From 3cc1856249ed659a600a5f00050d84e622fd86b4 Mon Sep 17 00:00:00 2001 From: olivroy Date: Wed, 6 Dec 2023 08:24:44 -0500 Subject: [PATCH 1/4] Add gh actions --- .Rbuildignore | 1 + .github/.gitignore | 1 + .github/workflows/R-CMD-check.yaml | 49 +++++++++++++++++++++++++++ .github/workflows/pkgdown.yaml | 48 ++++++++++++++++++++++++++ .github/workflows/test-coverage.yaml | 50 ++++++++++++++++++++++++++++ .travis.yml | 25 -------------- 6 files changed, 149 insertions(+), 25 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check.yaml create mode 100644 .github/workflows/pkgdown.yaml create mode 100644 .github/workflows/test-coverage.yaml delete mode 100644 .travis.yml diff --git a/.Rbuildignore b/.Rbuildignore index 7ee14d2..7e77372 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,4 @@ ^Meta$ ^CRAN-RELEASE$ ^CRAN-SUBMISSION$ +^\.github$ 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.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..a3ac618 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,49 @@ +# 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] + 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: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..ed7650c --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,48 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + release: + types: [published] + workflow_dispatch: + +name: pkgdown + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} + + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.4.1 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..27d4528 --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,50 @@ +# 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] + pull_request: + branches: [main, master] + +name: test-coverage + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr + needs: coverage + + - name: Test coverage + run: | + covr::codecov( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + shell: Rscript {0} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v3 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 31259c1..0000000 --- a/.travis.yml +++ /dev/null @@ -1,25 +0,0 @@ -# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r - -language: r -r: - - 3.6.0 - - release - - devel -warnings_are_errors: true -sudo: required -cache: packages - -r_github_packages: - - jimhester/covr - -env: - global: - - CRAN: http://cran.rstudio.com - -notifications: - email: - on_success: change - on_failure: change - -after_success: - - Rscript -e 'covr::codecov()' From 5b3dea6ccb6a253603ab7f036b806c7b1c3c9c39 Mon Sep 17 00:00:00 2001 From: olivroy Date: Wed, 6 Dec 2023 08:26:06 -0500 Subject: [PATCH 2/4] Update readme --- README.Rmd | 41 +++++++++++++++++++++++------------------ 1 file changed, 23 insertions(+), 18 deletions(-) diff --git a/README.Rmd b/README.Rmd index 6515c3c..bd7f2b0 100644 --- a/README.Rmd +++ b/README.Rmd @@ -2,6 +2,19 @@ output: github_document --- +# Anomalize is being Superceded by Timetk: + +# anomalize + + +[![R-CMD-check](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml) +[![Lifecycle Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html) +[![Coverage status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master) +[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize) +![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen) +![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen) + + ```{r setup, include = FALSE} @@ -14,12 +27,9 @@ knitr::opts_chunk$set( message = F, warning = F ) - -devtools::load_all() -library(tidyverse) +library(anomalize) ``` -# Anomalize is being Superceded by Timetk: The `anomalize` package functionality has been superceded by `timetk`. We suggest you begin to use the `timetk::anomalize()` to benefit from enhanced functionality to get improvements going forward. [Learn more about Anomaly Detection with `timetk` here.](https://business-science.github.io/timetk/articles/TK08_Automatic_Anomaly_Detection.html) @@ -36,13 +46,7 @@ plot_anomalies <- anomalize::plot_anomalies -# anomalize -[![Lifecycle Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html) -[![Coverage status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master) -[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize) -![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen) -![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen) > Tidy anomaly detection @@ -95,6 +99,7 @@ Next, let's get some data. `anomalize` ships with a data set called `tidyverse_ Suppose we want to determine which daily download "counts" are anomalous. It's as easy as using the three main functions (`time_decompose()`, `anomalize()`, and `time_recompose()`) along with a visualization function, `plot_anomalies()`. ```{r tidyverse_anoms_1, fig.height=8} +library(magrittr) tidyverse_cran_downloads %>% # Data Manipulation / Anomaly Detection time_decompose(count, method = "stl") %>% @@ -102,7 +107,7 @@ tidyverse_cran_downloads %>% time_recompose() %>% # Anomaly Visualization plot_anomalies(time_recomposed = TRUE, ncol = 3, alpha_dots = 0.25) + - labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") + ggplot2::labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") ``` Check out the [`anomalize` Quick Start Guide](https://business-science.github.io/anomalize/articles/anomalize_quick_start_guide.html). @@ -112,16 +117,16 @@ Check out the [`anomalize` Quick Start Guide](https://business-science.github.io Yes! Anomalize has a new function, `clean_anomalies()`, that can be used to repair time series prior to forecasting. We have a [brand new vignette - Reduce Forecast Error (by 32%) with Cleaned Anomalies](https://business-science.github.io/anomalize/articles/forecasting_with_cleaned_anomalies.html). ```{r} tidyverse_cran_downloads %>% - filter(package == "lubridate") %>% - ungroup() %>% + dplyr::filter(package == "lubridate") %>% + dplyr::ungroup() %>% time_decompose(count) %>% anomalize(remainder) %>% # New function that cleans & repairs anomalies! clean_anomalies() %>% - select(date, anomaly, observed, observed_cleaned) %>% - filter(anomaly == "Yes") + dplyr::select(date, anomaly, observed, observed_cleaned) %>% + dplyr::filter(anomaly == "Yes") ``` @@ -133,12 +138,12 @@ There are a several extra capabilities: ```{r, fig.height=7} tidyverse_cran_downloads %>% - filter(package == "lubridate") %>% - ungroup() %>% + dplyr::filter(package == "lubridate") %>% + dplyr::ungroup() %>% time_decompose(count) %>% anomalize(remainder) %>% plot_anomaly_decomposition() + - labs(title = "Decomposition of Anomalized Lubridate Downloads") + ggplot2::labs(title = "Decomposition of Anomalized Lubridate Downloads") ``` For more information on the `anomalize` methods and the inner workings, please see ["Anomalize Methods" Vignette](https://business-science.github.io/anomalize/articles/anomalize_methods.html). From e5bcda073d259c89ff82fdbd41d820de2da4f04f Mon Sep 17 00:00:00 2001 From: olivroy Date: Wed, 6 Dec 2023 08:26:16 -0500 Subject: [PATCH 3/4] devtools::build_readme() --- README.md | 45 ++++++++++++--------- man/figures/README-tidyverse_anoms_1-1.png | Bin 1004690 -> 1004701 bytes man/figures/README-unnamed-chunk-3-1.png | Bin 377384 -> 377395 bytes 3 files changed, 25 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index eb7b6dc..a609925 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,22 @@ - - # Anomalize is being Superceded by Timetk: +# anomalize + + + +[![R-CMD-check](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml) +[![Lifecycle +Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html) +[![Coverage +status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master) +[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize) +![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen) +![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen) + + + + The `anomalize` package functionality has been superceded by `timetk`. We suggest you begin to use the `timetk::anomalize()` to benefit from enhanced functionality to get improvements going forward. [Learn more @@ -24,16 +38,6 @@ plot_anomalies <- anomalize::plot_anomalies -# anomalize - -[![Lifecycle -Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html) -[![Coverage -status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master) -[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize) -![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen) -![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen) - > Tidy anomaly detection `anomalize` enables a tidy workflow for detecting anomalies in data. The @@ -98,6 +102,7 @@ anomalous. It’s as easy as using the three main functions visualization function, `plot_anomalies()`. ``` r +library(magrittr) tidyverse_cran_downloads %>% # Data Manipulation / Anomaly Detection time_decompose(count, method = "stl") %>% @@ -105,7 +110,7 @@ tidyverse_cran_downloads %>% time_recompose() %>% # Anomaly Visualization plot_anomalies(time_recomposed = TRUE, ncol = 3, alpha_dots = 0.25) + - labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") + ggplot2::labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") ``` @@ -122,16 +127,16 @@ Anomalies](https://business-science.github.io/anomalize/articles/forecasting_wit ``` r tidyverse_cran_downloads %>% - filter(package == "lubridate") %>% - ungroup() %>% + dplyr::filter(package == "lubridate") %>% + dplyr::ungroup() %>% time_decompose(count) %>% anomalize(remainder) %>% # New function that cleans & repairs anomalies! clean_anomalies() %>% - select(date, anomaly, observed, observed_cleaned) %>% - filter(anomaly == "Yes") + dplyr::select(date, anomaly, observed, observed_cleaned) %>% + dplyr::filter(anomaly == "Yes") #> # A time tibble: 19 × 4 #> # Index: date #> date anomaly observed observed_cleaned @@ -166,12 +171,12 @@ There are a several extra capabilities: ``` r tidyverse_cran_downloads %>% - 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covr, knitr, - rmarkdown, - devtools, - roxygen2 + rmarkdown VignetteBuilder: knitr diff --git a/vignettes/anomalize_methods.Rmd b/vignettes/anomalize_methods.Rmd index ffeb474..c7c78cd 100644 --- a/vignettes/anomalize_methods.Rmd +++ b/vignettes/anomalize_methods.Rmd @@ -19,7 +19,7 @@ knitr::opts_chunk$set( fig.align = "center" ) -devtools::load_all() +library(anomalize) library(tidyverse) ``` diff --git a/vignettes/forecasting_with_cleaned_anomalies.Rmd b/vignettes/forecasting_with_cleaned_anomalies.Rmd index 7cf3cd8..a5c95e8 100644 --- a/vignettes/forecasting_with_cleaned_anomalies.Rmd +++ b/vignettes/forecasting_with_cleaned_anomalies.Rmd @@ -17,7 +17,8 @@ knitr::opts_chunk$set( fig.align = "center" ) -devtools::load_all() +library(anomalize) +library(tidyverse) ```