update R-CMD-check and test-coverage workflows

AlineTalhouk · Jan 31, 2025 · 7dbd9e1 · 7dbd9e1
1 parent e89f244
commit 7dbd9e1
Show file tree

Hide file tree

Showing 4 changed files with 41 additions and 23 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,11 +42,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, mixedClust=?ignore
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-        env:
-          _R_CHECK_FORCE_SUGGESTS_: false
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,46 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - 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, mixedClust=?ignore
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/README.Rmd b/README.Rmd
@@ -16,9 +16,10 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![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)
-[![Codecov test coverage](https://codecov.io/gh/AlineTalhouk/diceR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/AlineTalhouk/diceR?branch=master)
+[![Codecov test coverage](https://codecov.io/gh/AlineTalhouk/diceR/graph/badge.svg)](https://app.codecov.io/gh/AlineTalhouk/diceR)
 [![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)
+
 <!-- badges: end -->
 
 ## Overview

diff --git a/README.md b/README.md
@@ -7,11 +7,12 @@
 
 [![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)
 [![Codecov test
-coverage](https://codecov.io/gh/AlineTalhouk/diceR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/AlineTalhouk/diceR?branch=master)
+coverage](https://codecov.io/gh/AlineTalhouk/diceR/graph/badge.svg)](https://app.codecov.io/gh/AlineTalhouk/diceR)
 [![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)
+
 <!-- badges: end -->
 
 ## Overview
@@ -88,19 +89,24 @@ internal evaluation indices:
 knitr::kable(obj$indices$ii$`4`)
 ```
 
-|                 | 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 |
+|  | 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
 
 This figure is a visual schematic of the pipeline that `dice()`
 implements.
 
-![Ensemble Clustering pipeline.](man/figures/pipeline.png)
+<figure>
+<img src="man/figures/pipeline.png"
+alt="Ensemble Clustering pipeline." />
+<figcaption aria-hidden="true">Ensemble Clustering
+pipeline.</figcaption>
+</figure>
 
 Please visit the
 [overview](https://alinetalhouk.github.io/diceR/articles/overview.html "diceR overview")