attempt using renv as a workaround to run github actions

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/workflows/publish.yml

@@ -21,29 +21,46 @@ jobs:
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
+
+      # attempt with pixi:
+
+      # - name: Install pixi
+      #   run: curl -fsSL https://pixi.sh/install.sh | bash
 
-      - name: Install pixi
-        run: curl -fsSL https://pixi.sh/install.sh | bash
+      # - name: Cache several folders
+      #   uses: actions/cache@v2
+      #   with:
+      #     path: |
+      #       _freeze
+      #       .pixi
+      #     key: ${{ runner.os }}
 
-      - name: Cache several folders
+      # - name: Set up dependencies
+      #   run: pixi install -e dev
+
+      # - name: Render slides
+      #   run: pixi run render_slides
+
+      # attempt with renv
+      - name: Set up renv
+        uses: r-lib/actions/setup-renv@v2
+
+      - name: Cache _freeze
         uses: actions/cache@v2
         with:
           path: |
             _freeze
-            .pixi
-          key: ${{ runner.os }}
       
-      - name: Set up dependencies
-        run: pixi install -e dev
-
       - name: Render slides
-        run: pixi run render_slides
+        run: |
+          source renv/python/virtualenvs/renv-python-3.12/bin/activate
+          quarto render
 
       - name: Deploy 🚀
         if: github.event_name != 'pull_request'
         uses: JamesIves/github-pages-deploy-action@v4
         with:
-          folder: _site
+          folder: _book
           branch: gh-pages
           force: false
           clean-exclude: pr-preview/
@@ -52,7 +69,7 @@ jobs:
         if: github.event_name == 'pull_request'
         uses: rossjrw/pr-preview-action@v1
         with:
-          source-dir: _site
+          source-dir: _book
           preview-branch: gh-pages
           umbrella-dir: pr-preview
           action: auto

README.md

@@ -51,3 +51,52 @@ To render the slides correctly in the workshop book site using [embedio](https:/
 ```bash
 pixi r render_slides
 ```
+
+## renv
+
+I'm currently experiencing issues with getting `pixi` to install `rpy2`. As a temporary workaround, I'm using `renv` to manage the R dependencies. 
+
+### First time setup
+
+To install the R and Python dependencies, use the following command:
+
+```R
+install.packages("renv")
+renv::restore()
+```
+
+### Adding new packages
+If you want to install a new R package, use the following command:
+
+```R
+renv::install("anndata")
+```
+
+If you want to install a new Python package, use the following command:
+
+```bash
+reticulate::py_install(c("rich>=13.7,<13.8", "anndata>=0.10.8,<0.11", "numpy>=1.24,<2", "scanpy>=1.10,<2", "mudata>=0.3,<0.4", "rpy2>=3.4,<4", "jupyter"))
+```
+
+After installing a new package, use the following command to update the `renv.lock` file:
+
+```R
+renv::snapshot()
+```
+
+### Using the environment
+
+To use the environment, use the following command:
+
+```bash
+# ensure that jupyter can also use the renv environment
+source renv/python/virtualenvs/renv-python-3.12/bin/activate
+quarto preview
+```
+
+Or to render the slides:
+
+```bash
+source renv/python/virtualenvs/renv-python-3.12/bin/activate
+quarto render
+```