Merge pull request #30 from AlexsLemonade/jashapiro/skip-download

Prevent unnecessary redownloads for vignettes

Author: jashapiro

vignettes/ScPCAr.Rmd

@@ -311,29 +311,19 @@ file_paths <- ScPCAr::download_sample(
   destination = "scpca_data",
   format = "sce"
 )
-```
-
-```
-## Downloading SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17.zip ...
-```
 
-```
-## Unzipping to scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17...
-```
-
-``` r
 # List the files that were downloaded
 file_paths
 ```
 
 ```
 ## [1] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/README.md"                       
-## [2] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/single_cell_metadata.tsv"        
-## [3] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_celltype-report.html"
-## [4] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_filtered.rds"        
-## [5] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_processed.rds"       
-## [6] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_qc.html"             
-## [7] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_unfiltered.rds"
+## [2] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_celltype-report.html"
+## [3] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_filtered.rds"        
+## [4] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_processed.rds"       
+## [5] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_qc.html"             
+## [6] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_unfiltered.rds"      
+## [7] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/single_cell_metadata.tsv"
 ```
 
 ## Understanding the downloaded file structure

vignettes/ScPCAr.Rmd.orig

@@ -168,6 +168,7 @@ The function will download and unpack the files associated with that sample, and
 Let's start with SingleCellExperiment format:
 
 ```{r download-sce}
+#| message: FALSE
 # Download SingleCellExperiment data for our sample
 # This will create a directory structure under "scpca_data/"
 file_paths <- ScPCAr::download_sample(

vignettes/precompile.R

@@ -9,7 +9,6 @@
 devtools::load_all()
 
 # Pre-compiled vignettes that depend on data downloads
-unlink(here::here("vignettes/scpca_data"), recursive = TRUE)
 knitr::knit(here::here("vignettes/ScPCAr.Rmd.orig"), output = here::here("vignettes/ScPCAr.Rmd"))
 
 # move figures