test the R workflow

.github/workflows/publish.yml

@@ -39,6 +39,7 @@ jobs:
           packages: |
             any::BiocManager
             any::alabaster
+            any::scRNAseq
       # - run: Rscript r_requirements.r
 
       - name: Render

chapters/interop.qmd

@@ -1,6 +1,6 @@
 # Interop with R
 
-The [rds2py](https://github.com/BiocPy/rds2py) package serves as a Python interface to the [rds2cpp](https://github.com/LTLA/rds2cpp) library, enabling direct reading of RDS files within Python. This eliminates the need for additional data conversion tools or intermediate formats, streamlining the transition between Python and R for seamless analysis.
+The [rds2py](https://github.com/BiocPy/rds2py) package provides Python bindings to the [rds2cpp](https://github.com/LTLA/rds2cpp) library, enabling direct reading of RDS files within Python. This eliminates the need for additional data conversion tools or intermediate formats, streamlining the transition between Python and R for seamless analysis.
 
 One notable feature is the use of memory views (excluding strings) to access the same memory from C++ in Python, facilitated through Cython. This approach is particularly advantageous for handling large datasets, as it avoids unnecessary duplication of data.
 

chapters/workflow.qmd

@@ -0,0 +1,17 @@
+```{r}
+library(scRNA-seq)
+
+sce <- ZilionisLungData()
+
+library(alabaster)
+dir_path <- paste(getwd(), "datasets", sep="/")
+saveObject(sce, path=paste(dir_path, "zilinoislung", sep="/"))
+```
+
+
+```{python}
+from dolomite_base import read_object
+
+obj = read_object("./datasets/zilinoislung")
+print(obj)
+```

r_requirements.r

@@ -1,5 +1,6 @@
-# install.packages(c("BiocManager", "devtools"), repos='http://cran.us.r-project.org')
-BiocManager::install(version = "3.18")
+install.packages(c("BiocManager", "devtools"), repos='http://cran.us.r-project.org')
+BiocManager::install(version = "3.18", ask=FALSE)
 
 # install alabaster
-BiocManager::install(c("alabaster"))
+BiocManager::install(c("alabaster", "scRNAseq"))
+