# 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, dev_SeuratV5]
  pull_request:
    branches: [main, master, dev_SeuratV5]
  release:
    types: [published]
  workflow_dispatch:

name: pkgdown

jobs:
  pkgdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v2

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

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, any::reticulate, local::., any::devtools
          needs: website

      - uses: actions/setup-python@v2
        with:
          python-version: '3.10'
          
      - name: Setup hummuspy env
        run: |
          reticulate::conda_create("r-reticulate", packages="python==3.10")
          reticulate::py_install("hummuspy", envname = "r-reticulate", pip=TRUE)
        shell: Rscript {0}

      - name: ubuntu setup for Monocle3
        run: sudo apt-get install libgdal-dev libgeos-dev libproj-dev
      
      - name: Install Monocle3
        run: devtools::install_github('cole-trapnell-lab/monocle3')
        shell: Rscript {0}
        
      - name: Install Cicero
        run: devtools::install_github("cole-trapnell-lab/cicero-release", ref = "monocle3")
        shell: Rscript {0}

      - name: Build site
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Deploy to GitHub pages 🚀
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4.4.1
        with:
          clean: false
          branch: gh-pages
          folder: docs
