add test coverage

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

README.Rmd

@@ -13,6 +13,10 @@ knitr::opts_chunk$set(
 )
 ```
 
+<!-- badges: start -->
+  [![R-CMD-check](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml)
+  <!-- badges: end -->
+
 # BioGA <a href="https://danymukesha.github.io/BioGA/"><img src="man/figures/logo.png" align="right" height="139" alt="BioGA website" /></a>
 
 The `BioGA` package provides a set of functions for genetic algorithm 

README.md

@@ -1,5 +1,9 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/danymukesha/BioGA/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
 
 # BioGA <a href="https://danymukesha.github.io/BioGA/"><img src="man/figures/logo.png" align="right" height="139" alt="BioGA website" /></a>
 
@@ -15,20 +19,63 @@ package:
 
 ``` r
 devtools::install_github("danymukesha/BioGA")
-#> Using GitHub PAT from the git credential store.
 #> Downloading GitHub repo danymukesha/BioGA@HEAD
-#> Skipping 16 packages ahead of CRAN: BiocGenerics, graph, S4Arrays, IRanges, S4Vectors, MatrixGenerics, GenomeInfoDbData, zlibbioc, XVector, GenomeInfoDb, RBGL, Biobase, DelayedArray, GenomicRanges, biocViews, SummarizedExperiment
+#> fs          (1.6.3   -> 1.6.4  ) [CRAN]
+#> fastmap     (1.1.1   -> 1.2.0  ) [CRAN]
+#> cachem      (1.0.8   -> 1.1.0  ) [CRAN]
+#> xfun        (0.42    -> 0.44   ) [CRAN]
+#> tinytex     (0.50    -> 0.51   ) [CRAN]
+#> knitr       (1.45    -> 1.46   ) [CRAN]
+#> htmltools   (0.5.7   -> 0.5.8.1) [CRAN]
+#> bslib       (0.6.1   -> 0.7.0  ) [CRAN]
+#> rmarkdown   (2.26    -> 2.27   ) [CRAN]
+#> matrixStats (1.2.0   -> 1.3.0  ) [CRAN]
+#> munsell     (0.5.0   -> 0.5.1  ) [CRAN]
+#> farver      (2.1.1   -> 2.1.2  ) [CRAN]
+#> BiocManager (1.30.22 -> 1.30.23) [CRAN]
+#> bookdown    (0.38    -> 0.39   ) [CRAN]
+#> gtable      (0.3.4   -> 0.3.5  ) [CRAN]
+#> ggplot2     (3.5.0   -> 3.5.1  ) [CRAN]
+#> Skipping 17 packages ahead of CRAN: BiocGenerics, graph, S4Arrays, IRanges, S4Vectors, MatrixGenerics, GenomeInfoDbData, zlibbioc, XVector, GenomeInfoDb, RBGL, Biobase, DelayedArray, GenomicRanges, BiocStyle, biocViews, SummarizedExperiment
+#> Installing 16 packages: fs, fastmap, cachem, xfun, tinytex, knitr, htmltools, bslib, rmarkdown, matrixStats, munsell, farver, BiocManager, bookdown, gtable, ggplot2
+#> Installing packages into 'C:/Users/dany.mukesha/AppData/Local/Temp/Rtmp63bptc/temp_libpath8488528329e2'
+#> (as 'lib' is unspecified)
+#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3:
+#>   cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3/PACKAGES'
+#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3:
+#>   cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/windows/contrib/4.3/PACKAGES'
+#> Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3:
+#>   cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/windows/contrib/4.3/PACKAGES'
+#> package 'fs' successfully unpacked and MD5 sums checked
+#> package 'fastmap' successfully unpacked and MD5 sums checked
+#> package 'cachem' successfully unpacked and MD5 sums checked
+#> package 'xfun' successfully unpacked and MD5 sums checked
+#> package 'tinytex' successfully unpacked and MD5 sums checked
+#> package 'knitr' successfully unpacked and MD5 sums checked
+#> package 'htmltools' successfully unpacked and MD5 sums checked
+#> package 'bslib' successfully unpacked and MD5 sums checked
+#> package 'rmarkdown' successfully unpacked and MD5 sums checked
+#> package 'matrixStats' successfully unpacked and MD5 sums checked
+#> package 'munsell' successfully unpacked and MD5 sums checked
+#> package 'farver' successfully unpacked and MD5 sums checked
+#> package 'BiocManager' successfully unpacked and MD5 sums checked
+#> package 'bookdown' successfully unpacked and MD5 sums checked
+#> package 'gtable' successfully unpacked and MD5 sums checked
+#> package 'ggplot2' successfully unpacked and MD5 sums checked
+#> 
+#> The downloaded binary packages are in
+#>  C:\Users\dany.mukesha\AppData\Local\Temp\RtmpWuKbDY\downloaded_packages
 #> ── R CMD build ─────────────────────────────────────────────────────────────────
-#>          checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpeMTOmQ\remotes6e2c19f3527f\danymukesha-BioGA-39ae5be/DESCRIPTION' ...     checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpeMTOmQ\remotes6e2c19f3527f\danymukesha-BioGA-39ae5be/DESCRIPTION' ...   ✔  checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpeMTOmQ\remotes6e2c19f3527f\danymukesha-BioGA-39ae5be/DESCRIPTION' (387ms)
+#>       ✔  checking for file 'C:\Users\dany.mukesha\AppData\Local\Temp\RtmpWuKbDY\remotes99a020a46bb9\danymukesha-BioGA-9b9a1cc/DESCRIPTION' (776ms)
 #>       ─  preparing 'BioGA':
 #>    checking DESCRIPTION meta-information ...     checking DESCRIPTION meta-information ...   ✔  checking DESCRIPTION meta-information
 #> ─  cleaning src
 #>       ─  checking for LF line-endings in source and make files and shell scripts
 #>       ─  checking for empty or unneeded directories
 #>      Omitted 'LazyData' from DESCRIPTION
-#>       ─  building 'BioGA_0.99.0.tar.gz'
+#>       ─  building 'BioGA_0.99.5.tar.gz'
 #>      
 #> 
-#> Installing package into 'C:/Users/dany.mukesha/AppData/Local/Temp/RtmpQ9yEQT/temp_libpath43e05a565418'
+#> Installing package into 'C:/Users/dany.mukesha/AppData/Local/Temp/Rtmp63bptc/temp_libpath8488528329e2'
 #> (as 'lib' is unspecified)
 ```