re-install monocle3 and cicero #145
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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, 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 |