Add force=TRUE when installing local repo [skip ci]

Author: bschilder

.Rhistory

@@ -57,7 +57,8 @@ Suggests:
     jsonlite,
     BiocStyle,
     BiocPkgTools,
-    biocViews
+    biocViews,
+    reticulate
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

DESCRIPTION

@@ -12,9 +12,21 @@
     - `channels`
   - New function to construct conda env yaml files:
     - `construct_conda_yml`
+  - New unit tests to test `construct_conda_yml` and building conda envs 
+  from the generated yamls.
 * `fill_yaml` 
   - Add subfunction `is_default`
 
+## Bug fixes
+
+* `no visible global function definition for internal function check_miniconda_args`
+  - This weird error only came up during Rstudio R CMD checks. 
+  The function `check_miniconda_args` was clearly defined in its own file. 
+  The only way to fix it was copying the function into the same one where it
+  was called `fill_yaml`.
+  - Thought it might be a permissions issues with *check_miniconda_args.R* but 
+  the permissions are identical with all the others.
+
 # rworkflows 0.99.13
 
 ## New features

NEWS.md

@@ -0,0 +1,4 @@
+conda_installed <- function(){
+  requireNamespace("reticulate")
+  utils::getFromNamespace("conda_installed","reticulate")()
+}

R/check_miniconda_args.R

@@ -0,0 +1,4 @@
+condaenv_exists <- function(...){
+  requireNamespace("reticulate")
+ utils::getFromNamespace("condaenv_exists","reticulate")(...) 
+}

R/conda_installed.R

@@ -17,9 +17,11 @@
 #' @export
 #' @importFrom yaml read_yaml
 #' @examples
-#' yml <- construct_conda_yml(name="sc_env",
+#' yml <- construct_conda_yml(name="myenv",
 #'                            dependencies=c("anndata","scanpy"),
-#'                            return_path = FALSE)
+#'                            return_path = FALSE,  
+#'                            ## Writing to temp only for example
+#'                            save_path=tempfile(fileext="myenv_conda.yml"))
 construct_conda_yml <- function(name = "test",
                                 channels = list("conda-forge", 
                                                 "nodefaults"),
@@ -34,13 +36,16 @@ construct_conda_yml <- function(name = "test",
                                 ){
   # devoptera::args2vars(construct_conda_yml) 
 
+  if(is.vector(dependencies)) dependencies <- as.list(dependencies)
+  if(is.vector(pip)) pip <- as.list(pip)
   yml <- list(
     name=name,
     channels=channels,
     dependencies=dependencies
   )
   if(!is.null(pip)){
-    yml[["pip"]] <- pip
+    yml[["dependencies"]] <- c(unique(c(yml[["dependencies"]],"pip")),
+                               list(list(pip=pip))) 
   }
   #### Preview ####
   if(isTRUE(preview)){
@@ -50,6 +55,7 @@ construct_conda_yml <- function(name = "test",
   path_or_yaml <- return_yaml(yml=yml,
                               path=save_path,
                               return_path=return_path,
-                              verbose=verbose)
+                              verbose=verbose, 
+                              indent.mapping.sequence = TRUE)
   return(path_or_yaml)
 }

R/condaenv_exists.R

@@ -106,3 +106,50 @@ fill_yaml <- function(## function-level args
   }
   return(yml) 
 }
+
+
+#' Check Miniconda arguments
+#' 
+#' Check Miniconda arguments for compatibility with one another.
+#' @inheritParams use_workflow
+#' @returns Named list of updated args.
+#' 
+#' @keywords internal
+check_miniconda_args <- function(runners, 
+                                 miniforge_variant,
+                                 miniforge_version,
+                                 activate_environment,
+                                 environment_file,
+                                 channels,
+                                 verbose=TRUE){
+  
+  for(a in c("miniforge_version",
+             "environment_file",
+             "activate_environment")){
+    if(!is_default(arg=a, val=get(a), func="use_workflow") && 
+       isFALSE(miniforge_variant)){
+      messager(a,"supplied. Enabling miniforge.", v=verbose)
+      miniforge_variant <- TRUE
+    }
+  }
+  #### Check if python-version set ####
+  if(isTRUE(miniforge_variant)) { 
+    #### Check runners ####
+    for(r in runners){
+      if(is.null(r$`python-version`)){
+        messager("python-version not set for runner",
+                 paste0("os=",shQuote(r$os),"."),
+                 "Using default.",v=verbose)
+      }
+    }
+  }
+  if(isTRUE(miniforge_variant)) miniforge_variant <- ""
+  return(list( 
+    miniforge_variant=miniforge_variant,
+    miniforge_version=miniforge_version,
+    activate_environment=activate_environment,
+    environment_file=environment_file,
+    channels=channels
+  ))
+}
+

R/construct_conda_yml.R

@@ -1,11 +1,15 @@
 return_yaml <- function(yml,
                         path,
                         return_path,
-                        verbose=TRUE){
+                        handlers=NULL,
+                        verbose=TRUE, 
+                        ...){
   if(!is.null(path)){  
     save_yaml(yml=yml,
               path=path,
-              verbose=verbose)
+              handlers=handlers,
+              verbose=verbose,
+              ...)
     #### Return ####
     if(isTRUE(return_path)){
       return(path)

R/fill_yaml.R

@@ -1,14 +1,16 @@
 save_yaml <- function(yml,
                       path,
-                      verbose=TRUE){
+                      handlers=NULL,
+                      verbose=TRUE,
+                      ...){
 
   dir.create(dirname(path),showWarnings = FALSE, recursive = TRUE)
   messager("Saving yaml ==>",path,v=verbose)
   #### Write bools as true/false rather than yes/no (default) ####
-  handlers2 <- list('bool#yes' = function(x){"${{ true }}"},
-                    'bool#no' = function(x){"${{ false }}"})
-  yml2 <- yaml::yaml.load(yaml::as.yaml(yml), 
-                          handlers = handlers2)
-  yaml::write_yaml(x = yml2,
+  if(!is.null(handlers)){
+    yml <- yaml::yaml.load(yaml::as.yaml(yml), 
+                           handlers = handlers)
+  } 
+  yaml::write_yaml(x = yml,
                    file = path)
 }