRAN’s time series +- [CRAN’s time series view](https://cran.r-project.org/web/views/TimeSeries.html) ## Implementations - - Partitional, hierarchical and fuzzy clustering - - k-Shape clustering - - Shape-based distance - - Shape extraction for time series - - TADPole clustering - - An optimized version of DTW - - Keogh’s and Lemire’s DTW lower bounds - - Global alignment kernel (GAK) distance - - DTW Barycenter Averaging - - Soft-DTW (distance and centroid) - - Some multivariate support (GAK, DTW and soft-DTW) - - Cluster validity indices (crisp and fuzzy, internal and external) - - Parallelization for most functions +- Partitional, hierarchical and fuzzy clustering + - k-Shape clustering + - Shape-based distance + - Shape extraction for time series + - TADPole clustering +- An optimized version of DTW +- Keogh’s and Lemire’s DTW lower bounds +- Global alignment kernel (GAK) distance +- DTW Barycenter Averaging +- Soft-DTW (distance and centroid) +- Some multivariate support (GAK, DTW and soft-DTW) +- Cluster validity indices (crisp and fuzzy, internal and external) +- Parallelization for most functions ## Installation