Merge pull request #65 from poissonconsulting/upkeep

Upkeep

.github/workflows/R-CMD-check.yaml

@@ -8,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -43,16 +45,8 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
-
-      - if: runner.os != 'Windows'
-        uses: r-lib/actions/check-r-package@v2
-        with:
-          upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
 
-      - if: runner.os == 'Windows'
-        uses: r-lib/actions/check-r-package@v2
+      - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-build-vignettes")'
-          args: 'c("--ignore-vignettes", "--no-manual")'
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest

.github/workflows/test-coverage.yaml

@@ -8,6 +8,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -23,18 +25,27 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          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(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: |

README.Rmd

@@ -20,7 +20,7 @@ library(bboutools)
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/poissonconsulting/bboutools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/bboutools/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/bboutools/branch/main/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bboutools?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/bboutools/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bboutools)
 <!-- badges: end -->
 
 `bboutools` is an R package to estimate the annual survival, recruitment and population growth for boreal caribou populations using Bayesian and Maximum Likelihood models with fixed and random effects.

README.md

@@ -9,7 +9,7 @@
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/poissonconsulting/bboutools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/bboutools/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/poissonconsulting/bboutools/branch/main/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bboutools?branch=main)
+coverage](https://codecov.io/gh/poissonconsulting/bboutools/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/bboutools)
 <!-- badges: end -->
 
 `bboutools` is an R package to estimate the annual survival, recruitment
@@ -64,7 +64,7 @@ glance(surv_fit)
 #> # A tibble: 1 × 8
 #>       n     K nchains niters nthin   ess  rhat converged
 #>   <int> <int>   <int>  <int> <dbl> <int> <dbl> <lgl>    
-#> 1   363     5       3   1000    10   111  1.03 FALSE
+#> 1   363     5       3   1000    10   111  1.03 TRUE
 ```
 
 Predictions can then be generated using `bb_predict_survival()`.