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ci(covr): add coverage reports uploaded to codecov
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jamespeapen committed Oct 14, 2024
1 parent 7d13ed9 commit be8b864
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1 change: 1 addition & 0 deletions .Rbuildignore
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.direnv

.git
^codecov\.yml$
68 changes: 68 additions & 0 deletions .github/workflows/test-coverage.yaml
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# 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.yaml

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: Install deps
run: |
sudo apt-get install libhts-dev
echo "-------------------HTSLIB-----------------------"
pkg-config --cflags --libs htslib
echo "------------------------------------------------"
- 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
1 change: 1 addition & 0 deletions README.md
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<!-- badges: start -->
[![R-CMD-check](https://github.com/huishenlab/iscream/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/huishenlab/iscream/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/huishenlab/iscream/graph/badge.svg)](https://app.codecov.io/gh/huishenlab/iscream)
<!-- badges: end -->

Analysis and visualization of Whole Genome Bisulfite Sequencing (WGBS) data
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14 changes: 14 additions & 0 deletions codecov.yml
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comment: false

coverage:
status:
project:
default:
target: auto
threshold: 1%
informational: true
patch:
default:
target: auto
threshold: 1%
informational: true
4 changes: 4 additions & 0 deletions default.nix
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# dev dependencies
bench
covr
devtools
lobstr
pkgbuild
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styler
usethis
testthat
covr
DT
htmltools

# RCMD check
# V8
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