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[pre-commit.ci] pre-commit autoupdate #877

[pre-commit.ci] pre-commit autoupdate

[pre-commit.ci] pre-commit autoupdate #877

Workflow file for this run

# The purpose of this action is to calculate the code coverage and add the results on codecov.io
# codecov.io provides a badge showing the current coverage and generates coverage reports for each pull requests.
#
# 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
jobs:
test-coverage:
runs-on: self-hosted # ubuntu-22.04
env:
GITHUB_PAT: ${{ secrets.TOKEN }}
CIBERSORTX_EMAIL: ${{ secrets.CIBERSORTX_EMAIL }}
CIBERSORTX_TOKEN: ${{ secrets.CIBERSORTX_TOKEN }}
CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
steps:
- uses: actions/checkout@v4
- name: Update system dependencies
# due to recent versions of GLIBC missing
run: |
sudo apt-get update && sudo apt-get install cmake libstdc++6 \
libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev \
libharfbuzz-dev libfribidi-dev \
libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
- name: Install pak
run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')"
# - name: Install SpatialExperiment
# run: Rscript -e "pak::pkg_install('drighelli/SpatialExperiment')"
- name: Install Devtools
run: Rscript -e "pak::pkg_install('devtools')"
- name: Install SpatialExperiment
run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')"
- name: Install Immunedeconv
run: Rscript -e "pak::pkg_install('omnideconv/immunedeconv')"
- name: Install Omnideconv
run: Rscript -e "pak::pkg_install('omnideconv/omnideconv')"
- name: Install OmnipathR
run: Rscript -e "pak::pkg_install('OmnipathR')"
- uses: r-lib/actions/setup-r-dependencies@v2
with:
dependencies: '"hard"' # do not install suggests
extra-packages: any::covr, any::devtools
needs: coverage
- name: Test coverage
run: covr::codecov(quiet = FALSE)
shell: Rscript {0}