fix use_vignette_ funcs

Author: bschilder

.Rhistory

@@ -31,12 +31,6 @@ jobs:
           r: latest
           bioc: release
     steps:
-    - if: ${{ env.ACT }}
-      name: Hack container for local development
-      run: |
-        curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
-        sudo apt-get install -y nodejs
-      shell: bash {0}
     - uses: neurogenomics/rworkflows@master
       with:
         run_bioccheck: ${{ false }}
@@ -53,4 +47,4 @@ jobs:
         docker_org: neurogenomicslab
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
-        cache_version: cache-v1
+        cache_version: cache-master

.github/workflows/rworkflows.yml

@@ -37,7 +37,8 @@ Suggests:
     BiocStyle,
     covr,
     testthat (>= 3.0.0),
-    hexSticker
+    hexSticker,
+    htmltools
 RoxygenNote: 7.2.2
 VignetteBuilder: knitr
 License: GPL-3

DESCRIPTION

@@ -11,7 +11,8 @@
 
 ## Bug fixes
 
-  - Make `badger` a *Import*
+* Make `badger` a *Import*
+* Use Dockerfile stored in *inst/templates* instead of getting from GitHub.
 
 # rworkflows 0.99.1
 

NEWS.md

@@ -59,7 +59,8 @@ fill_yaml <- function(yml,
     yml$env <- with2
   } else if(name=="rworkflows"){
     #### replace with: args ####
-    yml$jobs[[1]]$steps[[2]]$with <- with2
+    steps <- yml$jobs[[1]]$steps
+    steps[[length(steps)]]$with <- with2
   }
   return(yml) 
 }

R/fill_yaml.R

@@ -4,7 +4,7 @@ get_hex <- function(branch,
                     add_html=TRUE,
                     verbose=TRUE){
 
-  if("URL" %in% desc:::desc_fields()){
+  if("URL" %in% desc::desc_fields()){
     URL <- desc::desc_get_field(key = "URL")
   } else {
     wrn <- "URL key not found in DESCRIPTION file."

R/get_hex.R

@@ -3,17 +3,25 @@ get_yaml <- function(name){
   workflow_nms <- c("rworkflows","rworkflows_static")
   handlers <- list('bool#yes' = function(x) { if (x == "on") x else TRUE})
   #### Check name and read in #####
+  #### Dynamic action ####
   if(is.null(name) || 
      name=="rworkflows"){
       yml <- yaml::read_yaml(
         system.file("templates","rworkflows_template.yml",
                     package = "rworkflows"),
         handlers = handlers)
+    #### Static workflow ####
     } else if(name=="rworkflows_static"){
       yml <- yaml::read_yaml(
         system.file("templates","rworkflows_template_static.yml",
                     package = "rworkflows"),
-        handlers = handlers)
+        handlers = handlers)  
+      #### Read in action to avoid code redundancy ####
+      ## Import the latest version of action.yml
+      action <- yaml::read_yaml(
+        "https://github.com/neurogenomics/rworkflows/raw/master/action.yml")
+      #### Add action steps to static workflow ####
+      yml$jobs$rworkflows_static$steps <- action$runs$steps
     } else {
       stp <- paste("`name` must be one of:",
                    paste("\n -",shQuote(workflow_nms),collapse = ""))

R/get_yaml.R

@@ -0,0 +1,14 @@
+set_vignette_index <- function(yml,
+                               pattern="%\\VignetteIndexEntry{docker}",
+                               vignette_index_entry){
+  yml$vignette <- gsub(
+    "} ","}\n",
+    gsub(
+      pattern, 
+      paste0("%\\VignetteIndexEntry{",vignette_index_entry,"}"), 
+      yml$vignette, 
+      fixed = TRUE),
+    fixed=TRUE
+  )
+  return(yml)
+}

R/set_vignette_index.R

@@ -20,14 +20,16 @@ use_dockerfile <- function(save_dir=getwd(),
                            show=FALSE,
                            verbose=TRUE){
 
-  if(file.exists(path) & isFALSE(force_new)){
+  if(file.exists(path) &&
+     isFALSE(force_new)){
     messager("Using existing Docker file:",path,v=verbose)
   } else {
     messager("Creating new Docker file ==>",path,v=verbose)
-    dir.create(dirname(path), showWarnings = FALSE, recursive = TRUE)
-    utils::download.file(
-      url = "https://github.com/neurogenomics/rworkflows/raw/master/Dockerfile", 
-      destfile = path) 
+    dir.create(dirname(path), showWarnings = FALSE, recursive = TRUE) 
+    file.copy(from = system.file("templates","Dockerfile",
+                                 package = "rworkflows"), 
+              to = path,  
+              overwrite = TRUE)
   }
   if(isTRUE(show)){
     messager("Docker file preview:",v=verbose)

R/use_dockerfile.R

@@ -54,11 +54,9 @@ use_vignette_docker <- function(docker_org,
     yml$params$docker_org$value <- docker_org
     ## vignette title
     yml$title <- title
-    yml$vignette <- gsub(
-      "%\\VignetteIndexEntry{docker}", 
-      paste0("%\\VignetteIndexEntry{",vignette_index_entry,"}"), 
-      yml$vignette, 
-      fixed = TRUE)
+    yml <- set_vignette_index(yml = yml,
+                              pattern = "%\\VignetteIndexEntry{docker}",
+                              vignette_index_entry = vignette_index_entry)
     #### Render to text ####
     yml_txt <- gsub("''","\"",yaml::as.yaml(yml))
     new_rmd <-c("---",strsplit(yml_txt,"\n")[[1]],"---",