From 6a1902a9d52eb0af819e55261b260fef15b58207 Mon Sep 17 00:00:00 2001 From: Derek Chiu Date: Mon, 13 Mar 2023 12:01:46 -0700 Subject: [PATCH] update README and github action workflows --- .github/workflows/R-CMD-check.yaml | 13 +++++------ .github/workflows/test-coverage.yaml | 32 ++++++++++++++++++++++------ README.Rmd | 1 + README.md | 13 +++++------ 4 files changed, 41 insertions(+), 18 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 5bef95c..f4b17a4 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,4 +1,4 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# 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: @@ -15,14 +15,15 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: rcmdcheck + extra-packages: any::rcmdcheck + needs: check - - uses: r-lib/actions/check-r-package@v1 + - uses: r-lib/actions/check-r-package@v2 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 3c0da1c..2c5bb50 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,4 +1,4 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# 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: @@ -15,16 +15,36 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: covr + extra-packages: any::covr + needs: coverage - name: Test coverage - run: covr::codecov() + run: | + covr::codecov( + quiet = FALSE, + clean = FALSE, + install_path = file.path(Sys.getenv("RUNNER_TEMP"), "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: ${{ runner.temp }}/package diff --git a/README.Rmd b/README.Rmd index 47c4b53..d5724f6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -19,6 +19,7 @@ knitr::opts_chunk$set( [![Codecov test coverage](https://codecov.io/gh/AlineTalhouk/diceR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/AlineTalhouk/diceR?branch=master) [![CRAN status](https://www.r-pkg.org/badges/version/diceR)](https://CRAN.R-project.org/package=diceR) [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/diceR?color=orange)](https://r-pkg.org/pkg/diceR) +[![R-CMD-check](https://github.com/AlineTalhouk/diceR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/AlineTalhouk/diceR/actions/workflows/R-CMD-check.yaml) ## Overview diff --git a/README.md b/README.md index ed906c3..a4cb979 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,7 @@ coverage](https://codecov.io/gh/AlineTalhouk/diceR/branch/master/graph/badge.svg status](https://www.r-pkg.org/badges/version/diceR)](https://CRAN.R-project.org/package=diceR) [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/diceR?color=orange)](https://r-pkg.org/pkg/diceR) +[![R-CMD-check](https://github.com/AlineTalhouk/diceR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/AlineTalhouk/diceR/actions/workflows/R-CMD-check.yaml) ## Overview @@ -88,12 +89,12 @@ internal evaluation indices: knitr::kable(obj$indices$ii$`4`) ``` -| | Algorithms | calinski_harabasz | dunn | pbm | tau | gamma | c_index | davies_bouldin | mcclain_rao | sd_dis | ray_turi | g_plus | silhouette | s_dbw | Compactness | Connectivity | -|:----------------|:----------------|------------------:|----------:|---------:|----------:|----------:|----------:|---------------:|------------:|----------:|----------:|----------:|-----------:|------:|------------:|-------------:| -| HC_Euclidean | HC_Euclidean | 3.104106 | 0.2608547 | 59.73711 | 0.1994677 | 0.6349401 | 0.2844073 | 1.839182 | 0.8009149 | 0.1306062 | 1.4765665 | 0.0180141 | NaN | NaN | 24.83225 | 41.62183 | -| DIANA_Euclidean | DIANA_Euclidean | 53.647400 | 0.3348103 | 33.87817 | 0.4296601 | 0.6314448 | 0.1589442 | 2.824201 | 0.8051915 | 0.2119281 | 3.2978986 | 0.0853202 | 0.0692233 | NaN | 21.93396 | 241.66310 | -| kmodes | kmodes | 55.336853 | 0.3396909 | 50.73168 | 0.4553051 | 0.6600223 | 0.1455632 | 2.010999 | 0.7974362 | 0.1180643 | 1.1528004 | 0.0808925 | 0.1250821 | NaN | 21.90504 | 204.58333 | -| majority | majority | 19.373248 | 0.3544371 | 85.05173 | 0.3694313 | 0.6529652 | 0.2102487 | 1.622799 | 0.8019453 | 0.1108674 | 0.9200511 | 0.0555431 | 0.1884934 | NaN | 23.85408 | 64.04921 | +| | Algorithms | calinski_harabasz | dunn | gamma | c_index | davies_bouldin | sd | s_dbw | silhouette | Compactness | Connectivity | +|:----------------|:----------------|------------------:|----------:|-----------:|----------:|---------------:|---------:|---------:|-----------:|------------:|-------------:| +| HC_Euclidean | HC_Euclidean | 3.104106 | 0.2608547 | 0.6349401 | 0.2844073 | 1.839182 | 2.846480 | 1.678968 | -0.1418603 | 24.83225 | 41.62183 | +| DIANA_Euclidean | DIANA_Euclidean | 53.647400 | 0.3348103 | -1.9749903 | 0.1589442 | 2.824201 | 3.450173 | 1.809561 | 0.0564065 | 21.93396 | 241.66310 | +| kmodes | kmodes | 55.138600 | 0.3396909 | -1.8704101 | 0.1453599 | 2.006752 | 3.986950 | 1.967467 | 0.1369288 | 21.91494 | 201.42540 | +| majority | majority | 19.373248 | 0.3544371 | 0.6529653 | 0.2102487 | 1.622799 | 4.039708 | 1.982210 | 0.1504666 | 23.85408 | 64.04921 | ## Pipeline