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quick upgrade

quick upgrade #197

Workflow file for this run

name: deploy
on:
workflow_dispatch:
pull_request:
types:
- closed
defaults:
run:
shell: bash -l {0}
permissions:
contents: read
pages: write
id-token: write
concurrency:
group: "pages"
cancel-in-progress: false
jobs:
build:
if: github.event.pull_request.merged == true
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: CheckoutRepo
uses: actions/checkout@v3
with:
fetch-depth: 0
- name: MicromambaCreateEnv
uses: mamba-org/setup-micromamba@main
with:
environment-name: Rseurat
environment-file: configs/conda.yml
cache-env: true
- name: MicromambaActivateEnv
run: micromamba activate Rseurat
- name: RemoteInstallGH
run: |
Rscript -e "remotes::install_github('satijalab/seurat-data')"
Rscript -e "SeuratData::InstallData('ifnb')" # if this fails, download file.tar.gz w/ cURL, then install.packages('file.tar.gz', repos=NULL, type='source')
Rscript -e "SeuratData::InstallData('pbmc3k')"
- name: DownloadZenodo
working-directory: ./rmd
run: |
Rscript -e "utils::download.file('https://zenodo.org/record/7891484/files/panc_sub_processed.RDS?download=1',destfile='datasets/preprocessed_rds/panc_sub_processed.RDS',method='wget')"
- name: RmarkdownRenderSite
run: Rscript -e "rmarkdown::render_site('rmd')"
- name: Upload artifact
uses: actions/upload-pages-artifact@v1
with:
path: ./rmd/site
deploy:
needs: build
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
runs-on: ubuntu-latest
steps:
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v2