Merge branch 'dev-jtm_gene_conversion-intersect' into jtm_gene_conver…

…sion

.github/workflows/bioc_branch.yml

@@ -0,0 +1,4 @@
+name: Update Bioconductor package files
+
+on:
+  workflow_dispatch:

NAMESPACE

@@ -3,7 +3,6 @@
 export(TF_syntax_to_R)
 export(add_rl_column)
 export(build_domino)
-export(cache)
 export(circos_ligand_receptor)
 export(cor_heatmap)
 export(cor_scatter)

R/utils.R

@@ -248,17 +248,6 @@ dom_network_items <- function(dom, clusters = NULL, return = NULL) {
     }
 }
 
-#' Specify the cache
-#' 
-#' @param path Path to tstore cache on
-#' @return BiocFileCache
-#' @export
-cache <- function(path = tools::R_user_dir(package = "domino2")) {
-  bfc <- BiocFileCache::BiocFileCache(path, ask = FALSE)
-
-  bfc
-}
-
 #' Convert python True/False syntax to TRUE/FALSE
 #' 
 #' @param x character vector. If it consists of only "True" and "False" strings, the vector is converted to an R logical vector

tests/testthat/test-cache.r

@@ -1,8 +1,14 @@
 test_that("can add to a new cache", {
-  tf <- tempfile(tmpdir = tempdir(check = TRUE))
-  file.create(tf)
-  bfc <- cache(path = tempdir())
+  bfc <- BiocFileCache::BiocFileCache(tempdir(), ask = FALSE)
   expect_equal(length(bfc), 0)
-  BiocFileCache::cleanbfc(bfc, ask = FALSE)
+
+  #from Bioc example
+  savepath <- BiocFileCache::bfcnew(bfc, "NewResource", ext = ".RData")
+  df <- data.frame(list("a"=c(1, 2), "b"=c(3, 4)))
+  save(df, file = savepath)
+
+  expect_equal(length(bfc), 1)
+
+  #cleanup
   BiocFileCache::removebfc(bfc, ask = FALSE)
 })

vignettes/domino2.Rmd

@@ -32,7 +32,7 @@ set.seed(123)
 ```
 
 ``` {r files, include=FALSE}
-bfc <- cache()
+bfc <- BiocFileCache::BiocFileCache(ask = FALSE)
 
 data_url <- "https://zenodo.org/records/10222767/files"
 

vignettes/domino_object_vignette.Rmd

@@ -25,7 +25,7 @@ library(domino2)
 ```
 
 ```{r setup, include = FALSE}
-bfc <- cache()
+bfc <- BiocFileCache::BiocFileCache(ask = FALSE)
 data_url <- "https://zenodo.org/records/10222767/files/pbmc_domino_built.rds"
 tmp_path <- BiocFileCache::bfcrpath(bfc, data_url)
 dom <- readRDS(tmp_path)

vignettes/plotting_vignette.Rmd

@@ -29,7 +29,7 @@ library(patchwork)
 In addition to the numerous plotting options available in the original [Domino](https://github.com/Elisseeff-Lab/domino), domino2 has added more functionality and new methods to improve visualization and interpretation of analysis results. Here, we will go over the different plotting functions available, as well as different options that can be utilized, and options for customization. We will be using the domino object (loaded as `dom`) from our example analysis in [Getting Started](vignette("domino2")).
 
 ```{r load data, include = FALSE}
-bfc <- cache()
+bfc <- BiocFileCache::BiocFileCache(ask = FALSE)
 data_url <- "https://zenodo.org/records/10222767/files/pbmc_domino_built.rds"
 tmp_path <- BiocFileCache::bfcrpath(bfc, data_url)
 dom <- readRDS(tmp_path)