feat: add upload to codecov.io #21

feat: add upload to codecov.io

Author: akselthomsen

.github/linters/.lycheeignore

@@ -1,2 +1,4 @@
 # Dead irrelevant path in pkgdown/favicon
 http://svgjs.dev/svgjs
+# Path to RSPM yet to be derived
+https://packagemanager.posit.co/cran/$%7B%7Bmatrix.config.date 

.github/linters/.mega-linter.yml

@@ -1,8 +1,10 @@
 APPLY_FIXES: all
 DISABLE_LINTERS:
   - REPOSITORY_GIT_DIFF
+  - REPOSITORY_CHECKOV
 ADDITIONAL_EXCLUDED_DIRECTORIES:
   - dev
+REPOSITORY_KICS_ARGUMENTS: "--exclude-queries 555ab8f9-2001-455e-a077-f2d0f41e2fb9"
 SPELL_LYCHEE_ARGUMENTS: "--exclude-path man/figures --exclude-path docs --exclude-path pkgdown/favicon"
 SPELL_LYCHEE_FILE_EXTENSIONS: 
   - "*"

.github/workflows/coverage.yaml

@@ -12,6 +12,11 @@ on:
   workflow_dispatch:
   workflow_call:
     inputs:
+      use_codecov:
+        description: Upload code coverage results to codecov.io
+        required: false
+        type: boolean
+        default: false
       use_local_setup_action:
         description: Use composite .github/actions/setup/action.yaml to setup package specific needs
         required: false
@@ -21,7 +26,7 @@ permissions:
   contents: read
   pull-requests: write
 jobs:
-  test-coverage-internal:
+  test-coverage:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -75,3 +80,12 @@ jobs:
           recreate: true
           header: coverage
           path: coverage.md
+      - name: Upload coverage reports to Codecov
+        if:  ${{ inputs.use_codecov }}
+        uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          files: "./cobertura.xml"
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: ${{ github.repository }}
+          verbose: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: r.workflows
 Title: R package workflows
-Version: 0.0.1.9000
+Version: 0.0.1.9001
 Authors@R: c(
     person("Cervan", "Girard", , "cgid@novonordisk.com", role = c("aut", "cre")),
     person("Aksel", "Thomsen", , "oath@novonordisk.com", role = c("aut"))

README.md

@@ -6,7 +6,7 @@ It contains the following workflows:
 
 1. [R-CMD-check standard](.github/workflows/check_current_version.yaml): Standard R CMD check, that checks the package for current version of R on MacOs and Windows, and for the previous, current, and development version of R on Linux.
 2. [R-CMD-check NN versions](.github/workflows/check_nn_versions.yaml): Same as 1., but uses the R version and packages available as per given lock dates.
-3. [Test coverage](.github/workflows/coverage.yaml): Derives test coverage for the package and publishes a summary table to the pull request.
+3. [Test coverage](.github/workflows/coverage.yaml): Derives test coverage for the package and publishes a summary table to the pull request. For Open-Source repositories this also gives you the option to upload code coverage results to [codecov.io](https://codecov.io).
 4. [pkgdown](.github/workflows/pkgdown.yaml): Renders and publishes a `pkgdown` website for your package (to your `gh-pages` branch). For a pull request the page is published to `{base url of package}/dev/{pr number}`, and a link to this development webpage is posted as a comment to your pull request.
 5. [megalinter](.github/workflows/megalinter.yaml): Lints your entire project using the [megalinter](https://megalinter.io/) tool. Note that for the [cspell](https://github.com/streetsidesoftware/cspell) linter words in `inst/WORDLIST` are automatically added as a dictionary if the file exists.
 
@@ -43,6 +43,9 @@ jobs:
   coverage:
     name: Coverage report
     uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/coverage.yaml@main
+    secrets: inherit # Required if use_code below is true, in order to access organisational codecov token
+    with:
+      use_codecov: false # Change to true if you want to upload coverage results to codecov.io.
   megalinter:
     name: Megalinter
     uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/megalinter.yaml@main

inst/WORDLIST

@@ -0,0 +1,7 @@
+Aksel
+Cervan
+Girard
+roxygen
+Roxygen
+testthat
+Thomsen