Add .Rprofile

Author: bschilder

.Rprofile

@@ -0,0 +1 @@
+options(repos = BiocManager::repositories())

.github/workflows/rworkflows.yml

@@ -55,4 +55,4 @@ jobs:
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
         free_diskspace: ${{ true }}
-        miniforge_variant: "Mambaforge"
+        miniforge_variant: false

.github/workflows/rworkflows_dev.yml

@@ -57,4 +57,4 @@ jobs:
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
         free_diskspace: ${{ true }}
-        miniforge_variant: "Mambaforge"
+        miniforge_variant: false

.github/workflows/rworkflows_static.yml

@@ -94,7 +94,7 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         mkdir -p /__w/_temp/Library
-        echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
+        echo ".libPaths('/__w/_temp/Library')" >> ~/.Rprofile
         git config --global --add safe.directory '*'
       shell: bash {0}
     - name: ⏬ Checkout repository

NAMESPACE

@@ -14,6 +14,7 @@ export(infer_biocviews)
 export(infer_deps)
 export(is_gha)
 export(use_badges)
+export(use_codespace)
 export(use_dockerfile)
 export(use_issue_template)
 export(use_readme)

NEWS.md

@@ -3,7 +3,23 @@
 ## New features
 
 * Add *.devcontainer/devcontainer.json*
-
+* `use_vignette_docker`
+  - New helper func: `infer_docker_org`
+
+## Bug fixes 
+
+* `infer_deps` 
+  - Pass `infer_deps` the *DESCRIPTION* path directly 
+    within the `fill_description` func. 
+  - Fix unit tests.
+* `conda_*`
+  - Try to get reticularte to find the path to conda 
+  installed by `setup-miniconda`.
+* New func: `use_codespace`
+  - Create dev container config file.
+* *.Rprofile*
+  - Added to avoid CRAN issues with bioc packages.
+  
 # rworkflows 0.99.14
 
 ## New features

R/fill_description.R

@@ -94,9 +94,11 @@ fill_description <- function(path = here::here("DESCRIPTION"),
                                                      depth = 2)$r,
                                ")"
                              ),
-                             imports = infer_deps(which = "Imports",
+                             imports = infer_deps(path = path,
+                                                  which = "Imports",
                                                   add_newlines = TRUE),
-                             suggests = infer_deps(which = "Suggests",
+                             suggests = infer_deps(path = path,
+                                                   which = "Suggests",
                                                    add_newlines = TRUE),
                              remotes = NULL,
                              version = NULL,

R/infer_deps.R

@@ -20,8 +20,13 @@
 #' @importFrom desc desc
 #' @importFrom renv dependencies
 #' @examples 
-#' deps <- infer_deps()
-infer_deps <- function(path = here::here(),
+#' #### Get example DESCRIPTION file ####
+#' url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION" 
+#' path <- tempfile(fileext = "DESCRIPTION")
+#' utils::download.file(url,path)
+#' 
+#' deps <- infer_deps(path = path)
+infer_deps <- function(path = here::here("DESCRIPTION"),
                        which = c("Imports","Suggests"),
                        imports_thresh = 2,
                        imports = NULL,

R/infer_docker_org.R

@@ -0,0 +1,20 @@
+infer_docker_org <- function(docker_org,
+                             docker_registry,
+                             verbose=TRUE){
+  if(!is.null(docker_org)){
+    return(docker_org)
+  } else if(is.null(docker_org) && 
+     grepl("ghcr.io",docker_registry)){
+    ## Infer docker_org from DESCRIPTION
+    desc_file <- get_description(verbose = verbose)
+    gh_url <- get_github_url_desc(desc_file = desc_file[[1]])
+    if(!is.null(gh_url)){
+      docker_org <- rev(strsplit(gh_url,"/")[[1]])[2]
+      return(docker_org)
+    } else {
+      stopper("docker_org must be supplied.")
+    }
+  } else {
+    stopper("docker_org must be supplied.")
+  }
+}

R/use_codespace.R

@@ -0,0 +1,60 @@
+#' Use Codespace
+#' 
+#' Generate a dev container config file to set up a 
+#' \href{https://docs.github.com/en/codespaces}{GitHub Codespace}.
+#' @param template Dev container config template to use.
+#' @param image Base Docker image to use for the Codespace.
+#' @param features Named list of features to add to the Codespace.
+#' See \href{https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/configuring-dev-containers/adding-features-to-a-devcontainer-file}{here}
+#'  for details.
+#' @param customizations Named list of customizations to add to the Codespace.
+#' See \href{https://containers.dev/supporting}{here}
+#'  for details.
+#' @inheritParams use_vignette_docker
+#' @returns Path to dev container config file.
+#' 
+#' @export
+#' @examples
+#' path <- use_codespace(save_dir=tempdir())
+use_codespace <- function(template="devcontainer.json",
+                          image="ghcr.io/neurogenomics/rworkflows:dev",
+                          features=list(
+                            "ghcr.io/devcontainers/features/conda:1"=list()
+                          ),
+                          customizations=list(
+                            vscode=list(
+                              settings=list(),
+                              extensions=
+                                list("reditorsupport.r",
+                                     "visualstudioexptteam.vscodeintellicode",
+                                     "ionutvmi.path-autocomplete")
+                              )
+                            ),
+                          save_dir=here::here(".devcontainer"),
+                          path=file.path(save_dir,
+                                         template),
+                          force_new=FALSE,
+                          show=FALSE,
+                          verbose=TRUE){
+  # devoptera::args2vars(use_codespace)
+  
+  #### Create or use existing file ####
+  if(file.exists(path) &&
+     isFALSE(force_new)){
+    messager("Using existing dev container config file ==>",path,v=verbose)
+  } else {
+    requireNamespace("jsonlite")
+    messager("Creating new dev container config file ==>",path,v=verbose)
+    tmp <- system.file("templates","devcontainer.json",package="rworkflows")
+    jsn <- jsonlite::read_json(tmp)
+    jsn$features <- features
+    jsn$customizations <- customizations
+    jsonlite::write_json(jsn,path)
+  }
+  #### Preview ####
+  if(isTRUE(show)){
+    messager("Config file preview:",v=verbose)
+    cat(paste(readLines(path),collapse ="\n"))
+  }
+  return(path)
+}