Skip to content

Commit

Permalink
Add github action job: check-standard
Browse files Browse the repository at this point in the history
  • Loading branch information
asardaes committed Apr 18, 2021
1 parent f5d0ca7 commit f22e49c
Show file tree
Hide file tree
Showing 5 changed files with 127 additions and 19 deletions.
1 change: 1 addition & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
^.*\.Rproj$
^\.Rproj\.user$
^\.github$

^man-examples
^man-roxygen
Expand Down
1 change: 1 addition & 0 deletions .github/.gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
*.html
98 changes: 98 additions & 0 deletions .github/workflows/check-standard.yaml
Original file line number Diff line number Diff line change
@@ -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
1 change: 1 addition & 0 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
45 changes: 26 additions & 19 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,13 @@
---
output:
md_document:
variant: gfm
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

[![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
Expand All @@ -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

Expand Down

0 comments on commit f22e49c

Please sign in to comment.