Merge branch 'main' into add-csv-files

UCD-SERG · Jan 8, 2025 · acb9f0b · acb9f0b
2 parents 7b7f23b + ac31268
commit acb9f0b
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Showing 6 changed files with 15 additions and 7 deletions.
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -39,7 +39,8 @@ jobs:
 
       - uses: codecov/codecov-action@v4
         with:
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          # 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

diff --git a/NEWS.md b/NEWS.md
@@ -32,6 +32,9 @@
 (from <https://github.com/bcgov/ssdtools>) (#265)
 
 ## Internal changes
+
+* Updated `test-coverage.yml` GHA action to current `r-lib` standard (#330)
+
 * Change default pipe setting (#312)
 
 * Add test for missing strata in `est.incidence.by` (#227)

diff --git a/README.md b/README.md
@@ -8,7 +8,8 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/UCD-SERG/serocalculator/graph/badge.svg?token=85CXV6GN2T)](https://codecov.io/gh/UCD-SERG/serocalculator)
+[![Codecov test
+coverage](https://codecov.io/gh/UCD-SERG/serocalculator/graph/badge.svg)](https://app.codecov.io/gh/UCD-SERG/serocalculator)
 <!-- badges: end -->
 
 <div id="fig-website-QR">

diff --git a/README.qmd b/README.qmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/UCD-SERG/serocalculator/graph/badge.svg?token=85CXV6GN2T)](https://codecov.io/gh/UCD-SERG/serocalculator)
+[![Codecov test coverage](https://codecov.io/gh/UCD-SERG/serocalculator/graph/badge.svg)](https://app.codecov.io/gh/UCD-SERG/serocalculator)
 <!-- badges: end -->
 
 ```{r svg}

diff --git a/codecov.yml b/codecov.yml
@@ -1,14 +1,15 @@
 coverage:
   status:
-    project: #add everything under here, more options at https://docs.codecov.com/docs/commit-status
+    project: # add everything under here, more options at
+     # https://docs.codecov.com/docs/commit-status
       default:
         # basic
-        target: auto #default
+        target: auto # default
         threshold: 1%
         base: auto
-        informational: true
+        informational: false # default
     patch:
       default:
         target: auto
         threshold: 1%
-        informational: true
+        informational: false
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -8,6 +8,7 @@ CMD
 Campylobacter
 Ceper
 Chiang
+Codecov
 De
 Dhulikhel
 Diekmann
@@ -17,6 +18,7 @@ FIC
 Falkenhorst
 Fogarty
 Friesema
+GHA
 Gageldonk
 Graaf
 Gras