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billdenney committed Aug 19, 2024
1 parent d3c5272 commit 114ccf2
Showing 4 changed files with 33 additions and 18 deletions.
13 changes: 6 additions & 7 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -6,7 +6,9 @@ on:
pull_request:
branches: [main, master]

name: R-CMD-check
name: R-CMD-check.yaml

permissions: read-all

jobs:
R-CMD-check:
@@ -22,17 +24,14 @@ jobs:
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
#- {os: ubuntu-latest, r: 'oldrel-1'}
- {os: ubuntu-latest, r: 'oldrel-1'}

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
_R_CHECK_FORCE_SUGGESTS_: false
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

@@ -44,7 +43,6 @@ jobs:

- uses: r-lib/actions/setup-r-dependencies@v2
with:
pak-version: devel
extra-packages: |
any::rcmdcheck
nlmixr2/lotri
@@ -57,3 +55,4 @@ jobs:
- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
10 changes: 7 additions & 3 deletions .github/workflows/pkgdown.yaml
Original file line number Diff line number Diff line change
@@ -9,7 +9,9 @@ on:
types: [published]
workflow_dispatch:

name: pkgdown
name: pkgdown.yaml

permissions: read-all

jobs:
pkgdown:
@@ -19,8 +21,10 @@ jobs:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

@@ -46,7 +50,7 @@ jobs:

- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/github-pages-deploy-action@v4.4.1
uses: JamesIves/github-pages-deploy-action@v4.5.0
with:
clean: false
branch: gh-pages
24 changes: 18 additions & 6 deletions .github/workflows/test-coverage.yaml
Original file line number Diff line number Diff line change
@@ -6,7 +6,9 @@ on:
pull_request:
branches: [main, master]

name: test-coverage
name: test-coverage.yaml

permissions: read-all

jobs:
test-coverage:
@@ -15,7 +17,7 @@ jobs:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-r@v2
with:
@@ -25,6 +27,7 @@ jobs:
with:
extra-packages: |
any::covr
any::xml2
nlmixr2/lotri
nlmixr2/rxode2ll
nlmixr2/rxode2
@@ -34,23 +37,32 @@ jobs:

- 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_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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
find '${{ 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: ${{ runner.temp }}/package
4 changes: 2 additions & 2 deletions README.Rmd
Original file line number Diff line number Diff line change
@@ -16,8 +16,8 @@ knitr::opts_chunk$set(
# nlmixr2extra

<!-- badges: start -->
[![R-CMD-check](https://github.com/nlmixr2/nlmixr2extra/workflows/R-CMD-check/badge.svg)](https://github.com/nlmixr2/nlmixr2extra/actions)
[![Codecov test coverage](https://codecov.io/gh/nlmixr2/nlmixr2extra/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nlmixr2/nlmixr2extra?branch=main)
[![R-CMD-check](https://github.com/nlmixr2/nlmixr2extra/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/nlmixr2extra/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/nlmixr2/nlmixr2extra/graph/badge.svg)](https://app.codecov.io/gh/nlmixr2/nlmixr2extra)
[![CRAN version](http://www.r-pkg.org/badges/version/nlmixr2extra)](https://cran.r-project.org/package=nlmixr2extra)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/nlmixr2extra)](https://cran.r-project.org/package=nlmixr2extra)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/nlmixr2extra)](https://cran.r-project.org/package=nlmixr2extra)

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